Starting phenix.real_space_refine on Tue Jan 21 21:54:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfe_39221/01_2025/8yfe_39221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfe_39221/01_2025/8yfe_39221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yfe_39221/01_2025/8yfe_39221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfe_39221/01_2025/8yfe_39221.map" model { file = "/net/cci-nas-00/data/ceres_data/8yfe_39221/01_2025/8yfe_39221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfe_39221/01_2025/8yfe_39221.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 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 11109 2.51 5 N 2939 2.21 5 O 3203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17315 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5651 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 45, 'TRANS': 641} Chain breaks: 4 Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3051 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 2 Chain: "C" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5519 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 43, 'TRANS': 628} Chain breaks: 5 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3094 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 16, 'TRANS': 360} Time building chain proxies: 8.91, per 1000 atoms: 0.51 Number of scatterers: 17315 At special positions: 0 Unit cell: (150.894, 140.436, 119.52, 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 3203 8.00 N 2939 7.00 C 11109 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: 3.91 Conformation dependent library (CDL) restraints added in 2.1 seconds 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 17 sheets defined 47.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 4.257A pdb=" N TRP A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.820A pdb=" N GLY A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.640A pdb=" N HIS A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 92 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.637A pdb=" N SER A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.966A pdb=" N ILE A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.677A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.554A pdb=" N SER A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.562A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 removed outlier: 4.267A pdb=" N PHE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.676A pdb=" N GLU A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.608A pdb=" N ASP A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 328 " --> pdb=" O CYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 370 through 407 removed outlier: 3.521A pdb=" N ARG A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 3.858A pdb=" N TYR A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 583 removed outlier: 3.763A pdb=" N LEU A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.050A pdb=" N ALA A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 689 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.620A pdb=" N LEU A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 Processing helix chain 'A' and resid 857 through 868 removed outlier: 5.079A pdb=" N ASP A 866 " --> pdb=" O GLN A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.969A pdb=" N ILE B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.989A pdb=" N VAL B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.588A pdb=" N SER B 187 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 4.193A pdb=" N ARG B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 241 through 263 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 306 through 326 removed outlier: 4.130A pdb=" N SER B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.665A pdb=" N SER B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 72 through 92 removed outlier: 3.821A pdb=" N MET C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 129 removed outlier: 3.763A pdb=" N ASN C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 184 removed outlier: 3.520A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.583A pdb=" N SER C 189 " --> pdb=" O PRO C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 217 removed outlier: 3.711A pdb=" N ILE C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 243 removed outlier: 4.212A pdb=" N PHE C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 302 Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.828A pdb=" N PHE C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 343 through 356 Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.537A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 541 through 552 removed outlier: 3.896A pdb=" N ARG C 545 " --> pdb=" O GLY C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 581 removed outlier: 3.950A pdb=" N VAL C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 removed outlier: 3.502A pdb=" N GLU C 608 " --> pdb=" O ASN C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 627 removed outlier: 3.505A pdb=" N SER C 627 " --> pdb=" O GLU C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 647 removed outlier: 3.539A pdb=" N MET C 645 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 656 Processing helix chain 'C' and resid 681 through 690 removed outlier: 3.577A pdb=" N LYS C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 688 " --> pdb=" O ARG C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 696 removed outlier: 4.986A pdb=" N ASP C 694 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 703 Processing helix chain 'C' and resid 718 through 728 removed outlier: 4.313A pdb=" N THR C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 819 removed outlier: 4.088A pdb=" N ILE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.550A pdb=" N ASP C 866 " --> pdb=" O GLN C 862 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.724A pdb=" N ILE D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 69 through 75 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.660A pdb=" N GLY D 128 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 149 Processing helix chain 'D' and resid 153 through 167 removed outlier: 3.952A pdb=" N GLN D 157 " --> pdb=" O HIS D 153 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 225 through 229 removed outlier: 4.263A pdb=" N ARG D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 229' Processing helix chain 'D' and resid 241 through 263 Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 306 through 326 removed outlier: 3.586A pdb=" N SER D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 363 Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.521A pdb=" N LYS D 368 " --> pdb=" O PRO D 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.329A pdb=" N ILE A 229 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N GLU A 253 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 53 removed outlier: 6.424A pdb=" N ILE A 97 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER A 196 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 99 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA4, first strand: chain 'A' and resid 662 through 663 Processing sheet with id=AA5, first strand: chain 'A' and resid 759 through 760 removed outlier: 4.354A pdb=" N ILE A 776 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.504A pdb=" N LEU B 346 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 7 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 119 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 removed outlier: 4.181A pdb=" N GLY B 202 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 25 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 200 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B 23 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 19 removed outlier: 4.181A pdb=" N GLY B 202 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR B 195 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 98 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLY B 211 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR B 100 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ALA B 213 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.298A pdb=" N TYR B 230 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 268 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B 232 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY B 270 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS B 234 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG B 272 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR B 236 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 282 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 280 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.566A pdb=" N ILE C 229 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N GLU C 253 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR C 230 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR C 51 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP C 48 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 96 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 193 " --> pdb=" O VAL C 712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AB3, first strand: chain 'C' and resid 662 through 663 Processing sheet with id=AB4, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 8 removed outlier: 4.760A pdb=" N VAL D 331 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP D 332 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL D 123 " --> pdb=" O TRP D 332 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 119 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 36 removed outlier: 5.859A pdb=" N GLN D 23 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG D 200 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D 194 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR D 195 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 98 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY D 211 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 100 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ALA D 213 " --> pdb=" O THR D 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AB8, first strand: chain 'D' and resid 216 through 217 removed outlier: 4.411A pdb=" N LYS D 266 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 232 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 269 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 282 " --> pdb=" O TYR D 269 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2025 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: 5.55 Time building geometry restraints manager: 4.56 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: 5581 1.34 - 1.46: 4090 1.46 - 1.58: 7970 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 17747 Sorted by residual: bond pdb=" CA ILE D 289 " pdb=" CB ILE D 289 " ideal model delta sigma weight residual 1.539 1.549 -0.010 5.40e-03 3.43e+04 3.12e+00 bond pdb=" CA ASP C 837 " pdb=" C ASP C 837 " ideal model delta sigma weight residual 1.529 1.519 0.010 1.04e-02 9.25e+03 9.60e-01 bond pdb=" CB PHE C 838 " pdb=" CG PHE C 838 " ideal model delta sigma weight residual 1.502 1.523 -0.021 2.30e-02 1.89e+03 8.09e-01 bond pdb=" CE2 TYR D 315 " pdb=" CZ TYR D 315 " ideal model delta sigma weight residual 1.378 1.359 0.019 2.40e-02 1.74e+03 6.54e-01 bond pdb=" CA ASP B 329 " pdb=" CB ASP B 329 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.41e-01 ... (remaining 17742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 23827 2.68 - 5.35: 162 5.35 - 8.03: 7 8.03 - 10.70: 1 10.70 - 13.38: 1 Bond angle restraints: 23998 Sorted by residual: angle pdb=" N ILE A 817 " pdb=" CA ILE A 817 " pdb=" C ILE A 817 " ideal model delta sigma weight residual 113.53 108.64 4.89 9.80e-01 1.04e+00 2.49e+01 angle pdb=" CB MET D 105 " pdb=" CG MET D 105 " pdb=" SD MET D 105 " ideal model delta sigma weight residual 112.70 99.32 13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 114.56 110.25 4.31 1.27e+00 6.20e-01 1.15e+01 angle pdb=" N GLU B 85 " pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " ideal model delta sigma weight residual 110.28 115.33 -5.05 1.55e+00 4.16e-01 1.06e+01 angle pdb=" C ASP B 328 " pdb=" N ASP B 329 " pdb=" CA ASP B 329 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.10e+00 ... (remaining 23993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 9642 17.24 - 34.49: 904 34.49 - 51.73: 178 51.73 - 68.98: 23 68.98 - 86.22: 15 Dihedral angle restraints: 10762 sinusoidal: 4535 harmonic: 6227 Sorted by residual: dihedral pdb=" CA PHE A 325 " pdb=" C PHE A 325 " pdb=" N PHE A 326 " pdb=" CA PHE A 326 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA THR A 810 " pdb=" C THR A 810 " pdb=" N GLN A 811 " pdb=" CA GLN A 811 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PHE C 325 " pdb=" C PHE C 325 " pdb=" N PHE C 326 " pdb=" CA PHE C 326 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 10759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1920 0.044 - 0.088: 464 0.088 - 0.131: 160 0.131 - 0.175: 2 0.175 - 0.219: 1 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB VAL A 255 " pdb=" CA VAL A 255 " pdb=" CG1 VAL A 255 " pdb=" CG2 VAL A 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA GLU B 89 " pdb=" N GLU B 89 " pdb=" C GLU B 89 " pdb=" CB GLU B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 2544 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 352 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C GLU D 352 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU D 352 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN D 353 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 637 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO C 638 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 638 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 638 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 857 " 0.010 2.00e-02 2.50e+03 9.90e-03 1.96e+00 pdb=" CG TYR A 857 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 857 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 857 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 857 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 857 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 857 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 857 " -0.001 2.00e-02 2.50e+03 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 371 2.68 - 3.24: 17652 3.24 - 3.79: 27649 3.79 - 4.35: 37031 4.35 - 4.90: 58246 Nonbonded interactions: 140949 Sorted by model distance: nonbonded pdb=" OH TYR C 547 " pdb=" OD2 ASP C 602 " model vdw 2.126 3.040 nonbonded pdb=" OD1 ASP C 386 " pdb=" OH TYR C 542 " model vdw 2.169 3.040 nonbonded pdb=" OH TYR C 622 " pdb=" OE1 GLU C 700 " model vdw 2.171 3.040 nonbonded pdb=" O ASP D 118 " pdb=" OH TYR D 138 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASP A 386 " pdb=" OH TYR A 542 " model vdw 2.190 3.040 ... (remaining 140944 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 5 through 63 or resid 69 through 129 or resid 156 through \ 257 or resid 283 through 406 or resid 533 through 824 or resid 836 through 867)) \ selection = (chain 'C' and (resid 5 through 824 or resid 836 through 867)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 2 through 147 or resid 150 through 301 or resid 304 throug \ h 376)) } 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.380 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.002 0.023 17747 Z= 0.142 Angle : 0.537 13.379 23998 Z= 0.273 Chirality : 0.042 0.219 2547 Planarity : 0.004 0.039 3087 Dihedral : 13.896 86.221 6738 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 2077 helix: 0.61 (0.19), residues: 799 sheet: -0.82 (0.34), residues: 241 loop : -0.22 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 288 HIS 0.006 0.001 HIS C 227 PHE 0.015 0.001 PHE D 158 TYR 0.025 0.001 TYR A 857 ARG 0.008 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.885 Fit side-chains REVERT: A 50 LEU cc_start: 0.9147 (tp) cc_final: 0.8803 (tp) REVERT: A 566 MET cc_start: 0.7381 (tmm) cc_final: 0.7076 (tmm) REVERT: A 647 ASP cc_start: 0.8358 (m-30) cc_final: 0.8146 (m-30) REVERT: B 105 MET cc_start: 0.9428 (mmp) cc_final: 0.9213 (mmm) REVERT: B 339 ARG cc_start: 0.8249 (ppt170) cc_final: 0.7933 (ppt170) REVERT: C 76 MET cc_start: 0.8752 (ptt) cc_final: 0.8105 (pmm) REVERT: C 77 MET cc_start: 0.7104 (mmt) cc_final: 0.6763 (mmt) REVERT: C 664 MET cc_start: 0.6363 (tmm) cc_final: 0.6136 (tmm) REVERT: D 122 ASP cc_start: 0.7806 (m-30) cc_final: 0.7575 (p0) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2868 time to fit residues: 48.7831 Evaluate side-chains 84 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.5980 chunk 158 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 106 optimal weight: 0.0370 chunk 84 optimal weight: 0.3980 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 244 HIS ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN C 583 GLN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.075774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053783 restraints weight = 74624.326| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.64 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17747 Z= 0.251 Angle : 0.597 9.739 23998 Z= 0.309 Chirality : 0.044 0.181 2547 Planarity : 0.004 0.041 3087 Dihedral : 4.135 17.747 2325 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.47 % Allowed : 7.35 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 2077 helix: 0.80 (0.18), residues: 838 sheet: -0.98 (0.31), residues: 264 loop : -0.31 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 320 HIS 0.007 0.001 HIS C 719 PHE 0.024 0.001 PHE C 7 TYR 0.021 0.001 TYR C 841 ARG 0.004 0.001 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 2.058 Fit side-chains REVERT: A 330 ASP cc_start: 0.8796 (p0) cc_final: 0.8053 (t0) REVERT: A 380 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8361 (tp30) REVERT: A 566 MET cc_start: 0.7429 (tmm) cc_final: 0.7096 (tmm) REVERT: A 647 ASP cc_start: 0.8259 (m-30) cc_final: 0.8053 (m-30) REVERT: A 783 MET cc_start: 0.8291 (ptp) cc_final: 0.8014 (ptp) REVERT: A 838 PHE cc_start: 0.7755 (m-10) cc_final: 0.7435 (m-10) REVERT: A 857 TYR cc_start: 0.9089 (t80) cc_final: 0.8820 (t80) REVERT: B 105 MET cc_start: 0.9431 (mmp) cc_final: 0.9224 (mmm) REVERT: B 252 LEU cc_start: 0.9254 (mm) cc_final: 0.8975 (mm) REVERT: C 354 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8361 (mm-40) REVERT: D 122 ASP cc_start: 0.7858 (m-30) cc_final: 0.7641 (p0) outliers start: 9 outliers final: 4 residues processed: 96 average time/residue: 0.2611 time to fit residues: 41.5900 Evaluate side-chains 83 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 340 ASN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.075704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.053576 restraints weight = 74428.403| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.65 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17747 Z= 0.234 Angle : 0.556 8.427 23998 Z= 0.285 Chirality : 0.043 0.165 2547 Planarity : 0.004 0.040 3087 Dihedral : 4.058 17.690 2325 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.68 % Allowed : 10.92 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 2077 helix: 0.94 (0.18), residues: 837 sheet: -0.90 (0.31), residues: 264 loop : -0.29 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 320 HIS 0.007 0.001 HIS A 719 PHE 0.016 0.001 PHE D 158 TYR 0.018 0.001 TYR C 841 ARG 0.005 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.860 Fit side-chains REVERT: A 203 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: A 205 GLU cc_start: 0.8280 (pm20) cc_final: 0.7848 (pm20) REVERT: A 330 ASP cc_start: 0.8721 (p0) cc_final: 0.8254 (t0) REVERT: A 380 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8360 (tp30) REVERT: A 548 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: A 566 MET cc_start: 0.7454 (tmm) cc_final: 0.7084 (tmm) REVERT: A 783 MET cc_start: 0.8299 (ptp) cc_final: 0.8026 (ptp) REVERT: A 838 PHE cc_start: 0.7710 (m-10) cc_final: 0.7384 (m-10) REVERT: A 857 TYR cc_start: 0.9194 (t80) cc_final: 0.8813 (t80) REVERT: B 252 LEU cc_start: 0.9296 (mm) cc_final: 0.8999 (mm) REVERT: C 126 ASP cc_start: 0.7798 (m-30) cc_final: 0.7348 (p0) REVERT: C 354 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8333 (mm-40) REVERT: D 122 ASP cc_start: 0.7864 (m-30) cc_final: 0.7640 (p0) outliers start: 13 outliers final: 3 residues processed: 96 average time/residue: 0.2536 time to fit residues: 40.2347 Evaluate side-chains 82 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 669 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 95 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 557 GLN C 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052067 restraints weight = 74954.441| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.61 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17747 Z= 0.364 Angle : 0.621 9.235 23998 Z= 0.319 Chirality : 0.044 0.166 2547 Planarity : 0.004 0.054 3087 Dihedral : 4.294 20.656 2325 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.57 % Allowed : 13.23 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 2077 helix: 0.81 (0.18), residues: 838 sheet: -1.02 (0.32), residues: 252 loop : -0.30 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 256 HIS 0.007 0.001 HIS A 719 PHE 0.017 0.001 PHE D 158 TYR 0.016 0.001 TYR C 841 ARG 0.004 0.000 ARG C 703 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 2.229 Fit side-chains REVERT: A 330 ASP cc_start: 0.8687 (p0) cc_final: 0.8201 (t0) REVERT: A 356 LEU cc_start: 0.9203 (mt) cc_final: 0.9001 (mp) REVERT: A 380 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8456 (tp30) REVERT: A 548 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8422 (pm20) REVERT: A 566 MET cc_start: 0.7678 (tmm) cc_final: 0.7263 (tmm) REVERT: A 783 MET cc_start: 0.8309 (ptp) cc_final: 0.8029 (ptp) REVERT: A 838 PHE cc_start: 0.7547 (m-10) cc_final: 0.7307 (m-10) REVERT: B 105 MET cc_start: 0.9356 (mmm) cc_final: 0.9083 (mmm) REVERT: B 252 LEU cc_start: 0.9326 (mm) cc_final: 0.9021 (mm) REVERT: B 269 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6604 (t80) REVERT: C 126 ASP cc_start: 0.7726 (m-30) cc_final: 0.7297 (p0) REVERT: C 192 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7162 (mp0) outliers start: 30 outliers final: 16 residues processed: 104 average time/residue: 0.2540 time to fit residues: 44.8695 Evaluate side-chains 96 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 158 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.075062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.053007 restraints weight = 75377.060| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.64 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17747 Z= 0.246 Angle : 0.555 9.965 23998 Z= 0.284 Chirality : 0.043 0.171 2547 Planarity : 0.004 0.036 3087 Dihedral : 4.138 18.512 2325 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.99 % Allowed : 13.33 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2077 helix: 0.97 (0.18), residues: 839 sheet: -1.00 (0.32), residues: 252 loop : -0.31 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 320 HIS 0.007 0.001 HIS A 719 PHE 0.016 0.001 PHE D 158 TYR 0.017 0.001 TYR C 841 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 1.887 Fit side-chains REVERT: A 241 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 297 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: A 330 ASP cc_start: 0.8664 (p0) cc_final: 0.8067 (t0) REVERT: A 356 LEU cc_start: 0.9240 (mt) cc_final: 0.8900 (mp) REVERT: A 380 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8417 (tp30) REVERT: A 548 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: A 566 MET cc_start: 0.7451 (tmm) cc_final: 0.7026 (tmt) REVERT: A 783 MET cc_start: 0.8335 (ptp) cc_final: 0.8033 (ptp) REVERT: A 838 PHE cc_start: 0.7567 (m-10) cc_final: 0.7302 (m-10) REVERT: A 857 TYR cc_start: 0.9136 (t80) cc_final: 0.8567 (t80) REVERT: B 67 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7851 (pp) REVERT: B 105 MET cc_start: 0.9344 (mmm) cc_final: 0.9016 (mmm) REVERT: B 157 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7984 (mp10) REVERT: B 252 LEU cc_start: 0.9360 (mm) cc_final: 0.9122 (mm) REVERT: B 269 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.6442 (t80) REVERT: C 110 MET cc_start: 0.8580 (mmm) cc_final: 0.8319 (mmm) REVERT: C 126 ASP cc_start: 0.7641 (m-30) cc_final: 0.7285 (p0) REVERT: C 192 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7214 (mp0) outliers start: 38 outliers final: 22 residues processed: 111 average time/residue: 0.2576 time to fit residues: 48.5877 Evaluate side-chains 106 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 152 optimal weight: 0.0470 chunk 59 optimal weight: 0.0050 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 167 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.0254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.076169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054345 restraints weight = 74341.841| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.60 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17747 Z= 0.157 Angle : 0.532 11.115 23998 Z= 0.268 Chirality : 0.042 0.166 2547 Planarity : 0.003 0.034 3087 Dihedral : 3.931 16.039 2325 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.10 % Allowed : 13.75 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2077 helix: 1.19 (0.19), residues: 837 sheet: -0.92 (0.31), residues: 262 loop : -0.18 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 288 HIS 0.005 0.001 HIS C 227 PHE 0.015 0.001 PHE D 158 TYR 0.010 0.001 TYR C 841 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 2.030 Fit side-chains REVERT: A 203 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 205 GLU cc_start: 0.7874 (pm20) cc_final: 0.7590 (pm20) REVERT: A 297 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8539 (m-10) REVERT: A 330 ASP cc_start: 0.8594 (p0) cc_final: 0.8036 (t0) REVERT: A 356 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 380 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8586 (tp30) REVERT: A 548 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: A 566 MET cc_start: 0.7440 (tmm) cc_final: 0.7061 (tmm) REVERT: A 783 MET cc_start: 0.8304 (ptp) cc_final: 0.7989 (ptp) REVERT: A 838 PHE cc_start: 0.7441 (m-10) cc_final: 0.7167 (m-10) REVERT: B 67 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7785 (pp) REVERT: B 87 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8476 (mm-30) REVERT: B 108 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8633 (pp) REVERT: B 157 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: B 252 LEU cc_start: 0.9358 (mm) cc_final: 0.9117 (mm) REVERT: B 269 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.6381 (t80) REVERT: C 110 MET cc_start: 0.8500 (mmm) cc_final: 0.8237 (mmm) REVERT: C 126 ASP cc_start: 0.7609 (m-30) cc_final: 0.7221 (p0) REVERT: C 192 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: C 297 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8622 (m-10) outliers start: 40 outliers final: 16 residues processed: 122 average time/residue: 0.2598 time to fit residues: 52.2369 Evaluate side-chains 108 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 139 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN C 649 ASN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.074002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.051982 restraints weight = 75400.786| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.59 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17747 Z= 0.376 Angle : 0.630 11.699 23998 Z= 0.318 Chirality : 0.044 0.161 2547 Planarity : 0.004 0.044 3087 Dihedral : 4.211 20.498 2325 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.26 % Allowed : 14.33 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 2077 helix: 1.00 (0.18), residues: 839 sheet: -1.07 (0.32), residues: 256 loop : -0.30 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 101 HIS 0.007 0.001 HIS A 719 PHE 0.017 0.002 PHE D 158 TYR 0.023 0.001 TYR C 841 ARG 0.006 0.000 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 81 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: A 241 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8948 (mm) REVERT: A 297 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8641 (m-10) REVERT: A 330 ASP cc_start: 0.8652 (p0) cc_final: 0.8057 (t0) REVERT: A 356 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 380 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8513 (tp30) REVERT: A 548 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: A 566 MET cc_start: 0.7703 (tmm) cc_final: 0.7344 (tmm) REVERT: A 783 MET cc_start: 0.8288 (ptp) cc_final: 0.8021 (ptp) REVERT: A 838 PHE cc_start: 0.7567 (m-10) cc_final: 0.7322 (m-10) REVERT: B 67 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 87 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: B 252 LEU cc_start: 0.9424 (mm) cc_final: 0.9202 (mm) REVERT: B 269 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6740 (t80) REVERT: C 110 MET cc_start: 0.8559 (mmm) cc_final: 0.8332 (mmm) REVERT: C 126 ASP cc_start: 0.7680 (m-30) cc_final: 0.7380 (p0) REVERT: C 192 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: C 645 MET cc_start: 0.8885 (tmm) cc_final: 0.8346 (tmm) outliers start: 43 outliers final: 30 residues processed: 117 average time/residue: 0.2463 time to fit residues: 48.6748 Evaluate side-chains 117 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 136 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.074890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052975 restraints weight = 74706.115| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 4.54 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17747 Z= 0.245 Angle : 0.571 12.223 23998 Z= 0.288 Chirality : 0.043 0.163 2547 Planarity : 0.004 0.033 3087 Dihedral : 4.117 18.456 2325 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.57 % Allowed : 14.28 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 2077 helix: 1.07 (0.19), residues: 840 sheet: -1.01 (0.32), residues: 250 loop : -0.28 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 320 HIS 0.010 0.001 HIS A 719 PHE 0.016 0.001 PHE D 158 TYR 0.022 0.001 TYR C 841 ARG 0.005 0.000 ARG C 761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 83 time to evaluate : 2.034 Fit side-chains revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 205 GLU cc_start: 0.7916 (pm20) cc_final: 0.7507 (pm20) REVERT: A 241 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8863 (mm) REVERT: A 297 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8578 (m-10) REVERT: A 330 ASP cc_start: 0.8672 (p0) cc_final: 0.8084 (t0) REVERT: A 356 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8809 (mp) REVERT: A 380 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8448 (tp30) REVERT: A 548 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: A 566 MET cc_start: 0.7573 (tmm) cc_final: 0.7201 (tmm) REVERT: A 783 MET cc_start: 0.8344 (ptp) cc_final: 0.8010 (ptp) REVERT: A 838 PHE cc_start: 0.7543 (m-10) cc_final: 0.7276 (m-10) REVERT: A 857 TYR cc_start: 0.9168 (t80) cc_final: 0.8473 (t80) REVERT: B 67 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7897 (pp) REVERT: B 87 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: B 105 MET cc_start: 0.9473 (mmm) cc_final: 0.9226 (mmm) REVERT: B 157 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: B 252 LEU cc_start: 0.9420 (mm) cc_final: 0.9183 (mm) REVERT: B 269 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6660 (t80) REVERT: C 110 MET cc_start: 0.8533 (mmm) cc_final: 0.8302 (mmm) REVERT: C 126 ASP cc_start: 0.7767 (m-30) cc_final: 0.7421 (p0) REVERT: C 192 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: C 297 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: C 645 MET cc_start: 0.8963 (tmm) cc_final: 0.8354 (tmm) outliers start: 49 outliers final: 29 residues processed: 126 average time/residue: 0.2488 time to fit residues: 52.3926 Evaluate side-chains 121 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 139 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 182 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.075767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.053916 restraints weight = 74550.857| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.54 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17747 Z= 0.179 Angle : 0.558 12.756 23998 Z= 0.277 Chirality : 0.042 0.161 2547 Planarity : 0.003 0.033 3087 Dihedral : 3.971 16.917 2325 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.36 % Allowed : 14.65 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 2077 helix: 1.15 (0.19), residues: 842 sheet: -0.89 (0.32), residues: 250 loop : -0.20 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 288 HIS 0.011 0.001 HIS A 719 PHE 0.015 0.001 PHE D 158 TYR 0.022 0.001 TYR C 841 ARG 0.004 0.000 ARG C 761 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 83 time to evaluate : 1.915 Fit side-chains REVERT: A 203 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 205 GLU cc_start: 0.7903 (pm20) cc_final: 0.7530 (pm20) REVERT: A 241 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8875 (mm) REVERT: A 330 ASP cc_start: 0.8635 (p0) cc_final: 0.8062 (t0) REVERT: A 356 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8800 (mp) REVERT: A 380 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8435 (tp30) REVERT: A 548 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: A 566 MET cc_start: 0.7457 (tmm) cc_final: 0.7045 (tmt) REVERT: A 783 MET cc_start: 0.8355 (ptp) cc_final: 0.8031 (ptp) REVERT: A 838 PHE cc_start: 0.7494 (m-10) cc_final: 0.7228 (m-10) REVERT: A 857 TYR cc_start: 0.9147 (t80) cc_final: 0.8485 (t80) REVERT: B 67 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7860 (pp) REVERT: B 87 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: B 105 MET cc_start: 0.9458 (mmm) cc_final: 0.9188 (mmm) REVERT: B 157 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: B 252 LEU cc_start: 0.9439 (mm) cc_final: 0.9185 (mm) REVERT: B 269 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6604 (t80) REVERT: C 110 MET cc_start: 0.8498 (mmm) cc_final: 0.8268 (mmm) REVERT: C 126 ASP cc_start: 0.7553 (m-30) cc_final: 0.7213 (p0) REVERT: C 192 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: C 297 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.8588 (m-10) REVERT: C 645 MET cc_start: 0.8950 (tmm) cc_final: 0.8377 (tmm) outliers start: 45 outliers final: 27 residues processed: 121 average time/residue: 0.2437 time to fit residues: 49.9559 Evaluate side-chains 117 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 146 optimal weight: 3.9990 chunk 36 optimal weight: 0.0670 chunk 48 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 0.0980 chunk 12 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 GLN ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 153 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.075695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053811 restraints weight = 74539.641| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.61 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17747 Z= 0.197 Angle : 0.575 13.503 23998 Z= 0.284 Chirality : 0.042 0.178 2547 Planarity : 0.004 0.033 3087 Dihedral : 3.940 16.506 2325 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.10 % Allowed : 14.96 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 2077 helix: 1.19 (0.19), residues: 845 sheet: -0.83 (0.32), residues: 252 loop : -0.19 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 256 HIS 0.012 0.001 HIS A 719 PHE 0.015 0.001 PHE D 158 TYR 0.022 0.001 TYR C 841 ARG 0.004 0.000 ARG C 761 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 2.107 Fit side-chains REVERT: A 203 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7398 (tm-30) REVERT: A 205 GLU cc_start: 0.7942 (pm20) cc_final: 0.7566 (pm20) REVERT: A 241 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8881 (mm) REVERT: A 330 ASP cc_start: 0.8634 (p0) cc_final: 0.8069 (t0) REVERT: A 356 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 380 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8619 (tp30) REVERT: A 548 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: A 566 MET cc_start: 0.7416 (tmm) cc_final: 0.7054 (tmm) REVERT: A 783 MET cc_start: 0.8303 (ptp) cc_final: 0.7989 (ptp) REVERT: A 838 PHE cc_start: 0.7517 (m-10) cc_final: 0.7287 (m-10) REVERT: A 857 TYR cc_start: 0.9161 (t80) cc_final: 0.8502 (t80) REVERT: B 67 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7885 (pp) REVERT: B 87 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: B 105 MET cc_start: 0.9527 (mmm) cc_final: 0.9307 (mmm) REVERT: B 157 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: B 252 LEU cc_start: 0.9436 (mm) cc_final: 0.9195 (mm) REVERT: B 269 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.6607 (t80) REVERT: C 110 MET cc_start: 0.8501 (mmm) cc_final: 0.8285 (mmm) REVERT: C 126 ASP cc_start: 0.7203 (m-30) cc_final: 0.6985 (m-30) REVERT: C 192 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: C 297 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8522 (m-10) REVERT: C 645 MET cc_start: 0.8957 (tmm) cc_final: 0.8375 (tmm) outliers start: 40 outliers final: 26 residues processed: 116 average time/residue: 0.2519 time to fit residues: 49.8952 Evaluate side-chains 119 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 143 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 97 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 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 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.076371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.054578 restraints weight = 73807.879| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 4.53 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 17747 Z= 0.161 Angle : 0.563 13.302 23998 Z= 0.277 Chirality : 0.042 0.203 2547 Planarity : 0.003 0.033 3087 Dihedral : 3.862 15.768 2325 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.99 % Allowed : 15.28 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 2077 helix: 1.18 (0.19), residues: 855 sheet: -0.77 (0.31), residues: 263 loop : -0.19 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 288 HIS 0.010 0.001 HIS A 719 PHE 0.014 0.001 PHE D 158 TYR 0.020 0.001 TYR C 841 ARG 0.004 0.000 ARG C 761 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5719.58 seconds wall clock time: 103 minutes 37.40 seconds (6217.40 seconds total)