Starting phenix.real_space_refine on Mon Oct 14 10:02:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfe_39221/10_2024/8yfe_39221.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfe_39221/10_2024/8yfe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfe_39221/10_2024/8yfe_39221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfe_39221/10_2024/8yfe_39221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfe_39221/10_2024/8yfe_39221.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfe_39221/10_2024/8yfe_39221.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 11109 2.51 5 N 2939 2.21 5 O 3203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 17315 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5651 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 45, 'TRANS': 641} Chain breaks: 4 Chain: "B" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3051 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 15, 'TRANS': 355} Chain breaks: 2 Chain: "C" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5519 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 43, 'TRANS': 628} Chain breaks: 5 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3094 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 16, 'TRANS': 360} Time building chain proxies: 9.87, per 1000 atoms: 0.57 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: 4.02 Conformation dependent library (CDL) restraints added in 2.3 seconds 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4024 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 17 sheets defined 47.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 4.257A pdb=" N TRP A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.820A pdb=" N GLY A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.640A pdb=" N HIS A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 92 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.637A pdb=" N SER A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.966A pdb=" N ILE A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.677A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 removed outlier: 3.554A pdb=" N SER A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.562A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 243 removed outlier: 4.267A pdb=" N PHE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.676A pdb=" N GLU A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.608A pdb=" N ASP A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 328 " --> pdb=" O CYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 370 through 407 removed outlier: 3.521A pdb=" N ARG A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 3.858A pdb=" N TYR A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 583 removed outlier: 3.763A pdb=" N LEU A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.050A pdb=" N ALA A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 689 " --> pdb=" O LEU A 685 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 691 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.620A pdb=" N LEU A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 842 Processing helix chain 'A' and resid 857 through 868 removed outlier: 5.079A pdb=" N ASP A 866 " --> pdb=" O GLN A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.969A pdb=" N ILE B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.989A pdb=" N VAL B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.588A pdb=" N SER B 187 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 4.193A pdb=" N ARG B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 241 through 263 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 306 through 326 removed outlier: 4.130A pdb=" N SER B 310 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.665A pdb=" N SER B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 72 through 92 removed outlier: 3.821A pdb=" N MET C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 129 removed outlier: 3.763A pdb=" N ASN C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 184 removed outlier: 3.520A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.583A pdb=" N SER C 189 " --> pdb=" O PRO C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 217 removed outlier: 3.711A pdb=" N ILE C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 243 removed outlier: 4.212A pdb=" N PHE C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 302 Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.828A pdb=" N PHE C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 326 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'C' and resid 343 through 356 Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.537A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 541 through 552 removed outlier: 3.896A pdb=" N ARG C 545 " --> pdb=" O GLY C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 581 removed outlier: 3.950A pdb=" N VAL C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 removed outlier: 3.502A pdb=" N GLU C 608 " --> pdb=" O ASN C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 627 removed outlier: 3.505A pdb=" N SER C 627 " --> pdb=" O GLU C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 647 removed outlier: 3.539A pdb=" N MET C 645 " --> pdb=" O PHE C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 656 Processing helix chain 'C' and resid 681 through 690 removed outlier: 3.577A pdb=" N LYS C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 688 " --> pdb=" O ARG C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 696 removed outlier: 4.986A pdb=" N ASP C 694 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 703 Processing helix chain 'C' and resid 718 through 728 removed outlier: 4.313A pdb=" N THR C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 819 removed outlier: 4.088A pdb=" N ILE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.550A pdb=" N ASP C 866 " --> pdb=" O GLN C 862 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 867 " --> pdb=" O ILE C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 removed outlier: 3.724A pdb=" N ILE D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 69 through 75 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.660A pdb=" N GLY D 128 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 149 Processing helix chain 'D' and resid 153 through 167 removed outlier: 3.952A pdb=" N GLN D 157 " --> pdb=" O HIS D 153 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 225 through 229 removed outlier: 4.263A pdb=" N ARG D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 229' Processing helix chain 'D' and resid 241 through 263 Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 306 through 326 removed outlier: 3.586A pdb=" N SER D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 363 Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.521A pdb=" N LYS D 368 " --> pdb=" O PRO D 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.329A pdb=" N ILE A 229 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N GLU A 253 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 53 removed outlier: 6.424A pdb=" N ILE A 97 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER A 196 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 99 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA4, first strand: chain 'A' and resid 662 through 663 Processing sheet with id=AA5, first strand: chain 'A' and resid 759 through 760 removed outlier: 4.354A pdb=" N ILE A 776 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.504A pdb=" N LEU B 346 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 7 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 119 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 19 removed outlier: 4.181A pdb=" N GLY B 202 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 25 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 200 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B 23 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 19 removed outlier: 4.181A pdb=" N GLY B 202 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR B 195 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 98 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLY B 211 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR B 100 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ALA B 213 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.298A pdb=" N TYR B 230 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 268 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B 232 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY B 270 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS B 234 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG B 272 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR B 236 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 282 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 280 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.566A pdb=" N ILE C 229 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N GLU C 253 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TYR C 230 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR C 51 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP C 48 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 96 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 193 " --> pdb=" O VAL C 712 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 364 through 365 Processing sheet with id=AB3, first strand: chain 'C' and resid 662 through 663 Processing sheet with id=AB4, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 8 removed outlier: 4.760A pdb=" N VAL D 331 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP D 332 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL D 123 " --> pdb=" O TRP D 332 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 119 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 36 removed outlier: 5.859A pdb=" N GLN D 23 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG D 200 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D 194 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR D 195 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 98 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY D 211 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 100 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ALA D 213 " --> pdb=" O THR D 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AB8, first strand: chain 'D' and resid 216 through 217 removed outlier: 4.411A pdb=" N LYS D 266 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 232 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 269 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 282 " --> pdb=" O TYR D 269 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 4.69 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: 0.440 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.180 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17747 Z= 0.142 Angle : 0.537 13.379 23998 Z= 0.273 Chirality : 0.042 0.219 2547 Planarity : 0.004 0.039 3087 Dihedral : 13.896 86.221 6738 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 2077 helix: 0.61 (0.19), residues: 799 sheet: -0.82 (0.34), residues: 241 loop : -0.22 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 288 HIS 0.006 0.001 HIS C 227 PHE 0.015 0.001 PHE D 158 TYR 0.025 0.001 TYR A 857 ARG 0.008 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.091 Fit side-chains REVERT: A 50 LEU cc_start: 0.9147 (tp) cc_final: 0.8803 (tp) REVERT: A 566 MET cc_start: 0.7381 (tmm) cc_final: 0.7076 (tmm) REVERT: A 647 ASP cc_start: 0.8358 (m-30) cc_final: 0.8146 (m-30) REVERT: B 105 MET cc_start: 0.9428 (mmp) cc_final: 0.9213 (mmm) REVERT: B 339 ARG cc_start: 0.8249 (ppt170) cc_final: 0.7933 (ppt170) REVERT: C 76 MET cc_start: 0.8752 (ptt) cc_final: 0.8105 (pmm) REVERT: C 77 MET cc_start: 0.7104 (mmt) cc_final: 0.6763 (mmt) REVERT: C 664 MET cc_start: 0.6363 (tmm) cc_final: 0.6136 (tmm) REVERT: D 122 ASP cc_start: 0.7806 (m-30) cc_final: 0.7575 (p0) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2793 time to fit residues: 47.7305 Evaluate side-chains 84 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 176 optimal weight: 0.5980 chunk 158 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 106 optimal weight: 0.0370 chunk 84 optimal weight: 0.3980 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 244 HIS ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN C 583 GLN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17747 Z= 0.251 Angle : 0.597 9.739 23998 Z= 0.309 Chirality : 0.044 0.181 2547 Planarity : 0.004 0.041 3087 Dihedral : 4.135 17.747 2325 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.47 % Allowed : 7.35 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 2077 helix: 0.80 (0.18), residues: 838 sheet: -0.98 (0.31), residues: 264 loop : -0.31 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 320 HIS 0.007 0.001 HIS C 719 PHE 0.024 0.001 PHE C 7 TYR 0.021 0.001 TYR C 841 ARG 0.004 0.001 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 2.233 Fit side-chains REVERT: A 330 ASP cc_start: 0.8679 (p0) cc_final: 0.7919 (t0) REVERT: A 380 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8274 (tp30) REVERT: A 566 MET cc_start: 0.7314 (tmm) cc_final: 0.6967 (tmm) REVERT: A 647 ASP cc_start: 0.8319 (m-30) cc_final: 0.8092 (m-30) REVERT: A 783 MET cc_start: 0.8204 (ptp) cc_final: 0.7932 (ptp) REVERT: A 838 PHE cc_start: 0.7462 (m-10) cc_final: 0.7151 (m-10) REVERT: A 857 TYR cc_start: 0.9086 (t80) cc_final: 0.8828 (t80) REVERT: B 105 MET cc_start: 0.9460 (mmp) cc_final: 0.9221 (mmm) REVERT: B 252 LEU cc_start: 0.9260 (mm) cc_final: 0.8987 (mm) REVERT: C 354 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8354 (mm-40) outliers start: 9 outliers final: 4 residues processed: 96 average time/residue: 0.2614 time to fit residues: 41.6037 Evaluate side-chains 82 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 2.129 ------------------------------------------------------------------------------- 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 105 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 152 optimal weight: 0.0770 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 340 ASN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17747 Z= 0.170 Angle : 0.536 7.931 23998 Z= 0.273 Chirality : 0.042 0.167 2547 Planarity : 0.004 0.046 3087 Dihedral : 3.941 16.755 2325 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.79 % Allowed : 10.18 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2077 helix: 0.97 (0.18), residues: 841 sheet: -0.82 (0.32), residues: 264 loop : -0.23 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 320 HIS 0.008 0.001 HIS A 719 PHE 0.015 0.001 PHE D 158 TYR 0.018 0.001 TYR C 841 ARG 0.003 0.000 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 2.711 Fit side-chains REVERT: A 203 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: A 205 GLU cc_start: 0.8098 (pm20) cc_final: 0.7760 (pm20) REVERT: A 330 ASP cc_start: 0.8520 (p0) cc_final: 0.7933 (t0) REVERT: A 380 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8229 (tp30) REVERT: A 548 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: A 566 MET cc_start: 0.7229 (tmm) cc_final: 0.6893 (tmm) REVERT: A 647 ASP cc_start: 0.8340 (m-30) cc_final: 0.8126 (m-30) REVERT: A 783 MET cc_start: 0.8191 (ptp) cc_final: 0.7929 (ptp) REVERT: A 838 PHE cc_start: 0.7335 (m-10) cc_final: 0.7013 (m-10) REVERT: A 857 TYR cc_start: 0.9108 (t80) cc_final: 0.8811 (t80) REVERT: B 252 LEU cc_start: 0.9273 (mm) cc_final: 0.8984 (mm) REVERT: C 126 ASP cc_start: 0.7776 (m-30) cc_final: 0.7299 (p0) REVERT: C 354 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8281 (mm-40) outliers start: 15 outliers final: 4 residues processed: 102 average time/residue: 0.2729 time to fit residues: 46.1461 Evaluate side-chains 88 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 669 VAL 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 187 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 202 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17747 Z= 0.290 Angle : 0.577 9.268 23998 Z= 0.295 Chirality : 0.043 0.165 2547 Planarity : 0.004 0.043 3087 Dihedral : 4.061 18.293 2325 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.21 % Allowed : 12.13 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2077 helix: 1.00 (0.18), residues: 838 sheet: -0.91 (0.31), residues: 264 loop : -0.26 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 320 HIS 0.007 0.001 HIS A 719 PHE 0.016 0.001 PHE D 158 TYR 0.025 0.001 TYR C 841 ARG 0.003 0.000 ARG C 398 *********************** 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 101 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 2.070 Fit side-chains revert: symmetry clash REVERT: A 330 ASP cc_start: 0.8579 (p0) cc_final: 0.8154 (t0) REVERT: A 566 MET cc_start: 0.7411 (tmm) cc_final: 0.6967 (tmm) REVERT: A 783 MET cc_start: 0.8209 (ptp) cc_final: 0.7941 (ptp) REVERT: A 838 PHE cc_start: 0.7455 (m-10) cc_final: 0.7139 (m-10) REVERT: A 857 TYR cc_start: 0.9230 (t80) cc_final: 0.8794 (t80) REVERT: B 105 MET cc_start: 0.9360 (mmm) cc_final: 0.9047 (mmm) REVERT: B 252 LEU cc_start: 0.9313 (mm) cc_final: 0.8994 (mm) REVERT: B 269 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6453 (t80) REVERT: C 110 MET cc_start: 0.8614 (mmm) cc_final: 0.8265 (mmm) REVERT: C 126 ASP cc_start: 0.7686 (m-30) cc_final: 0.7253 (p0) REVERT: C 192 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6969 (mp0) outliers start: 23 outliers final: 15 residues processed: 96 average time/residue: 0.2490 time to fit residues: 40.6144 Evaluate side-chains 93 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain B residue 123 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 C residue 192 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 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 168 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 557 GLN C 583 GLN C 649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 17747 Z= 0.482 Angle : 0.687 10.284 23998 Z= 0.353 Chirality : 0.046 0.161 2547 Planarity : 0.005 0.060 3087 Dihedral : 4.551 23.271 2325 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.99 % Allowed : 13.44 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 2077 helix: 0.72 (0.18), residues: 836 sheet: -1.10 (0.33), residues: 245 loop : -0.43 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 101 HIS 0.007 0.002 HIS A 247 PHE 0.018 0.002 PHE B 253 TYR 0.027 0.002 TYR C 841 ARG 0.005 0.001 ARG C 703 *********************** 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 116 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 2.082 Fit side-chains REVERT: A 241 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 297 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8556 (m-10) REVERT: A 313 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 330 ASP cc_start: 0.8599 (p0) cc_final: 0.8135 (t0) REVERT: A 356 LEU cc_start: 0.9138 (mt) cc_final: 0.8751 (mp) REVERT: A 380 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8420 (tp30) REVERT: A 548 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: A 566 MET cc_start: 0.7671 (tmm) cc_final: 0.7306 (tmm) REVERT: A 783 MET cc_start: 0.8242 (ptp) cc_final: 0.7947 (ptp) REVERT: B 67 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7857 (pp) REVERT: B 105 MET cc_start: 0.9325 (mmm) cc_final: 0.9011 (mmm) REVERT: B 252 LEU cc_start: 0.9438 (mm) cc_final: 0.9172 (mm) REVERT: B 269 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6807 (t80) REVERT: C 110 MET cc_start: 0.8577 (mmm) cc_final: 0.8333 (mmm) REVERT: C 126 ASP cc_start: 0.7813 (m-30) cc_final: 0.7377 (p0) REVERT: C 192 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: C 645 MET cc_start: 0.8843 (tmm) cc_final: 0.8253 (tmm) outliers start: 38 outliers final: 22 residues processed: 108 average time/residue: 0.2507 time to fit residues: 45.7335 Evaluate side-chains 106 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 77 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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 313 LEU Chi-restraints excluded: chain A residue 323 ILE 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 136 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 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 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 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 67 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 202 optimal weight: 0.0050 chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 106 optimal weight: 0.0770 overall best weight: 0.9354 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17747 Z= 0.159 Angle : 0.537 11.030 23998 Z= 0.273 Chirality : 0.042 0.167 2547 Planarity : 0.004 0.034 3087 Dihedral : 4.098 17.524 2325 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.99 % Allowed : 13.81 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 2077 helix: 1.05 (0.18), residues: 842 sheet: -0.95 (0.32), residues: 258 loop : -0.27 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 288 HIS 0.006 0.001 HIS C 227 PHE 0.016 0.001 PHE D 158 TYR 0.020 0.001 TYR C 841 ARG 0.003 0.000 ARG A 252 *********************** 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 122 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 84 time to evaluate : 2.097 Fit side-chains REVERT: A 110 MET cc_start: 0.8475 (pmm) cc_final: 0.8247 (pmm) REVERT: A 203 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 205 GLU cc_start: 0.7814 (pm20) cc_final: 0.7145 (pm20) REVERT: A 330 ASP cc_start: 0.8480 (p0) cc_final: 0.7876 (t0) REVERT: A 356 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 380 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8331 (tp30) REVERT: A 548 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: A 566 MET cc_start: 0.7354 (tmm) cc_final: 0.6938 (tmt) REVERT: A 783 MET cc_start: 0.8168 (ptp) cc_final: 0.7859 (ptp) REVERT: A 857 TYR cc_start: 0.9190 (t80) cc_final: 0.8775 (t80) REVERT: B 108 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8655 (pp) REVERT: B 252 LEU cc_start: 0.9352 (mm) cc_final: 0.9111 (mm) REVERT: B 269 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.6486 (t80) REVERT: C 104 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8740 (t) REVERT: C 110 MET cc_start: 0.8484 (mmm) cc_final: 0.8234 (mmm) REVERT: C 126 ASP cc_start: 0.7568 (m-30) cc_final: 0.7239 (p0) REVERT: C 192 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7053 (mp0) outliers start: 38 outliers final: 17 residues processed: 117 average time/residue: 0.2535 time to fit residues: 49.1592 Evaluate side-chains 103 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 104 VAL 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 719 HIS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 194 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17747 Z= 0.157 Angle : 0.541 11.913 23998 Z= 0.267 Chirality : 0.042 0.165 2547 Planarity : 0.003 0.034 3087 Dihedral : 3.910 15.996 2325 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.57 % Allowed : 14.44 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2077 helix: 1.19 (0.19), residues: 847 sheet: -0.94 (0.31), residues: 261 loop : -0.21 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 256 HIS 0.004 0.001 HIS C 227 PHE 0.014 0.001 PHE D 158 TYR 0.018 0.001 TYR C 841 ARG 0.006 0.000 ARG C 761 *********************** 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 116 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 1.924 Fit side-chains revert: symmetry clash REVERT: A 203 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7383 (tm-30) REVERT: A 205 GLU cc_start: 0.7870 (pm20) cc_final: 0.7445 (pm20) REVERT: A 356 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8680 (mp) REVERT: A 380 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8513 (tp30) REVERT: A 548 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: A 566 MET cc_start: 0.7344 (tmm) cc_final: 0.6909 (tmt) REVERT: A 783 MET cc_start: 0.8167 (ptp) cc_final: 0.7845 (ptp) REVERT: A 857 TYR cc_start: 0.9249 (t80) cc_final: 0.8855 (t80) REVERT: B 67 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7757 (pp) REVERT: B 87 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8404 (mm-30) REVERT: B 252 LEU cc_start: 0.9352 (mm) cc_final: 0.9110 (mm) REVERT: B 269 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6466 (t80) REVERT: C 110 MET cc_start: 0.8452 (mmm) cc_final: 0.8222 (mmm) REVERT: C 126 ASP cc_start: 0.7542 (m-30) cc_final: 0.7179 (p0) REVERT: C 192 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: C 297 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8599 (m-10) outliers start: 30 outliers final: 17 residues processed: 113 average time/residue: 0.2491 time to fit residues: 47.1838 Evaluate side-chains 107 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 629 LEU 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 267 ILE Chi-restraints excluded: chain B residue 269 TYR 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 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 124 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 128 optimal weight: 0.2980 chunk 137 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN D 153 HIS D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17747 Z= 0.166 Angle : 0.543 12.080 23998 Z= 0.270 Chirality : 0.042 0.164 2547 Planarity : 0.003 0.034 3087 Dihedral : 3.857 15.893 2325 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.78 % Allowed : 14.33 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 2077 helix: 1.22 (0.19), residues: 849 sheet: -0.84 (0.31), residues: 263 loop : -0.22 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 288 HIS 0.009 0.001 HIS A 719 PHE 0.014 0.001 PHE D 158 TYR 0.018 0.001 TYR C 841 ARG 0.005 0.000 ARG C 761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 2.070 Fit side-chains REVERT: A 203 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 205 GLU cc_start: 0.7892 (pm20) cc_final: 0.7445 (pm20) REVERT: A 356 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 380 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8506 (tp30) REVERT: A 548 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: A 566 MET cc_start: 0.7380 (tmm) cc_final: 0.6919 (tmt) REVERT: A 783 MET cc_start: 0.8174 (ptp) cc_final: 0.7868 (ptp) REVERT: A 857 TYR cc_start: 0.9259 (t80) cc_final: 0.8845 (t80) REVERT: B 67 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7712 (pp) REVERT: B 87 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: B 105 MET cc_start: 0.9492 (mmm) cc_final: 0.9278 (mmm) REVERT: B 252 LEU cc_start: 0.9387 (mm) cc_final: 0.9131 (mm) REVERT: B 269 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6457 (t80) REVERT: C 110 MET cc_start: 0.8442 (mmm) cc_final: 0.8237 (mmm) REVERT: C 126 ASP cc_start: 0.7499 (m-30) cc_final: 0.7175 (p0) REVERT: C 192 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: C 297 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8615 (m-10) outliers start: 34 outliers final: 21 residues processed: 118 average time/residue: 0.2502 time to fit residues: 49.3992 Evaluate side-chains 110 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 629 LEU 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 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 192 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 147 optimal weight: 0.0470 chunk 57 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.002 0.061 17747 Z= 0.159 Angle : 0.546 12.802 23998 Z= 0.270 Chirality : 0.042 0.164 2547 Planarity : 0.003 0.034 3087 Dihedral : 3.786 15.869 2325 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.73 % Allowed : 14.80 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 2077 helix: 1.27 (0.19), residues: 846 sheet: -0.75 (0.31), residues: 263 loop : -0.18 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 288 HIS 0.004 0.001 HIS C 227 PHE 0.014 0.001 PHE D 158 TYR 0.018 0.001 TYR C 841 ARG 0.004 0.000 ARG C 761 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 2.045 Fit side-chains REVERT: A 356 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8665 (mp) REVERT: A 380 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8486 (tp30) REVERT: A 548 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: A 566 MET cc_start: 0.7337 (tmm) cc_final: 0.6933 (tmt) REVERT: A 783 MET cc_start: 0.8178 (ptp) cc_final: 0.7892 (ptp) REVERT: A 857 TYR cc_start: 0.9257 (t80) cc_final: 0.8854 (t80) REVERT: B 67 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7697 (pp) REVERT: B 87 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8423 (mm-30) REVERT: B 105 MET cc_start: 0.9474 (mmm) cc_final: 0.9270 (mmm) REVERT: B 252 LEU cc_start: 0.9386 (mm) cc_final: 0.9136 (mm) REVERT: B 269 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6562 (t80) REVERT: C 110 MET cc_start: 0.8438 (mmm) cc_final: 0.8216 (mmm) REVERT: C 126 ASP cc_start: 0.7110 (m-30) cc_final: 0.6839 (m-30) REVERT: C 192 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: C 297 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8731 (m-10) REVERT: C 566 MET cc_start: 0.7688 (mmp) cc_final: 0.7480 (mmp) REVERT: D 53 ASP cc_start: 0.8965 (t0) cc_final: 0.8477 (p0) outliers start: 33 outliers final: 20 residues processed: 115 average time/residue: 0.2474 time to fit residues: 48.3203 Evaluate side-chains 111 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 629 LEU 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 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 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 121 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 191 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17747 Z= 0.192 Angle : 0.567 13.422 23998 Z= 0.280 Chirality : 0.042 0.164 2547 Planarity : 0.003 0.033 3087 Dihedral : 3.811 15.560 2325 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.52 % Allowed : 15.22 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2077 helix: 1.25 (0.19), residues: 849 sheet: -0.76 (0.31), residues: 264 loop : -0.22 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.003 0.001 HIS A 719 PHE 0.014 0.001 PHE D 158 TYR 0.012 0.001 TYR C 841 ARG 0.004 0.000 ARG C 761 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 2.180 Fit side-chains REVERT: A 203 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 205 GLU cc_start: 0.7779 (pm20) cc_final: 0.7013 (pm20) REVERT: A 356 LEU cc_start: 0.9000 (mt) cc_final: 0.8639 (mp) REVERT: A 380 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8491 (tp30) REVERT: A 548 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: A 566 MET cc_start: 0.7356 (tmm) cc_final: 0.6944 (tmm) REVERT: A 783 MET cc_start: 0.8167 (ptp) cc_final: 0.7869 (ptp) REVERT: A 838 PHE cc_start: 0.7054 (m-10) cc_final: 0.6807 (m-10) REVERT: A 857 TYR cc_start: 0.9290 (t80) cc_final: 0.8860 (t80) REVERT: B 67 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7708 (pp) REVERT: B 87 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8430 (mm-30) REVERT: B 252 LEU cc_start: 0.9394 (mm) cc_final: 0.9145 (mm) REVERT: B 269 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6629 (t80) REVERT: C 110 MET cc_start: 0.8457 (mmm) cc_final: 0.8236 (mmm) REVERT: C 126 ASP cc_start: 0.7091 (m-30) cc_final: 0.6823 (m-30) REVERT: C 192 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: C 297 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8686 (m-10) REVERT: C 645 MET cc_start: 0.8792 (tmm) cc_final: 0.8246 (tmm) REVERT: D 53 ASP cc_start: 0.8968 (t0) cc_final: 0.8473 (p0) outliers start: 29 outliers final: 18 residues processed: 112 average time/residue: 0.2585 time to fit residues: 49.0740 Evaluate side-chains 107 residues out of total 1905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 579 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 629 LEU 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 267 ILE Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 297 TYR Chi-restraints excluded: chain C residue 326 PHE Chi-restraints excluded: chain C residue 669 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain D residue 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 50 optimal weight: 6.9990 chunk 152 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.0270 chunk 166 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** 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 = 0.3716 r_free = 0.3716 target = 0.076346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054507 restraints weight = 74147.663| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 4.56 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17747 Z= 0.183 Angle : 0.564 13.150 23998 Z= 0.278 Chirality : 0.042 0.162 2547 Planarity : 0.003 0.033 3087 Dihedral : 3.798 15.639 2325 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.68 % Allowed : 15.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2077 helix: 1.27 (0.19), residues: 845 sheet: -0.76 (0.31), residues: 264 loop : -0.21 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 288 HIS 0.003 0.001 HIS C 227 PHE 0.014 0.001 PHE D 158 TYR 0.015 0.001 TYR C 857 ARG 0.004 0.000 ARG C 761 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.66 seconds wall clock time: 52 minutes 14.13 seconds (3134.13 seconds total)