Starting phenix.real_space_refine on Wed Mar 4 14:41:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o4h_12718/03_2026/7o4h_12718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o4h_12718/03_2026/7o4h_12718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7o4h_12718/03_2026/7o4h_12718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o4h_12718/03_2026/7o4h_12718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7o4h_12718/03_2026/7o4h_12718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o4h_12718/03_2026/7o4h_12718.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 9246 2.51 5 N 2313 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s 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: 14195 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3705 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 15, 'TRANS': 449} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3765 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 452} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3748 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 449} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2977 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Time building chain proxies: 3.16, per 1000 atoms: 0.22 Number of scatterers: 14195 At special positions: 0 Unit cell: (112.32, 110.16, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2572 8.00 N 2313 7.00 C 9246 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: 1.23 Conformation dependent library (CDL) restraints added in 510.9 milliseconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 8 sheets defined 60.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 160 through 172 Processing helix chain 'A' and resid 175 through 187 removed outlier: 4.723A pdb=" N ILE A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.817A pdb=" N TRP A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 4.111A pdb=" N ARG A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 217' Processing helix chain 'A' and resid 232 through 241 removed outlier: 4.081A pdb=" N ASP A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 3.827A pdb=" N ASP A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 268 through 274 removed outlier: 4.473A pdb=" N ASN A 271 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 274 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 removed outlier: 3.881A pdb=" N GLU A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 292 through 323 removed outlier: 4.519A pdb=" N PHE A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.878A pdb=" N SER A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 402 removed outlier: 4.143A pdb=" N LEU A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 425 through 441 removed outlier: 3.674A pdb=" N GLU A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 removed outlier: 3.937A pdb=" N VAL A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 452' Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 482 through 491 removed outlier: 3.852A pdb=" N LEU A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 583 Processing helix chain 'A' and resid 586 through 604 removed outlier: 4.145A pdb=" N LYS A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY A 591 " --> pdb=" O PRO A 587 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 179 through 187 removed outlier: 4.268A pdb=" N PHE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.617A pdb=" N TRP B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 271 through 275 removed outlier: 4.056A pdb=" N ARG B 275 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.112A pdb=" N PHE B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 290 Processing helix chain 'B' and resid 295 through 321 removed outlier: 3.738A pdb=" N PHE B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 371 through 401 removed outlier: 3.996A pdb=" N PHE B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 377 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.053A pdb=" N GLU B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 442 removed outlier: 3.666A pdb=" N GLU B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 removed outlier: 4.318A pdb=" N LEU B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.516A pdb=" N ARG B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 482 through 491 removed outlier: 3.551A pdb=" N LEU B 486 " --> pdb=" O GLU B 482 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 575 through 584 Processing helix chain 'B' and resid 588 through 604 removed outlier: 4.082A pdb=" N MET B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 187 removed outlier: 3.589A pdb=" N THR C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 172 " --> pdb=" O PHE C 168 " (cutoff:3.500A) Proline residue: C 173 - end of helix removed outlier: 3.650A pdb=" N TYR C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 179 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET C 180 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 199 through 213 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.608A pdb=" N LEU C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.850A pdb=" N LEU C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 262 removed outlier: 4.269A pdb=" N ILE C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 removed outlier: 3.642A pdb=" N ILE C 268 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN C 271 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 293 through 324 Processing helix chain 'C' and resid 344 through 359 removed outlier: 3.917A pdb=" N VAL C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 402 removed outlier: 4.455A pdb=" N TYR C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 422 removed outlier: 3.921A pdb=" N GLU C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 421 " --> pdb=" O GLN C 417 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 442 removed outlier: 3.764A pdb=" N GLU C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 453 removed outlier: 3.637A pdb=" N VAL C 451 " --> pdb=" O ASP C 447 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 453 " --> pdb=" O ARG C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'C' and resid 588 through 603 removed outlier: 4.371A pdb=" N MET C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 791 removed outlier: 4.120A pdb=" N ILE D 788 " --> pdb=" O ASN D 784 " (cutoff:3.500A) Proline residue: D 789 - end of helix Processing helix chain 'D' and resid 794 through 798 removed outlier: 3.817A pdb=" N GLN D 797 " --> pdb=" O PHE D 794 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR D 798 " --> pdb=" O PRO D 795 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 794 through 798' Processing helix chain 'D' and resid 803 through 809 Processing helix chain 'D' and resid 884 through 897 Processing helix chain 'D' and resid 901 through 931 Processing helix chain 'D' and resid 941 through 956 removed outlier: 4.575A pdb=" N ILE D 947 " --> pdb=" O GLY D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 1001 Processing helix chain 'D' and resid 1002 through 1019 removed outlier: 4.267A pdb=" N TYR D1006 " --> pdb=" O ALA D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1022 No H-bonds generated for 'chain 'D' and resid 1020 through 1022' Processing helix chain 'D' and resid 1024 through 1040 removed outlier: 4.184A pdb=" N GLN D1028 " --> pdb=" O PRO D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1054 removed outlier: 3.873A pdb=" N GLN D1053 " --> pdb=" O GLU D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1067 Processing helix chain 'D' and resid 1070 through 1074 removed outlier: 4.008A pdb=" N LYS D1073 " --> pdb=" O ILE D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1091 removed outlier: 3.979A pdb=" N ILE D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE D1086 " --> pdb=" O ARG D1082 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASP D1087 " --> pdb=" O GLN D1083 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET D1088 " --> pdb=" O MET D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1148 Processing helix chain 'D' and resid 1151 through 1155 removed outlier: 3.667A pdb=" N ASN D1154 " --> pdb=" O GLY D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1183 Processing helix chain 'D' and resid 1186 through 1203 removed outlier: 3.895A pdb=" N ASN D1202 " --> pdb=" O LEU D1198 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS D1203 " --> pdb=" O ARG D1199 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 removed outlier: 3.662A pdb=" N ARG D1215 " --> pdb=" O ILE D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1217 through 1225 removed outlier: 4.270A pdb=" N LEU D1221 " --> pdb=" O GLY D1217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D1223 " --> pdb=" O PRO D1219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D1224 " --> pdb=" O LYS D1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 3.809A pdb=" N GLN A 494 " --> pdb=" O CYS A 573 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS A 573 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA3, first strand: chain 'B' and resid 494 through 495 removed outlier: 3.613A pdb=" N GLN B 494 " --> pdb=" O CYS B 573 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 534 through 535 removed outlier: 4.002A pdb=" N VAL B 534 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.995A pdb=" N ASP C 570 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 518 " --> pdb=" O ASP C 570 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 572 " --> pdb=" O ILE C 516 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C 516 " --> pdb=" O PHE C 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AA7, first strand: chain 'D' and resid 1093 through 1095 removed outlier: 3.530A pdb=" N ARG D1093 " --> pdb=" O ILE D1170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE D1115 " --> pdb=" O PHE D1169 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D1142 " --> pdb=" O TYR D1114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1134 through 1136 removed outlier: 4.458A pdb=" N VAL D1134 " --> pdb=" O VAL D1123 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D1121 " --> pdb=" O LEU D1136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN D1122 " --> pdb=" O VAL D1161 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D1161 " --> pdb=" O GLN D1122 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1923 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4452 1.34 - 1.46: 3353 1.46 - 1.58: 6612 1.58 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 14526 Sorted by residual: bond pdb=" C TYR C 586 " pdb=" N PRO C 587 " ideal model delta sigma weight residual 1.334 1.298 0.036 2.34e-02 1.83e+03 2.37e+00 bond pdb=" CG1 ILE D 990 " pdb=" CD1 ILE D 990 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CB TRP B 353 " pdb=" CG TRP B 353 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.89e+00 bond pdb=" CB PHE B 296 " pdb=" CG PHE B 296 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.88e+00 bond pdb=" C ILE D 788 " pdb=" N PRO D 789 " ideal model delta sigma weight residual 1.334 1.364 -0.031 2.34e-02 1.83e+03 1.71e+00 ... (remaining 14521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 19402 2.70 - 5.41: 286 5.41 - 8.11: 30 8.11 - 10.82: 7 10.82 - 13.52: 4 Bond angle restraints: 19729 Sorted by residual: angle pdb=" C PRO A 266 " pdb=" N GLU A 267 " pdb=" CA GLU A 267 " ideal model delta sigma weight residual 122.31 110.85 11.46 2.00e+00 2.50e-01 3.28e+01 angle pdb=" C ASN B 400 " pdb=" N MET B 401 " pdb=" CA MET B 401 " ideal model delta sigma weight residual 122.31 112.80 9.51 2.00e+00 2.50e-01 2.26e+01 angle pdb=" N LEU A 455 " pdb=" CA LEU A 455 " pdb=" C LEU A 455 " ideal model delta sigma weight residual 110.31 104.92 5.39 1.20e+00 6.94e-01 2.01e+01 angle pdb=" C HIS A 468 " pdb=" N LEU A 469 " pdb=" CA LEU A 469 " ideal model delta sigma weight residual 122.15 111.09 11.06 2.83e+00 1.25e-01 1.53e+01 angle pdb=" CB ARG D1195 " pdb=" CG ARG D1195 " pdb=" CD ARG D1195 " ideal model delta sigma weight residual 111.30 120.21 -8.91 2.30e+00 1.89e-01 1.50e+01 ... (remaining 19724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 7651 17.38 - 34.76: 765 34.76 - 52.14: 139 52.14 - 69.53: 16 69.53 - 86.91: 6 Dihedral angle restraints: 8577 sinusoidal: 3346 harmonic: 5231 Sorted by residual: dihedral pdb=" CA ASP B 370 " pdb=" C ASP B 370 " pdb=" N SER B 371 " pdb=" CA SER B 371 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA HIS B 468 " pdb=" C HIS B 468 " pdb=" N LEU B 469 " pdb=" CA LEU B 469 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASN B 294 " pdb=" C ASN B 294 " pdb=" N ILE B 295 " pdb=" CA ILE B 295 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 8574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1424 0.040 - 0.080: 596 0.080 - 0.120: 157 0.120 - 0.160: 38 0.160 - 0.200: 6 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CB ILE C 516 " pdb=" CA ILE C 516 " pdb=" CG1 ILE C 516 " pdb=" CG2 ILE C 516 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA ARG D1195 " pdb=" N ARG D1195 " pdb=" C ARG D1195 " pdb=" CB ARG D1195 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CB THR C 560 " pdb=" CA THR C 560 " pdb=" OG1 THR C 560 " pdb=" CG2 THR C 560 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 2218 not shown) Planarity restraints: 2475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1034 " -0.030 2.00e-02 2.50e+03 2.77e-02 1.92e+01 pdb=" CG TRP D1034 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP D1034 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP D1034 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D1034 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D1034 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D1034 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1034 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1034 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D1034 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D1218 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO D1219 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D1219 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D1219 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 157 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO B 158 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " 0.031 5.00e-02 4.00e+02 ... (remaining 2472 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 304 2.66 - 3.22: 15223 3.22 - 3.78: 21102 3.78 - 4.34: 26431 4.34 - 4.90: 40470 Nonbonded interactions: 103530 Sorted by model distance: nonbonded pdb=" O TYR C 238 " pdb=" OG1 THR C 241 " model vdw 2.106 3.040 nonbonded pdb=" N VAL C 368 " pdb=" OE2 GLU C 372 " model vdw 2.159 3.120 nonbonded pdb=" NH2 ARG A 512 " pdb=" O SER A 546 " model vdw 2.170 3.120 nonbonded pdb=" NH1 ARG B 512 " pdb=" O SER B 546 " model vdw 2.172 3.120 nonbonded pdb=" O LYS D1057 " pdb=" NZ LYS D1057 " model vdw 2.182 3.120 ... (remaining 103525 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 154 through 168 or (resid 169 and (name N or name CA or na \ me C or name O or name CB )) or resid 170 through 183 or (resid 184 through 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 21 \ 2 or (resid 213 and (name N or name CA or name C or name O or name CB )) or resi \ d 214 through 231 or (resid 232 and (name N or name CA or name C or name O or na \ me CB )) or resid 233 through 237 or (resid 238 through 239 and (name N or name \ CA or name C or name O or name CB )) or resid 240 through 243 or (resid 244 and \ (name N or name CA or name C or name O or name CB )) or resid 245 through 247 or \ (resid 248 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 9 through 266 or (resid 267 and (name N or name CA or name C or name O or name C \ B )) or resid 268 through 271 or (resid 272 and (name N or name CA or name C or \ name O or name CB )) or resid 273 through 296 or (resid 297 and (name N or name \ CA or name C or name O or name CB )) or resid 298 through 421 or (resid 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 434 or \ (resid 435 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 6 through 445 or (resid 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 through 456 or (resid 457 and (name N or name CA or name C or \ name O or name CB )) or resid 458 through 501 or (resid 502 and (name N or name \ CA or name C or name O or name CB )) or resid 503 through 506 or (resid 507 and \ (name N or name CA or name C or name O or name CB )) or resid 508 through 576 or \ (resid 577 through 578 and (name N or name CA or name C or name O or name CB )) \ or resid 579 through 584 or (resid 585 and (name N or name CA or name C or name \ O or name CB )) or resid 586 through 617)) selection = (chain 'B' and (resid 154 through 212 or (resid 213 and (name N or name CA or na \ me C or name O or name CB )) or resid 214 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 228 or (resid \ 229 and (name N or name CA or name C or name O or name CB )) or resid 230 throug \ h 237 or (resid 238 through 239 and (name N or name CA or name C or name O or na \ me CB )) or resid 240 through 247 or (resid 248 and (name N or name CA or name C \ or name O or name CB )) or resid 249 or (resid 250 and (name N or name CA or na \ me C or name O or name CB )) or resid 251 through 257 or (resid 258 and (name N \ or name CA or name C or name O or name CB )) or resid 259 through 263 or (resid \ 264 and (name N or name CA or name C or name O or name CB )) or resid 265 throug \ h 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) or \ resid 273 through 277 or (resid 278 and (name N or name CA or name C or name O o \ r name CB )) or resid 279 through 288 or (resid 289 and (name N or name CA or na \ me C or name O or name CB )) or resid 290 through 339 or (resid 340 and (name N \ or name CA or name C or name O or name CB )) or resid 341 through 345 or (resid \ 346 and (name N or name CA or name C or name O or name CB )) or resid 347 throug \ h 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) or \ resid 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) \ or resid 423 through 442 or (resid 443 through 444 and (name N or name CA or na \ me C or name O or name CB )) or resid 445 through 452 or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 454 through 456 or (resid \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 throug \ h 472 or (resid 473 and (name N or name CA or name C or name O or name CB )) or \ resid 474 through 505 or (resid 506 through 507 and (name N or name CA or name C \ or name O or name CB )) or resid 508 or (resid 509 and (name N or name CA or na \ me C or name O or name CB )) or resid 510 through 557 or (resid 558 and (name N \ or name CA or name C or name O or name CB )) or resid 559 through 576 or (resid \ 577 through 578 and (name N or name CA or name C or name O or name CB )) or resi \ d 579 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 597 or (resid 598 and (name N or name CA or name C \ or name O or name CB )) or resid 599 through 616 or (resid 617 and (name N or n \ ame CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 154 through 168 or (resid 169 and (name N or name CA or na \ me C or name O or name CB )) or resid 170 through 183 or (resid 184 through 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 21 \ 7 or (resid 218 and (name N or name CA or name C or name O or name CB )) or resi \ d 219 through 228 or (resid 229 and (name N or name CA or name C or name O or na \ me CB )) or resid 230 through 231 or (resid 232 and (name N or name CA or name C \ or name O or name CB )) or resid 233 through 238 or (resid 239 and (name N or n \ ame CA or name C or name O or name CB )) or resid 240 through 243 or (resid 244 \ and (name N or name CA or name C or name O or name CB )) or resid 245 through 24 \ 9 or (resid 250 and (name N or name CA or name C or name O or name CB )) or resi \ d 251 through 257 or (resid 258 and (name N or name CA or name C or name O or na \ me CB )) or resid 259 through 263 or (resid 264 and (name N or name CA or name C \ or name O or name CB )) or resid 265 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 277 or (resid 278 \ and (name N or name CA or name C or name O or name CB )) or resid 279 through 28 \ 8 or (resid 289 and (name N or name CA or name C or name O or name CB )) or resi \ d 290 through 296 or (resid 297 and (name N or name CA or name C or name O or na \ me CB )) or resid 298 through 339 or (resid 340 and (name N or name CA or name C \ or name O or name CB )) or resid 341 through 345 or (resid 346 and (name N or n \ ame CA or name C or name O or name CB )) or resid 347 through 419 or (resid 420 \ and (name N or name CA or name C or name O or name CB )) or resid 421 through 43 \ 4 or (resid 435 and (name N or name CA or name C or name O or name CB )) or resi \ d 436 through 442 or (resid 443 through 444 and (name N or name CA or name C or \ name O or name CB )) or resid 445 or (resid 446 and (name N or name CA or name C \ or name O or name CB )) or resid 447 through 452 or (resid 453 and (name N or n \ ame CA or name C or name O or name CB )) or resid 454 through 472 or (resid 473 \ and (name N or name CA or name C or name O or name CB )) or resid 474 through 50 \ 1 or (resid 502 and (name N or name CA or name C or name O or name CB )) or resi \ d 503 through 505 or (resid 506 through 507 and (name N or name CA or name C or \ name O or name CB )) or resid 508 or (resid 509 and (name N or name CA or name C \ or name O or name CB )) or resid 510 through 557 or (resid 558 and (name N or n \ ame CA or name C or name O or name CB )) or resid 559 through 577 or (resid 578 \ and (name N or name CA or name C or name O or name CB )) or resid 579 through 59 \ 7 or (resid 598 and (name N or name CA or name C or name O or name CB )) or resi \ d 599 through 617)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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: 0.010 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: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.005 0.057 14526 Z= 0.246 Angle : 0.847 13.519 19729 Z= 0.462 Chirality : 0.048 0.200 2221 Planarity : 0.005 0.074 2475 Dihedral : 13.959 86.907 5225 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.19), residues: 1770 helix: -0.10 (0.17), residues: 934 sheet: -3.13 (0.58), residues: 64 loop : -3.63 (0.19), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D1195 TYR 0.027 0.002 TYR D 923 PHE 0.032 0.002 PHE D1020 TRP 0.071 0.003 TRP D1034 HIS 0.006 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00540 (14526) covalent geometry : angle 0.84748 (19729) hydrogen bonds : bond 0.14399 ( 673) hydrogen bonds : angle 5.64546 ( 1923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 PRO cc_start: 0.8167 (Cg_endo) cc_final: 0.6483 (Cg_exo) REVERT: A 494 GLN cc_start: 0.7946 (mp10) cc_final: 0.7620 (mp10) REVERT: A 498 TYR cc_start: 0.6253 (t80) cc_final: 0.6037 (t80) REVERT: C 232 ARG cc_start: 0.8677 (mpp-170) cc_final: 0.8444 (mpt180) REVERT: C 449 ARG cc_start: 0.8945 (mmt180) cc_final: 0.8739 (mmt180) REVERT: C 452 LEU cc_start: 0.9323 (pp) cc_final: 0.8995 (tp) REVERT: C 453 LYS cc_start: 0.9325 (pttm) cc_final: 0.9121 (ptpp) REVERT: D 925 TRP cc_start: 0.5376 (t-100) cc_final: 0.5142 (t-100) REVERT: D 986 PHE cc_start: 0.8912 (t80) cc_final: 0.8450 (t80) REVERT: D 1011 MET cc_start: 0.9278 (mtp) cc_final: 0.8930 (mtp) REVERT: D 1044 MET cc_start: 0.8861 (mtp) cc_final: 0.8608 (mtp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1076 time to fit residues: 28.2887 Evaluate side-chains 135 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 466 ASN B 557 ASN C 312 ASN C 468 HIS C 494 GLN D 891 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.108628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.086465 restraints weight = 51339.700| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.76 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14526 Z= 0.153 Angle : 0.728 11.950 19729 Z= 0.373 Chirality : 0.044 0.204 2221 Planarity : 0.005 0.074 2475 Dihedral : 5.397 29.019 1960 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 1.53 % Allowed : 10.67 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.20), residues: 1770 helix: 0.37 (0.17), residues: 943 sheet: -2.90 (0.57), residues: 70 loop : -3.50 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 449 TYR 0.033 0.001 TYR D 950 PHE 0.024 0.002 PHE D1020 TRP 0.057 0.002 TRP D1034 HIS 0.008 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00322 (14526) covalent geometry : angle 0.72774 (19729) hydrogen bonds : bond 0.06648 ( 673) hydrogen bonds : angle 4.73935 ( 1923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 TRP cc_start: 0.7705 (OUTLIER) cc_final: 0.6752 (t60) REVERT: A 456 PRO cc_start: 0.8142 (Cg_endo) cc_final: 0.6689 (Cg_exo) REVERT: A 460 ARG cc_start: 0.7074 (mtm-85) cc_final: 0.6796 (mtm-85) REVERT: A 494 GLN cc_start: 0.8197 (mp10) cc_final: 0.7897 (mp10) REVERT: A 498 TYR cc_start: 0.6229 (t80) cc_final: 0.5884 (t80) REVERT: C 409 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 450 GLU cc_start: 0.9109 (pm20) cc_final: 0.8833 (pm20) REVERT: C 453 LYS cc_start: 0.9365 (pttm) cc_final: 0.9102 (ptpp) REVERT: C 496 GLN cc_start: 0.7235 (mp-120) cc_final: 0.6926 (mp-120) REVERT: D 1011 MET cc_start: 0.9208 (mtp) cc_final: 0.8827 (mtp) outliers start: 23 outliers final: 13 residues processed: 179 average time/residue: 0.1075 time to fit residues: 28.7789 Evaluate side-chains 155 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 803 HIS Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 995 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN A 610 ASN ** B 557 ASN ** 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 = 0.3955 r_free = 0.3955 target = 0.109826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.087690 restraints weight = 51611.508| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.80 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14526 Z= 0.136 Angle : 0.678 10.710 19729 Z= 0.343 Chirality : 0.044 0.435 2221 Planarity : 0.005 0.075 2475 Dihedral : 5.046 24.755 1960 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 2.33 % Allowed : 13.28 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.20), residues: 1770 helix: 0.61 (0.17), residues: 942 sheet: -2.88 (0.60), residues: 64 loop : -3.39 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 512 TYR 0.027 0.001 TYR D 950 PHE 0.022 0.001 PHE A 380 TRP 0.053 0.001 TRP D1034 HIS 0.006 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00286 (14526) covalent geometry : angle 0.67766 (19729) hydrogen bonds : bond 0.05869 ( 673) hydrogen bonds : angle 4.44638 ( 1923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7860 (t160) cc_final: 0.7656 (t0) REVERT: A 311 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.6783 (t60) REVERT: A 356 LEU cc_start: 0.8609 (tt) cc_final: 0.8357 (tp) REVERT: A 460 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6753 (mtm-85) REVERT: A 494 GLN cc_start: 0.8174 (mp10) cc_final: 0.7817 (mp10) REVERT: B 275 ARG cc_start: 0.8033 (mmt180) cc_final: 0.7675 (mpt180) REVERT: B 462 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8589 (mp0) REVERT: C 370 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.5965 (p0) REVERT: C 409 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8137 (tm-30) REVERT: C 416 LYS cc_start: 0.9047 (mtmm) cc_final: 0.8808 (mtmm) REVERT: C 450 GLU cc_start: 0.9134 (pm20) cc_final: 0.8875 (pm20) REVERT: C 453 LYS cc_start: 0.9379 (pttm) cc_final: 0.9082 (ptpp) REVERT: C 489 LEU cc_start: 0.8835 (mt) cc_final: 0.8534 (mp) REVERT: C 496 GLN cc_start: 0.7266 (mp-120) cc_final: 0.6542 (mp10) REVERT: D 1011 MET cc_start: 0.9249 (mtp) cc_final: 0.8814 (mtp) outliers start: 35 outliers final: 19 residues processed: 182 average time/residue: 0.1089 time to fit residues: 29.7437 Evaluate side-chains 166 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 803 HIS Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1044 MET Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 139 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.106368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.083855 restraints weight = 52358.821| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.80 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14526 Z= 0.226 Angle : 0.746 13.166 19729 Z= 0.387 Chirality : 0.046 0.315 2221 Planarity : 0.005 0.077 2475 Dihedral : 5.193 26.551 1960 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 3.34 % Allowed : 17.55 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.19), residues: 1770 helix: 0.40 (0.17), residues: 948 sheet: -2.88 (0.60), residues: 64 loop : -3.51 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 232 TYR 0.025 0.002 TYR D 950 PHE 0.022 0.002 PHE A 380 TRP 0.027 0.002 TRP D1034 HIS 0.007 0.002 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00514 (14526) covalent geometry : angle 0.74648 (19729) hydrogen bonds : bond 0.07207 ( 673) hydrogen bonds : angle 4.76424 ( 1923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4675 (t80) REVERT: A 267 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6537 (mt-10) REVERT: A 311 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.6788 (t60) REVERT: A 494 GLN cc_start: 0.8225 (mp10) cc_final: 0.7699 (mp10) REVERT: C 409 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8143 (tm-30) REVERT: C 450 GLU cc_start: 0.9202 (pm20) cc_final: 0.8973 (pm20) REVERT: C 489 LEU cc_start: 0.8814 (mt) cc_final: 0.8521 (mp) REVERT: C 494 GLN cc_start: 0.8296 (mp-120) cc_final: 0.8081 (mp10) REVERT: C 571 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8260 (pp) REVERT: D 1007 TYR cc_start: 0.9116 (t80) cc_final: 0.8690 (t80) REVERT: D 1011 MET cc_start: 0.9321 (mtp) cc_final: 0.9065 (mtp) outliers start: 50 outliers final: 30 residues processed: 181 average time/residue: 0.1025 time to fit residues: 28.3902 Evaluate side-chains 172 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 314 CYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 803 HIS Chi-restraints excluded: chain D residue 960 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1044 MET Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 400 ASN ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.109438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.086999 restraints weight = 51509.530| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 4.81 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14526 Z= 0.138 Angle : 0.697 16.925 19729 Z= 0.347 Chirality : 0.043 0.244 2221 Planarity : 0.005 0.076 2475 Dihedral : 4.892 23.806 1960 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 2.94 % Allowed : 18.88 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.20), residues: 1770 helix: 0.66 (0.17), residues: 949 sheet: -2.73 (0.59), residues: 70 loop : -3.42 (0.19), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 449 TYR 0.025 0.001 TYR D 950 PHE 0.022 0.001 PHE B 282 TRP 0.025 0.001 TRP D1034 HIS 0.006 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00300 (14526) covalent geometry : angle 0.69738 (19729) hydrogen bonds : bond 0.05938 ( 673) hydrogen bonds : angle 4.36236 ( 1923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.4965 (OUTLIER) cc_final: 0.4604 (t80) REVERT: A 267 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: A 311 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.6821 (t60) REVERT: A 356 LEU cc_start: 0.8618 (tt) cc_final: 0.8360 (tp) REVERT: A 400 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8281 (t0) REVERT: A 456 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.6338 (Cg_exo) REVERT: A 494 GLN cc_start: 0.8248 (mp10) cc_final: 0.7792 (mp10) REVERT: B 275 ARG cc_start: 0.8082 (mmt180) cc_final: 0.7764 (mmt180) REVERT: C 353 TRP cc_start: 0.7280 (t-100) cc_final: 0.6932 (t-100) REVERT: C 370 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6254 (p0) REVERT: C 409 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8071 (tm-30) REVERT: C 416 LYS cc_start: 0.9057 (mtmm) cc_final: 0.8802 (mtmm) REVERT: C 489 LEU cc_start: 0.8801 (mt) cc_final: 0.8494 (mp) REVERT: C 571 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8219 (pp) REVERT: D 1007 TYR cc_start: 0.9032 (t80) cc_final: 0.8623 (t80) REVERT: D 1011 MET cc_start: 0.9287 (mtp) cc_final: 0.9041 (mtp) outliers start: 44 outliers final: 25 residues processed: 184 average time/residue: 0.1033 time to fit residues: 29.2545 Evaluate side-chains 176 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 960 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1044 MET Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 130 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.109744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087436 restraints weight = 51530.079| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.80 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14526 Z= 0.137 Angle : 0.692 14.863 19729 Z= 0.346 Chirality : 0.043 0.262 2221 Planarity : 0.005 0.076 2475 Dihedral : 4.768 24.765 1960 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 2.87 % Allowed : 20.01 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1770 helix: 0.75 (0.17), residues: 949 sheet: -2.47 (0.63), residues: 64 loop : -3.35 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.024 0.001 TYR D 950 PHE 0.023 0.001 PHE B 282 TRP 0.053 0.001 TRP D1034 HIS 0.006 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00297 (14526) covalent geometry : angle 0.69236 (19729) hydrogen bonds : bond 0.05638 ( 673) hydrogen bonds : angle 4.26816 ( 1923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: A 311 TRP cc_start: 0.7648 (OUTLIER) cc_final: 0.6837 (t60) REVERT: A 356 LEU cc_start: 0.8605 (tt) cc_final: 0.8350 (tp) REVERT: A 494 GLN cc_start: 0.8154 (mp10) cc_final: 0.7678 (mp10) REVERT: B 401 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7596 (pmm) REVERT: C 409 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 416 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8786 (mtmm) REVERT: C 489 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8392 (mp) REVERT: C 571 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8290 (pp) REVERT: D 1007 TYR cc_start: 0.9028 (t80) cc_final: 0.8585 (t80) REVERT: D 1011 MET cc_start: 0.9280 (mtp) cc_final: 0.9006 (mtp) outliers start: 43 outliers final: 30 residues processed: 184 average time/residue: 0.1060 time to fit residues: 29.6603 Evaluate side-chains 180 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 960 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 109 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 116 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 140 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.110543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.088378 restraints weight = 51355.784| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 4.81 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14526 Z= 0.134 Angle : 0.690 14.857 19729 Z= 0.344 Chirality : 0.043 0.241 2221 Planarity : 0.005 0.075 2475 Dihedral : 4.678 25.118 1960 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 3.20 % Allowed : 19.61 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1770 helix: 0.75 (0.17), residues: 956 sheet: -2.44 (0.63), residues: 64 loop : -3.26 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.023 0.001 TYR D 950 PHE 0.026 0.001 PHE B 282 TRP 0.039 0.001 TRP D1034 HIS 0.006 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00287 (14526) covalent geometry : angle 0.69010 (19729) hydrogen bonds : bond 0.05323 ( 673) hydrogen bonds : angle 4.17749 ( 1923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6353 (mt-10) REVERT: A 311 TRP cc_start: 0.7678 (OUTLIER) cc_final: 0.6880 (t60) REVERT: A 356 LEU cc_start: 0.8593 (tt) cc_final: 0.8342 (tp) REVERT: A 494 GLN cc_start: 0.8102 (mp10) cc_final: 0.7631 (mp10) REVERT: B 275 ARG cc_start: 0.7691 (mmt180) cc_final: 0.7398 (mmt180) REVERT: B 401 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7549 (pmm) REVERT: C 409 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 416 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8801 (mtmm) REVERT: C 489 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 571 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8300 (pp) REVERT: D 803 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7240 (p-80) REVERT: D 1007 TYR cc_start: 0.9019 (t80) cc_final: 0.8588 (t80) outliers start: 48 outliers final: 33 residues processed: 185 average time/residue: 0.1060 time to fit residues: 30.0196 Evaluate side-chains 183 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 468 HIS Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 803 HIS Chi-restraints excluded: chain D residue 960 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 995 ASP Chi-restraints excluded: chain D residue 1044 MET Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 27 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 127 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 400 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** 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 = 0.3993 r_free = 0.3993 target = 0.112489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.090422 restraints weight = 50504.315| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.80 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14526 Z= 0.129 Angle : 0.693 16.127 19729 Z= 0.343 Chirality : 0.043 0.263 2221 Planarity : 0.004 0.075 2475 Dihedral : 4.452 23.735 1960 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 2.40 % Allowed : 20.75 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.20), residues: 1770 helix: 0.79 (0.17), residues: 951 sheet: -2.25 (0.65), residues: 64 loop : -3.09 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 512 TYR 0.023 0.001 TYR D 950 PHE 0.019 0.001 PHE A 380 TRP 0.036 0.001 TRP D1034 HIS 0.005 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00267 (14526) covalent geometry : angle 0.69261 (19729) hydrogen bonds : bond 0.04599 ( 673) hydrogen bonds : angle 4.06462 ( 1923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.4497 (OUTLIER) cc_final: 0.4165 (t80) REVERT: A 267 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6281 (mt-10) REVERT: A 311 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.6886 (t60) REVERT: A 339 ASP cc_start: 0.8483 (m-30) cc_final: 0.8270 (t70) REVERT: B 275 ARG cc_start: 0.7679 (mmt180) cc_final: 0.7443 (mpt180) REVERT: B 401 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7427 (pmm) REVERT: C 297 ARG cc_start: 0.8317 (ptm-80) cc_final: 0.7927 (ptm-80) REVERT: C 409 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 416 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8790 (mtmm) REVERT: C 489 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8434 (mp) REVERT: C 571 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8201 (pp) REVERT: D 1007 TYR cc_start: 0.9027 (t80) cc_final: 0.8614 (t80) REVERT: D 1188 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8922 (mmmt) outliers start: 36 outliers final: 25 residues processed: 191 average time/residue: 0.1023 time to fit residues: 29.7495 Evaluate side-chains 183 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 960 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 1044 MET Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 1 optimal weight: 5.9990 chunk 112 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 43 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.112497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.090409 restraints weight = 51182.583| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.83 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14526 Z= 0.127 Angle : 0.701 15.066 19729 Z= 0.347 Chirality : 0.043 0.261 2221 Planarity : 0.004 0.075 2475 Dihedral : 4.424 22.429 1960 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.40 % Allowed : 21.21 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.20), residues: 1770 helix: 0.79 (0.17), residues: 951 sheet: -2.69 (0.62), residues: 62 loop : -2.96 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 512 TYR 0.023 0.001 TYR D 923 PHE 0.018 0.001 PHE A 380 TRP 0.038 0.001 TRP D 925 HIS 0.005 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00275 (14526) covalent geometry : angle 0.70071 (19729) hydrogen bonds : bond 0.04551 ( 673) hydrogen bonds : angle 4.08439 ( 1923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.4531 (OUTLIER) cc_final: 0.4184 (t80) REVERT: A 267 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6332 (mt-10) REVERT: A 311 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.6907 (t60) REVERT: A 494 GLN cc_start: 0.8163 (mp10) cc_final: 0.7939 (mp10) REVERT: B 275 ARG cc_start: 0.7539 (mmt180) cc_final: 0.7290 (mpt180) REVERT: B 401 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7185 (pmm) REVERT: B 544 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: C 297 ARG cc_start: 0.8408 (ptm-80) cc_final: 0.8051 (ptm-80) REVERT: C 353 TRP cc_start: 0.7245 (t-100) cc_final: 0.6998 (t-100) REVERT: C 409 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 489 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8466 (mp) REVERT: C 571 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8164 (pp) REVERT: D 1007 TYR cc_start: 0.9067 (t80) cc_final: 0.8570 (t80) outliers start: 36 outliers final: 27 residues processed: 185 average time/residue: 0.1039 time to fit residues: 29.4735 Evaluate side-chains 181 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 960 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 1044 MET Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 139 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.110026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.087783 restraints weight = 51365.768| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 4.79 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14526 Z= 0.168 Angle : 0.739 16.462 19729 Z= 0.370 Chirality : 0.044 0.240 2221 Planarity : 0.005 0.074 2475 Dihedral : 4.583 23.232 1960 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.60 % Allowed : 21.21 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.20), residues: 1770 helix: 0.74 (0.17), residues: 948 sheet: -2.39 (0.65), residues: 58 loop : -3.03 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 512 TYR 0.022 0.001 TYR D 950 PHE 0.017 0.001 PHE A 380 TRP 0.073 0.002 TRP D1034 HIS 0.006 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00385 (14526) covalent geometry : angle 0.73890 (19729) hydrogen bonds : bond 0.05565 ( 673) hydrogen bonds : angle 4.27854 ( 1923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.4591 (OUTLIER) cc_final: 0.4259 (t80) REVERT: A 279 MET cc_start: 0.9204 (ptm) cc_final: 0.8613 (pmm) REVERT: A 494 GLN cc_start: 0.8198 (mp10) cc_final: 0.7990 (mp10) REVERT: C 297 ARG cc_start: 0.8467 (ptm-80) cc_final: 0.7977 (ptm-80) REVERT: C 409 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 489 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8559 (mp) REVERT: C 571 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8201 (pp) outliers start: 39 outliers final: 29 residues processed: 169 average time/residue: 0.1014 time to fit residues: 26.3163 Evaluate side-chains 169 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 TRP Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 960 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 1044 MET Chi-restraints excluded: chain D residue 1147 LEU Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1211 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 100 optimal weight: 8.9990 chunk 166 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.112414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090299 restraints weight = 50353.431| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.82 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14526 Z= 0.128 Angle : 0.707 15.143 19729 Z= 0.351 Chirality : 0.043 0.269 2221 Planarity : 0.004 0.074 2475 Dihedral : 4.432 21.100 1960 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.87 % Allowed : 21.88 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.20), residues: 1770 helix: 0.83 (0.18), residues: 945 sheet: -2.42 (0.66), residues: 54 loop : -2.97 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 512 TYR 0.023 0.001 TYR D 950 PHE 0.018 0.001 PHE A 380 TRP 0.067 0.002 TRP D1034 HIS 0.005 0.001 HIS C 310 Details of bonding type rmsd covalent geometry : bond 0.00277 (14526) covalent geometry : angle 0.70741 (19729) hydrogen bonds : bond 0.04721 ( 673) hydrogen bonds : angle 4.11626 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2395.63 seconds wall clock time: 41 minutes 59.61 seconds (2519.61 seconds total)