Starting phenix.real_space_refine on Thu Sep 18 14:24:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfe_39221/09_2025/8yfe_39221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfe_39221/09_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_39221/09_2025/8yfe_39221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfe_39221/09_2025/8yfe_39221.map" model { file = "/net/cci-nas-00/data/ceres_data/8yfe_39221/09_2025/8yfe_39221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfe_39221/09_2025/8yfe_39221.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.79, per 1000 atoms: 0.22 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: 1.48 Conformation dependent library (CDL) restraints added in 651.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.63 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: 3.32 Time building geometry restraints manager: 1.99 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: 0.620 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.110 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- 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= 0.103 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 : 10.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG D 106 TYR 0.025 0.001 TYR A 857 PHE 0.015 0.001 PHE D 158 TRP 0.021 0.001 TRP A 288 HIS 0.006 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00216 (17747) covalent geometry : angle 0.53691 (23998) hydrogen bonds : bond 0.24765 ( 722) hydrogen bonds : angle 8.17299 ( 2025) *********************** 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 : 0.724 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: 0.7932 (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: 0.1235 time to fit residues: 21.3944 Evaluate side-chains 85 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.075284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053216 restraints weight = 74889.590| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.65 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17747 Z= 0.201 Angle : 0.606 10.226 23998 Z= 0.314 Chirality : 0.044 0.167 2547 Planarity : 0.004 0.047 3087 Dihedral : 4.202 18.926 2325 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.52 % Allowed : 7.72 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 2077 helix: 0.78 (0.18), residues: 838 sheet: -1.02 (0.31), residues: 264 loop : -0.33 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 703 TYR 0.020 0.001 TYR C 841 PHE 0.023 0.001 PHE C 7 TRP 0.015 0.001 TRP A 320 HIS 0.007 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00445 (17747) covalent geometry : angle 0.60583 (23998) hydrogen bonds : bond 0.05779 ( 722) hydrogen bonds : angle 5.84413 ( 2025) *********************** 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: 10 poor density : 89 time to evaluate : 0.697 Fit side-chains REVERT: A 330 ASP cc_start: 0.8829 (p0) cc_final: 0.8214 (t0) REVERT: A 380 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8336 (tp30) REVERT: A 566 MET cc_start: 0.7497 (tmm) cc_final: 0.7093 (tmm) REVERT: A 647 ASP cc_start: 0.8209 (m-30) cc_final: 0.8009 (m-30) REVERT: A 783 MET cc_start: 0.8295 (ptp) cc_final: 0.8016 (ptp) REVERT: A 838 PHE cc_start: 0.7793 (m-10) cc_final: 0.7480 (m-10) REVERT: A 857 TYR cc_start: 0.9004 (t80) cc_final: 0.8738 (t80) REVERT: B 105 MET cc_start: 0.9435 (mmp) cc_final: 0.9233 (mmm) REVERT: B 252 LEU cc_start: 0.9270 (mm) cc_final: 0.8984 (mm) outliers start: 10 outliers final: 4 residues processed: 95 average time/residue: 0.1242 time to fit residues: 19.5738 Evaluate side-chains 82 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 557 GLN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 64 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.074350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.052209 restraints weight = 75471.899| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.63 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17747 Z= 0.237 Angle : 0.614 8.416 23998 Z= 0.316 Chirality : 0.044 0.144 2547 Planarity : 0.004 0.057 3087 Dihedral : 4.340 21.294 2325 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.15 % Allowed : 11.92 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 2077 helix: 0.81 (0.18), residues: 825 sheet: -1.05 (0.32), residues: 252 loop : -0.35 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 295 TYR 0.018 0.001 TYR C 841 PHE 0.017 0.002 PHE D 158 TRP 0.014 0.002 TRP A 320 HIS 0.008 0.001 HIS C 719 Details of bonding type rmsd covalent geometry : bond 0.00529 (17747) covalent geometry : angle 0.61369 (23998) hydrogen bonds : bond 0.05098 ( 722) hydrogen bonds : angle 5.47057 ( 2025) *********************** 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 104 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.714 Fit side-chains REVERT: A 203 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 205 GLU cc_start: 0.8337 (pm20) cc_final: 0.7820 (pm20) REVERT: A 330 ASP cc_start: 0.8725 (p0) cc_final: 0.8187 (t0) REVERT: A 356 LEU cc_start: 0.8820 (mt) cc_final: 0.8242 (mt) REVERT: A 359 MET cc_start: 0.8576 (mtm) cc_final: 0.8301 (mtm) REVERT: A 548 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: A 566 MET cc_start: 0.7649 (tmm) cc_final: 0.7256 (tmm) REVERT: A 783 MET cc_start: 0.8287 (ptp) cc_final: 0.7986 (ptp) REVERT: A 838 PHE cc_start: 0.7528 (m-10) cc_final: 0.7316 (m-10) REVERT: A 857 TYR cc_start: 0.9153 (t80) cc_final: 0.8704 (t80) REVERT: B 252 LEU cc_start: 0.9324 (mm) cc_final: 0.9010 (mm) REVERT: B 269 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6310 (t80) REVERT: C 126 ASP cc_start: 0.7820 (m-30) cc_final: 0.7347 (p0) REVERT: C 363 LEU cc_start: 0.9350 (mp) cc_final: 0.9011 (mp) outliers start: 22 outliers final: 11 residues processed: 99 average time/residue: 0.1224 time to fit residues: 20.0436 Evaluate side-chains 92 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 669 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 83 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.075094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053073 restraints weight = 74961.520| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.61 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17747 Z= 0.160 Angle : 0.552 9.294 23998 Z= 0.283 Chirality : 0.042 0.164 2547 Planarity : 0.004 0.035 3087 Dihedral : 4.173 18.627 2325 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.52 % Allowed : 13.33 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 2077 helix: 0.92 (0.18), residues: 834 sheet: -0.99 (0.31), residues: 262 loop : -0.27 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 376 TYR 0.017 0.001 TYR C 841 PHE 0.017 0.001 PHE D 158 TRP 0.012 0.001 TRP D 256 HIS 0.006 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00357 (17747) covalent geometry : angle 0.55232 (23998) hydrogen bonds : bond 0.04447 ( 722) hydrogen bonds : angle 5.17980 ( 2025) *********************** 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 114 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.588 Fit side-chains REVERT: A 297 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8603 (m-10) REVERT: A 330 ASP cc_start: 0.8666 (p0) cc_final: 0.8045 (t0) REVERT: A 356 LEU cc_start: 0.8868 (mt) cc_final: 0.8360 (mt) REVERT: A 359 MET cc_start: 0.8376 (mtm) cc_final: 0.8163 (mtm) REVERT: A 380 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8434 (tp30) REVERT: A 548 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: A 566 MET cc_start: 0.7455 (tmm) cc_final: 0.7080 (tmm) REVERT: A 783 MET cc_start: 0.8283 (ptp) cc_final: 0.7980 (ptp) REVERT: A 838 PHE cc_start: 0.7537 (m-10) cc_final: 0.7269 (m-10) REVERT: A 857 TYR cc_start: 0.9107 (t80) cc_final: 0.8644 (t80) REVERT: B 105 MET cc_start: 0.9334 (mmm) cc_final: 0.9096 (mmm) REVERT: B 252 LEU cc_start: 0.9324 (mm) cc_final: 0.8989 (mm) REVERT: B 269 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6387 (t80) REVERT: C 110 MET cc_start: 0.8591 (mmm) cc_final: 0.8253 (mmm) REVERT: C 126 ASP cc_start: 0.7706 (m-30) cc_final: 0.7274 (p0) REVERT: C 167 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7761 (mmp) REVERT: C 192 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7252 (mp0) outliers start: 29 outliers final: 15 residues processed: 106 average time/residue: 0.1042 time to fit residues: 18.9603 Evaluate side-chains 101 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 548 GLU Chi-restraints excluded: chain A residue 577 VAL 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 B residue 351 ASP Chi-restraints excluded: chain C residue 167 MET 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 326 PHE 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 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 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.0170 chunk 17 optimal weight: 0.0770 chunk 88 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 147 optimal weight: 0.0170 chunk 105 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 0.8218 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.076446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.054734 restraints weight = 72828.466| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 4.53 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17747 Z= 0.105 Angle : 0.523 10.302 23998 Z= 0.264 Chirality : 0.041 0.150 2547 Planarity : 0.003 0.034 3087 Dihedral : 3.958 16.492 2325 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.52 % Allowed : 13.86 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.19), residues: 2077 helix: 1.09 (0.19), residues: 842 sheet: -0.86 (0.32), residues: 256 loop : -0.22 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 252 TYR 0.017 0.001 TYR C 841 PHE 0.015 0.001 PHE D 158 TRP 0.012 0.001 TRP C 288 HIS 0.007 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00226 (17747) covalent geometry : angle 0.52301 (23998) hydrogen bonds : bond 0.04009 ( 722) hydrogen bonds : angle 4.89302 ( 2025) *********************** 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: 29 poor density : 88 time to evaluate : 0.667 Fit side-chains REVERT: A 203 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 205 GLU cc_start: 0.7843 (pm20) cc_final: 0.7550 (pm20) REVERT: A 297 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: A 330 ASP cc_start: 0.8597 (p0) cc_final: 0.8018 (t0) REVERT: A 356 LEU cc_start: 0.8835 (mt) cc_final: 0.8352 (mt) REVERT: A 380 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8353 (tp30) REVERT: A 548 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: A 566 MET cc_start: 0.7430 (tmm) cc_final: 0.7084 (tmm) REVERT: A 783 MET cc_start: 0.8279 (ptp) cc_final: 0.8005 (ptp) REVERT: A 838 PHE cc_start: 0.7416 (m-10) cc_final: 0.7140 (m-10) REVERT: A 857 TYR cc_start: 0.9139 (t80) cc_final: 0.8723 (t80) REVERT: B 67 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7833 (pp) REVERT: B 105 MET cc_start: 0.9349 (mmm) cc_final: 0.9032 (mmm) REVERT: B 157 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8137 (mp10) REVERT: B 252 LEU cc_start: 0.9335 (mm) cc_final: 0.9132 (mm) REVERT: C 110 MET cc_start: 0.8497 (mmm) cc_final: 0.8241 (mmm) REVERT: C 126 ASP cc_start: 0.7573 (m-30) cc_final: 0.7255 (p0) REVERT: C 167 MET cc_start: 0.8071 (mmp) cc_final: 0.7699 (mmp) REVERT: C 192 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: C 797 MET cc_start: 0.8909 (pmm) cc_final: 0.8574 (pmm) outliers start: 29 outliers final: 13 residues processed: 112 average time/residue: 0.1031 time to fit residues: 19.6957 Evaluate side-chains 104 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 297 TYR Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU 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 35 THR 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 26 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3681 r_free = 0.3681 target = 0.074710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.052696 restraints weight = 75158.834| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.56 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17747 Z= 0.211 Angle : 0.575 10.691 23998 Z= 0.292 Chirality : 0.043 0.144 2547 Planarity : 0.004 0.040 3087 Dihedral : 4.113 19.195 2325 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.31 % Allowed : 13.91 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.19), residues: 2077 helix: 1.08 (0.19), residues: 838 sheet: -0.95 (0.32), residues: 256 loop : -0.25 (0.21), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.019 0.001 TYR C 841 PHE 0.016 0.001 PHE D 158 TRP 0.011 0.001 TRP A 320 HIS 0.005 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00471 (17747) covalent geometry : angle 0.57546 (23998) hydrogen bonds : bond 0.04254 ( 722) hydrogen bonds : angle 4.96358 ( 2025) *********************** 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 128 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 84 time to evaluate : 0.612 Fit side-chains REVERT: A 241 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8918 (mm) REVERT: A 297 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8589 (m-10) REVERT: A 330 ASP cc_start: 0.8635 (p0) cc_final: 0.8090 (t0) REVERT: A 356 LEU cc_start: 0.8913 (mt) cc_final: 0.8542 (mt) REVERT: A 380 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8469 (tp30) REVERT: A 548 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: A 566 MET cc_start: 0.7551 (tmm) cc_final: 0.7201 (tmm) REVERT: A 783 MET cc_start: 0.8294 (ptp) cc_final: 0.8009 (ptp) REVERT: A 838 PHE cc_start: 0.7563 (m-10) cc_final: 0.7298 (m-10) REVERT: A 857 TYR cc_start: 0.9185 (t80) cc_final: 0.8679 (t80) REVERT: B 67 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7877 (pp) REVERT: B 87 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: B 105 MET cc_start: 0.9322 (mmm) cc_final: 0.9046 (mmm) REVERT: B 157 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: B 252 LEU cc_start: 0.9358 (mm) cc_final: 0.9135 (mm) REVERT: B 269 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6679 (t80) REVERT: C 110 MET cc_start: 0.8523 (mmm) cc_final: 0.8275 (mmm) REVERT: C 126 ASP cc_start: 0.7570 (m-30) cc_final: 0.7273 (p0) REVERT: C 167 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7862 (mmp) REVERT: C 192 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: C 645 MET cc_start: 0.8759 (tmm) cc_final: 0.8154 (tmm) REVERT: D 109 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8650 (mm) outliers start: 44 outliers final: 26 residues processed: 123 average time/residue: 0.1054 time to fit residues: 21.6994 Evaluate side-chains 119 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 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 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 167 MET 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 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 109 LEU Chi-restraints excluded: chain D residue 177 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 185 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 60 optimal weight: 0.0010 chunk 6 optimal weight: 0.0370 chunk 123 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 1.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 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 = 0.3702 r_free = 0.3702 target = 0.075667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.053806 restraints weight = 73746.049| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.58 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17747 Z= 0.122 Angle : 0.542 11.857 23998 Z= 0.271 Chirality : 0.042 0.169 2547 Planarity : 0.004 0.033 3087 Dihedral : 3.986 16.735 2325 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.52 % Allowed : 13.86 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 2077 helix: 1.15 (0.19), residues: 841 sheet: -0.91 (0.31), residues: 260 loop : -0.21 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 761 TYR 0.019 0.001 TYR C 841 PHE 0.015 0.001 PHE D 158 TRP 0.011 0.001 TRP D 256 HIS 0.004 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00273 (17747) covalent geometry : angle 0.54168 (23998) hydrogen bonds : bond 0.03927 ( 722) hydrogen bonds : angle 4.78757 ( 2025) *********************** 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 136 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 88 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 205 GLU cc_start: 0.7931 (pm20) cc_final: 0.7638 (pm20) REVERT: A 241 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8881 (mm) REVERT: A 297 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8541 (m-10) REVERT: A 330 ASP cc_start: 0.8644 (p0) cc_final: 0.8059 (t0) REVERT: A 356 LEU cc_start: 0.8806 (mt) cc_final: 0.8589 (mt) REVERT: A 380 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8590 (tp30) REVERT: A 548 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: A 566 MET cc_start: 0.7426 (tmm) cc_final: 0.6979 (tmt) REVERT: A 653 ILE cc_start: 0.9013 (tp) cc_final: 0.8679 (mm) REVERT: A 783 MET cc_start: 0.8329 (ptp) cc_final: 0.8015 (ptp) REVERT: A 838 PHE cc_start: 0.7476 (m-10) cc_final: 0.7207 (m-10) REVERT: A 857 TYR cc_start: 0.9176 (t80) cc_final: 0.8687 (t80) REVERT: B 67 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7801 (pp) REVERT: B 87 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8326 (mm-30) REVERT: B 157 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: B 252 LEU cc_start: 0.9368 (mm) cc_final: 0.9118 (mm) REVERT: B 269 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6469 (t80) REVERT: C 110 MET cc_start: 0.8503 (mmm) cc_final: 0.8293 (mmm) REVERT: C 126 ASP cc_start: 0.7575 (m-30) cc_final: 0.7222 (p0) REVERT: C 167 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7846 (mmp) REVERT: C 192 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: C 297 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8625 (m-10) outliers start: 48 outliers final: 23 residues processed: 129 average time/residue: 0.1032 time to fit residues: 22.7586 Evaluate side-chains 119 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 548 GLU Chi-restraints excluded: chain A residue 571 ILE 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 B residue 351 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU 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 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 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 176 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 91 optimal weight: 0.0670 chunk 44 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.074085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.052179 restraints weight = 75010.799| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.48 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17747 Z= 0.263 Angle : 0.647 12.536 23998 Z= 0.324 Chirality : 0.044 0.159 2547 Planarity : 0.004 0.043 3087 Dihedral : 4.256 20.957 2325 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.47 % Allowed : 14.23 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 2077 helix: 0.99 (0.18), residues: 843 sheet: -1.05 (0.32), residues: 256 loop : -0.29 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 761 TYR 0.026 0.001 TYR C 841 PHE 0.017 0.002 PHE D 158 TRP 0.013 0.002 TRP D 101 HIS 0.008 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00587 (17747) covalent geometry : angle 0.64731 (23998) hydrogen bonds : bond 0.04348 ( 722) hydrogen bonds : angle 5.04169 ( 2025) *********************** 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 131 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8960 (mm) REVERT: A 297 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8637 (m-10) REVERT: A 330 ASP cc_start: 0.8646 (p0) cc_final: 0.8041 (t0) REVERT: A 356 LEU cc_start: 0.8910 (mt) cc_final: 0.8365 (mt) REVERT: A 380 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8502 (tp30) REVERT: A 548 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: A 566 MET cc_start: 0.7594 (tmm) cc_final: 0.7239 (tmm) REVERT: A 653 ILE cc_start: 0.8940 (tp) cc_final: 0.8601 (mm) REVERT: A 783 MET cc_start: 0.8284 (ptp) cc_final: 0.8015 (ptp) REVERT: A 838 PHE cc_start: 0.7582 (m-10) cc_final: 0.7336 (m-10) REVERT: B 67 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7914 (pp) REVERT: B 87 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8339 (mm-30) REVERT: B 252 LEU cc_start: 0.9419 (mm) cc_final: 0.9199 (mm) REVERT: B 269 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.6803 (t80) REVERT: C 110 MET cc_start: 0.8553 (mmm) cc_final: 0.8336 (mmm) REVERT: C 126 ASP cc_start: 0.7652 (m-30) cc_final: 0.7374 (p0) REVERT: C 167 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7839 (mmp) REVERT: C 192 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: C 645 MET cc_start: 0.8897 (tmm) cc_final: 0.8369 (tmm) REVERT: C 719 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8558 (t-90) outliers start: 47 outliers final: 32 residues processed: 124 average time/residue: 0.1073 time to fit residues: 22.6918 Evaluate side-chains 124 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 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 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 167 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 76 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.076063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.054234 restraints weight = 74566.201| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.61 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.002 0.033 17747 Z= 0.108 Angle : 0.560 12.334 23998 Z= 0.277 Chirality : 0.042 0.167 2547 Planarity : 0.003 0.033 3087 Dihedral : 3.984 16.099 2325 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.05 % Allowed : 15.07 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.19), residues: 2077 helix: 1.20 (0.19), residues: 844 sheet: -0.92 (0.31), residues: 260 loop : -0.20 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 761 TYR 0.022 0.001 TYR C 841 PHE 0.015 0.001 PHE D 158 TRP 0.014 0.001 TRP A 671 HIS 0.011 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00234 (17747) covalent geometry : angle 0.55974 (23998) hydrogen bonds : bond 0.03830 ( 722) hydrogen bonds : angle 4.75823 ( 2025) *********************** 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 126 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.567 Fit side-chains REVERT: A 203 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: A 241 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8844 (mm) REVERT: A 356 LEU cc_start: 0.8985 (mt) cc_final: 0.8545 (mt) REVERT: A 380 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8597 (tp30) REVERT: A 548 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: A 566 MET cc_start: 0.7450 (tmm) cc_final: 0.7043 (tmt) REVERT: A 653 ILE cc_start: 0.8855 (tp) cc_final: 0.8497 (mm) REVERT: A 783 MET cc_start: 0.8324 (ptp) cc_final: 0.8020 (ptp) REVERT: A 838 PHE cc_start: 0.7493 (m-10) cc_final: 0.7250 (m-10) REVERT: A 857 TYR cc_start: 0.9262 (t80) cc_final: 0.8954 (t80) REVERT: B 67 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7790 (pp) REVERT: B 87 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8323 (mm-30) REVERT: B 105 MET cc_start: 0.9469 (mmm) cc_final: 0.9236 (mmm) REVERT: B 157 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: B 252 LEU cc_start: 0.9397 (mm) cc_final: 0.9128 (mm) REVERT: B 269 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6458 (t80) REVERT: C 110 MET cc_start: 0.8475 (mmm) cc_final: 0.8237 (mmm) REVERT: C 126 ASP cc_start: 0.7541 (m-30) cc_final: 0.7211 (p0) REVERT: C 167 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7740 (mmp) REVERT: C 192 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: C 297 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8632 (m-10) REVERT: C 645 MET cc_start: 0.8924 (tmm) cc_final: 0.8327 (tmm) outliers start: 39 outliers final: 24 residues processed: 120 average time/residue: 0.1083 time to fit residues: 21.9217 Evaluate side-chains 119 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 775 ASP 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 262 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 167 MET 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 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 262 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 160 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 136 optimal weight: 0.0870 chunk 157 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 overall best weight: 1.2360 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.076044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054123 restraints weight = 73946.316| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.59 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17747 Z= 0.119 Angle : 0.571 13.458 23998 Z= 0.280 Chirality : 0.042 0.156 2547 Planarity : 0.003 0.033 3087 Dihedral : 3.925 16.019 2325 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.89 % Allowed : 15.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 2077 helix: 1.23 (0.19), residues: 850 sheet: -0.79 (0.31), residues: 264 loop : -0.21 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 761 TYR 0.022 0.001 TYR C 841 PHE 0.014 0.001 PHE D 158 TRP 0.015 0.001 TRP A 671 HIS 0.012 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00267 (17747) covalent geometry : angle 0.57080 (23998) hydrogen bonds : bond 0.03790 ( 722) hydrogen bonds : angle 4.73360 ( 2025) ********************** 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 127 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.706 Fit side-chains REVERT: A 203 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 241 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8859 (mm) REVERT: A 351 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8413 (mp) REVERT: A 354 GLN cc_start: 0.8681 (mp10) cc_final: 0.8456 (mm-40) REVERT: A 356 LEU cc_start: 0.9013 (mt) cc_final: 0.8580 (mt) REVERT: A 380 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8247 (tm-30) REVERT: A 548 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: A 566 MET cc_start: 0.7421 (tmm) cc_final: 0.7039 (tmm) REVERT: A 653 ILE cc_start: 0.8858 (tp) cc_final: 0.8502 (mm) REVERT: A 783 MET cc_start: 0.8313 (ptp) cc_final: 0.8005 (ptp) REVERT: A 838 PHE cc_start: 0.7466 (m-10) cc_final: 0.7236 (m-10) REVERT: A 857 TYR cc_start: 0.9272 (t80) cc_final: 0.8972 (t80) REVERT: B 67 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7808 (pp) REVERT: B 87 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: B 157 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: B 252 LEU cc_start: 0.9391 (mm) cc_final: 0.9135 (mm) REVERT: B 269 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6626 (t80) REVERT: C 110 MET cc_start: 0.8464 (mmm) cc_final: 0.8244 (mmm) REVERT: C 126 ASP cc_start: 0.7147 (m-30) cc_final: 0.6894 (m-30) REVERT: C 167 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7735 (mmp) REVERT: C 192 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 297 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8656 (m-10) REVERT: C 645 MET cc_start: 0.8984 (tmm) cc_final: 0.8395 (tmm) REVERT: D 53 ASP cc_start: 0.9109 (t0) cc_final: 0.8529 (p0) outliers start: 36 outliers final: 19 residues processed: 121 average time/residue: 0.1086 time to fit residues: 22.2471 Evaluate side-chains 116 residues out of total 1905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 571 ILE 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 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 192 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.074941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052938 restraints weight = 75261.541| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.60 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2328 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= 0.191 Angle : 0.598 13.308 23998 Z= 0.297 Chirality : 0.043 0.156 2547 Planarity : 0.004 0.034 3087 Dihedral : 4.063 18.138 2325 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.89 % Allowed : 15.33 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.19), residues: 2077 helix: 1.16 (0.19), residues: 845 sheet: -0.80 (0.32), residues: 253 loop : -0.26 (0.21), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 761 TYR 0.024 0.001 TYR C 841 PHE 0.015 0.001 PHE D 158 TRP 0.015 0.001 TRP A 671 HIS 0.011 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00429 (17747) covalent geometry : angle 0.59816 (23998) hydrogen bonds : bond 0.04011 ( 722) hydrogen bonds : angle 4.82312 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.10 seconds wall clock time: 50 minutes 20.74 seconds (3020.74 seconds total)