Starting phenix.real_space_refine on Sun Aug 24 04:01:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9g_36986/08_2025/8k9g_36986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9g_36986/08_2025/8k9g_36986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2025/8k9g_36986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2025/8k9g_36986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2025/8k9g_36986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2025/8k9g_36986.map" } resolution = 3.49 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= 0.001 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 46 5.16 5 C 10498 2.51 5 N 2810 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16759 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "A" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3684 Classifications: {'peptide': 455} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3695 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.96, per 1000 atoms: 0.24 Number of scatterers: 16759 At special positions: 0 Unit cell: (85.28, 148.72, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 90 15.00 O 3315 8.00 N 2810 7.00 C 10498 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: 1.17 Conformation dependent library (CDL) restraints added in 447.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 20 sheets defined 40.0% alpha, 14.1% beta 2 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 97 through 105 removed outlier: 4.412A pdb=" N ILE A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.511A pdb=" N ARG A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.727A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.641A pdb=" N GLY A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.605A pdb=" N GLU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.869A pdb=" N ASN A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 7.102A pdb=" N ASP B 16 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.451A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.576A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.765A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.127A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.900A pdb=" N LEU B 194 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.582A pdb=" N LEU B 203 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.789A pdb=" N ILE B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N HIS B 225 " --> pdb=" O ASP B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.620A pdb=" N GLU B 231 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.588A pdb=" N GLU B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.666A pdb=" N ILE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.580A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.656A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.850A pdb=" N GLU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'E' and resid 22 through 30 Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.766A pdb=" N LYS E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 97 through 106 removed outlier: 3.839A pdb=" N ILE E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 132 removed outlier: 3.600A pdb=" N ASN E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 205 through 215 removed outlier: 4.034A pdb=" N GLN E 209 " --> pdb=" O GLN E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 248 through 265 Processing helix chain 'E' and resid 322 through 326 Processing helix chain 'E' and resid 331 through 351 Processing helix chain 'E' and resid 367 through 374 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 477 through 491 removed outlier: 3.700A pdb=" N ALA E 483 " --> pdb=" O THR E 479 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS E 485 " --> pdb=" O ARG E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 removed outlier: 4.191A pdb=" N TYR E 505 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 65 through 70 removed outlier: 4.339A pdb=" N LYS F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.640A pdb=" N LEU F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 3.861A pdb=" N VAL F 113 " --> pdb=" O ASN F 109 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 109 through 114' Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 190 through 194 removed outlier: 3.859A pdb=" N LEU F 194 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 removed outlier: 3.536A pdb=" N LEU F 203 " --> pdb=" O VAL F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.803A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 257 through 280 Processing helix chain 'F' and resid 353 through 366 removed outlier: 3.638A pdb=" N GLN F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS F 366 " --> pdb=" O ARG F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 385 Processing helix chain 'F' and resid 421 through 438 removed outlier: 3.776A pdb=" N GLU F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 449 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.876A pdb=" N LYS A 270 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 3.745A pdb=" N VAL A 92 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 282 removed outlier: 6.583A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 441 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 420 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 396 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.714A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.051A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS B 4 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 59 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.612A pdb=" N VAL B 334 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 404 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 403 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 188 Processing sheet with id=AB1, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.578A pdb=" N ALA B 292 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AB3, first strand: chain 'E' and resid 397 through 398 removed outlier: 5.580A pdb=" N LYS F 167 " --> pdb=" O MET F 414 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET F 414 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU F 169 " --> pdb=" O GLY F 412 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 4 " --> pdb=" O PHE F 411 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS F 413 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N TYR E 6 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N SER F 415 " --> pdb=" O TYR E 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.956A pdb=" N ILE E 12 " --> pdb=" O CYS E 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS E 20 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 95 removed outlier: 3.782A pdb=" N GLY E 45 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL E 141 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 303 through 304 removed outlier: 6.570A pdb=" N CYS E 279 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N HIS E 360 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU E 281 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 357 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL E 386 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE E 359 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 388 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA E 361 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 425 through 426 removed outlier: 4.018A pdb=" N VAL E 426 " --> pdb=" O SER E 431 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 31 through 33 removed outlier: 5.891A pdb=" N ILE F 5 " --> pdb=" O TRP F 33 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS F 4 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU F 61 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE F 6 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL F 63 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER F 8 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 285 through 286 removed outlier: 7.060A pdb=" N PHE F 291 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA F 325 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR F 293 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 323 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 285 through 286 removed outlier: 7.060A pdb=" N PHE F 291 " --> pdb=" O ALA F 325 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ALA F 325 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR F 293 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 323 " --> pdb=" O TYR F 293 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 334 " --> pdb=" O LYS F 328 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE F 401 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE F 403 " --> pdb=" O ILE F 391 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 207 through 210 553 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4067 1.33 - 1.45: 3844 1.45 - 1.57: 9190 1.57 - 1.69: 176 1.69 - 1.81: 70 Bond restraints: 17347 Sorted by residual: bond pdb=" N VAL B 395 " pdb=" CA VAL B 395 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N THR F 11 " pdb=" CA THR F 11 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.26e+00 bond pdb=" N THR B 11 " pdb=" CA THR B 11 " ideal model delta sigma weight residual 1.462 1.490 -0.029 9.50e-03 1.11e+04 9.21e+00 bond pdb=" C THR B 11 " pdb=" N PRO B 12 " ideal model delta sigma weight residual 1.331 1.354 -0.023 7.90e-03 1.60e+04 8.25e+00 bond pdb=" C THR F 11 " pdb=" N PRO F 12 " ideal model delta sigma weight residual 1.332 1.355 -0.023 8.20e-03 1.49e+04 7.75e+00 ... (remaining 17342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23275 2.35 - 4.69: 471 4.69 - 7.04: 65 7.04 - 9.38: 25 9.38 - 11.73: 10 Bond angle restraints: 23846 Sorted by residual: angle pdb=" N ASP B 386 " pdb=" CA ASP B 386 " pdb=" C ASP B 386 " ideal model delta sigma weight residual 111.71 105.69 6.02 1.15e+00 7.56e-01 2.74e+01 angle pdb=" CB ARG B 276 " pdb=" CG ARG B 276 " pdb=" CD ARG B 276 " ideal model delta sigma weight residual 111.30 122.10 -10.80 2.30e+00 1.89e-01 2.20e+01 angle pdb=" CA LYS B 280 " pdb=" CB LYS B 280 " pdb=" CG LYS B 280 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CA LYS F 400 " pdb=" CB LYS F 400 " pdb=" CG LYS F 400 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA LYS B 309 " pdb=" CB LYS B 309 " pdb=" CG LYS B 309 " ideal model delta sigma weight residual 114.10 123.00 -8.90 2.00e+00 2.50e-01 1.98e+01 ... (remaining 23841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8179 17.94 - 35.88: 1485 35.88 - 53.82: 534 53.82 - 71.77: 157 71.77 - 89.71: 33 Dihedral angle restraints: 10388 sinusoidal: 5059 harmonic: 5329 Sorted by residual: dihedral pdb=" C5' G G 5 " pdb=" C4' G G 5 " pdb=" C3' G G 5 " pdb=" O3' G G 5 " ideal model delta sinusoidal sigma weight residual 147.00 102.65 44.35 1 8.00e+00 1.56e-02 4.27e+01 dihedral pdb=" O4' G G 5 " pdb=" C4' G G 5 " pdb=" C3' G G 5 " pdb=" C2' G G 5 " ideal model delta sinusoidal sigma weight residual 24.00 -16.06 40.06 1 8.00e+00 1.56e-02 3.52e+01 dihedral pdb=" C3' G G 5 " pdb=" C4' G G 5 " pdb=" O4' G G 5 " pdb=" C1' G G 5 " ideal model delta sinusoidal sigma weight residual -2.00 33.77 -35.77 1 8.00e+00 1.56e-02 2.83e+01 ... (remaining 10385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2519 0.122 - 0.244: 87 0.244 - 0.366: 2 0.366 - 0.488: 2 0.488 - 0.610: 5 Chirality restraints: 2615 Sorted by residual: chirality pdb=" P DA H 36 " pdb=" OP1 DA H 36 " pdb=" OP2 DA H 36 " pdb=" O5' DA H 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" P DA H 31 " pdb=" OP1 DA H 31 " pdb=" OP2 DA H 31 " pdb=" O5' DA H 31 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" P DA D 36 " pdb=" OP1 DA D 36 " pdb=" OP2 DA D 36 " pdb=" O5' DA D 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 2612 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 15 " 0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ASP F 15 " -0.087 2.00e-02 2.50e+03 pdb=" O ASP F 15 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP F 16 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 272 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ALA F 272 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA F 272 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE F 273 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 276 " -0.240 9.50e-02 1.11e+02 1.07e-01 7.11e+00 pdb=" NE ARG F 276 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG F 276 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 276 " -0.008 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1578 2.74 - 3.28: 15893 3.28 - 3.82: 28524 3.82 - 4.36: 31846 4.36 - 4.90: 53629 Nonbonded interactions: 131470 Sorted by model distance: nonbonded pdb=" OG1 THR A 71 " pdb=" OE2 GLU B 426 " model vdw 2.201 3.040 nonbonded pdb=" NE1 TRP B 219 " pdb=" OE1 GLU B 398 " model vdw 2.220 3.120 nonbonded pdb=" O PRO A 404 " pdb=" OH TYR B 416 " model vdw 2.245 3.040 nonbonded pdb=" O3' DA D 36 " pdb=" NH2 ARG B 263 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR E 71 " pdb=" OE2 GLU F 426 " model vdw 2.250 3.040 ... (remaining 131465 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' selection = (chain 'E' and (resid 1 through 151 or resid 204 through 507)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.940 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17347 Z= 0.246 Angle : 0.852 11.726 23846 Z= 0.471 Chirality : 0.059 0.610 2615 Planarity : 0.006 0.107 2712 Dihedral : 21.185 89.707 6942 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.25 % Allowed : 35.10 % Favored : 64.65 % 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: -1.99 (0.18), residues: 1799 helix: -0.88 (0.19), residues: 633 sheet: -0.46 (0.32), residues: 271 loop : -1.92 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 193 TYR 0.024 0.002 TYR F 154 PHE 0.039 0.002 PHE E 313 TRP 0.038 0.002 TRP B 219 HIS 0.008 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00477 (17347) covalent geometry : angle 0.85234 (23846) hydrogen bonds : bond 0.17935 ( 555) hydrogen bonds : angle 7.99788 ( 1576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6470 (t80) outliers start: 4 outliers final: 2 residues processed: 161 average time/residue: 0.1411 time to fit residues: 33.3447 Evaluate side-chains 96 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 278 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 151 ASN B 258 ASN B 262 GLN B 349 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 446 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064500 restraints weight = 128518.044| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 5.15 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17347 Z= 0.159 Angle : 0.613 9.100 23846 Z= 0.328 Chirality : 0.043 0.214 2615 Planarity : 0.004 0.072 2712 Dihedral : 18.786 88.843 3180 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.15 % Allowed : 32.70 % Favored : 64.16 % 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: -1.33 (0.19), residues: 1799 helix: -0.02 (0.20), residues: 638 sheet: -0.39 (0.31), residues: 288 loop : -1.71 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.015 0.001 TYR F 154 PHE 0.014 0.001 PHE F 273 TRP 0.015 0.001 TRP E 370 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00335 (17347) covalent geometry : angle 0.61269 (23846) hydrogen bonds : bond 0.03886 ( 555) hydrogen bonds : angle 5.70112 ( 1576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9037 (mp0) REVERT: A 406 MET cc_start: 0.8953 (ppp) cc_final: 0.8735 (ppp) REVERT: A 435 MET cc_start: 0.8932 (tpp) cc_final: 0.8625 (tpp) REVERT: B 146 ASP cc_start: 0.8650 (t0) cc_final: 0.8406 (t0) REVERT: B 261 CYS cc_start: 0.9723 (OUTLIER) cc_final: 0.9394 (m) REVERT: B 287 MET cc_start: 0.9266 (tpp) cc_final: 0.8528 (tpt) REVERT: E 150 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8779 (t80) REVERT: E 331 LYS cc_start: 0.9855 (tppt) cc_final: 0.9641 (tppt) REVERT: E 435 MET cc_start: 0.8640 (tpp) cc_final: 0.8436 (mmm) REVERT: F 92 MET cc_start: 0.9440 (ttp) cc_final: 0.9134 (ttt) REVERT: F 287 MET cc_start: 0.9087 (mmm) cc_final: 0.8302 (mmm) outliers start: 51 outliers final: 19 residues processed: 155 average time/residue: 0.1356 time to fit residues: 31.5847 Evaluate side-chains 111 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 24 optimal weight: 0.0470 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 154 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.061204 restraints weight = 133090.846| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 5.38 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17347 Z= 0.173 Angle : 0.607 9.485 23846 Z= 0.320 Chirality : 0.043 0.200 2615 Planarity : 0.004 0.067 2712 Dihedral : 18.757 93.889 3174 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.19 % Allowed : 31.22 % Favored : 64.59 % 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: -1.09 (0.20), residues: 1799 helix: 0.32 (0.21), residues: 641 sheet: -0.49 (0.32), residues: 279 loop : -1.59 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 113 TYR 0.011 0.001 TYR F 154 PHE 0.014 0.001 PHE F 158 TRP 0.025 0.001 TRP E 370 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00381 (17347) covalent geometry : angle 0.60711 (23846) hydrogen bonds : bond 0.03420 ( 555) hydrogen bonds : angle 5.29618 ( 1576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 95 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9407 (OUTLIER) cc_final: 0.8982 (pp30) REVERT: A 134 GLU cc_start: 0.9292 (mm-30) cc_final: 0.9078 (mp0) REVERT: A 406 MET cc_start: 0.9009 (ppp) cc_final: 0.8780 (ppp) REVERT: A 435 MET cc_start: 0.8999 (tpp) cc_final: 0.8585 (tpp) REVERT: B 19 ARG cc_start: 0.9535 (OUTLIER) cc_final: 0.9069 (ttt-90) REVERT: B 92 MET cc_start: 0.9801 (mmm) cc_final: 0.9597 (mmm) REVERT: B 261 CYS cc_start: 0.9691 (OUTLIER) cc_final: 0.9447 (m) REVERT: B 287 MET cc_start: 0.9542 (tpp) cc_final: 0.9078 (tpp) REVERT: B 334 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 345 MET cc_start: 0.9310 (tmm) cc_final: 0.9052 (tmm) REVERT: E 150 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8909 (t80) REVERT: E 331 LYS cc_start: 0.9819 (tppt) cc_final: 0.9561 (tppt) REVERT: E 485 LYS cc_start: 0.9406 (ptmm) cc_final: 0.9195 (ptmm) REVERT: F 52 GLU cc_start: 0.9547 (OUTLIER) cc_final: 0.9228 (pm20) REVERT: F 92 MET cc_start: 0.9530 (ttp) cc_final: 0.9039 (ttp) REVERT: F 287 MET cc_start: 0.9156 (mmm) cc_final: 0.8516 (mmm) outliers start: 68 outliers final: 31 residues processed: 155 average time/residue: 0.1772 time to fit residues: 39.7915 Evaluate side-chains 125 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 187 optimal weight: 30.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.060120 restraints weight = 132178.455| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 5.41 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17347 Z= 0.163 Angle : 0.595 9.104 23846 Z= 0.311 Chirality : 0.042 0.162 2615 Planarity : 0.004 0.061 2712 Dihedral : 18.762 99.137 3174 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.01 % Allowed : 30.66 % Favored : 65.33 % 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: -0.93 (0.20), residues: 1799 helix: 0.48 (0.21), residues: 642 sheet: -0.60 (0.33), residues: 270 loop : -1.44 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 113 TYR 0.020 0.001 TYR F 154 PHE 0.019 0.001 PHE F 158 TRP 0.018 0.001 TRP E 370 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00360 (17347) covalent geometry : angle 0.59520 (23846) hydrogen bonds : bond 0.03254 ( 555) hydrogen bonds : angle 5.16134 ( 1576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 93 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9043 (mp0) REVERT: B 19 ARG cc_start: 0.9504 (OUTLIER) cc_final: 0.9015 (ttt180) REVERT: B 282 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8791 (p) REVERT: B 287 MET cc_start: 0.9600 (tpp) cc_final: 0.9135 (tpp) REVERT: B 334 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8837 (p) REVERT: B 345 MET cc_start: 0.9325 (tmm) cc_final: 0.8987 (tmm) REVERT: E 150 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8921 (t80) REVERT: E 435 MET cc_start: 0.8692 (mmm) cc_final: 0.8442 (tpp) REVERT: F 52 GLU cc_start: 0.9506 (OUTLIER) cc_final: 0.9189 (pm20) REVERT: F 92 MET cc_start: 0.9506 (ttp) cc_final: 0.8915 (ttp) REVERT: F 287 MET cc_start: 0.9222 (mmm) cc_final: 0.8923 (mmm) outliers start: 65 outliers final: 37 residues processed: 150 average time/residue: 0.1637 time to fit residues: 36.3045 Evaluate side-chains 126 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059201 restraints weight = 129624.087| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 5.25 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17347 Z= 0.163 Angle : 0.593 9.429 23846 Z= 0.308 Chirality : 0.042 0.174 2615 Planarity : 0.004 0.049 2712 Dihedral : 18.841 98.895 3174 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.13 % Allowed : 30.41 % Favored : 65.45 % 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: -0.86 (0.20), residues: 1799 helix: 0.54 (0.21), residues: 645 sheet: -0.67 (0.33), residues: 270 loop : -1.37 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 276 TYR 0.013 0.001 TYR E 346 PHE 0.013 0.001 PHE F 273 TRP 0.021 0.001 TRP E 370 HIS 0.023 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00363 (17347) covalent geometry : angle 0.59333 (23846) hydrogen bonds : bond 0.03232 ( 555) hydrogen bonds : angle 5.09023 ( 1576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 89 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8977 (pp30) REVERT: A 134 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9038 (mp0) REVERT: B 19 ARG cc_start: 0.9516 (OUTLIER) cc_final: 0.9159 (ttt180) REVERT: B 261 CYS cc_start: 0.9751 (OUTLIER) cc_final: 0.9536 (m) REVERT: B 277 MET cc_start: 0.9641 (ppp) cc_final: 0.9440 (ppp) REVERT: B 287 MET cc_start: 0.9574 (tpp) cc_final: 0.9058 (tpp) REVERT: E 57 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8897 (pp) REVERT: E 150 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8909 (t80) REVERT: E 331 LYS cc_start: 0.9723 (tppt) cc_final: 0.9509 (tppt) REVERT: E 364 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.9103 (mpp-170) REVERT: F 52 GLU cc_start: 0.9519 (OUTLIER) cc_final: 0.9177 (pm20) REVERT: F 92 MET cc_start: 0.9514 (ttp) cc_final: 0.8902 (ttp) REVERT: F 287 MET cc_start: 0.9150 (mmm) cc_final: 0.8883 (mmm) outliers start: 67 outliers final: 39 residues processed: 150 average time/residue: 0.1680 time to fit residues: 36.9299 Evaluate side-chains 132 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 86 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 163 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.0010 chunk 97 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059912 restraints weight = 132024.418| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 5.34 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17347 Z= 0.138 Angle : 0.577 10.646 23846 Z= 0.299 Chirality : 0.041 0.182 2615 Planarity : 0.004 0.049 2712 Dihedral : 18.812 99.001 3174 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.82 % Allowed : 30.35 % Favored : 65.82 % 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: -0.82 (0.20), residues: 1799 helix: 0.57 (0.21), residues: 645 sheet: -0.64 (0.33), residues: 269 loop : -1.34 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 186 TYR 0.011 0.001 TYR E 346 PHE 0.013 0.001 PHE E 30 TRP 0.019 0.001 TRP E 370 HIS 0.013 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00310 (17347) covalent geometry : angle 0.57652 (23846) hydrogen bonds : bond 0.03108 ( 555) hydrogen bonds : angle 5.00168 ( 1576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 92 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8975 (pp30) REVERT: A 134 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8984 (mp0) REVERT: A 285 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.5573 (m-80) REVERT: B 4 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8829 (mtpp) REVERT: B 19 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.9003 (ttt180) REVERT: B 287 MET cc_start: 0.9562 (tpp) cc_final: 0.9076 (tpp) REVERT: B 345 MET cc_start: 0.9367 (tmm) cc_final: 0.9024 (tmm) REVERT: E 57 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8882 (pp) REVERT: E 150 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8910 (t80) REVERT: E 331 LYS cc_start: 0.9753 (tppt) cc_final: 0.9543 (tppt) REVERT: E 364 ARG cc_start: 0.9412 (OUTLIER) cc_final: 0.9173 (mpp-170) REVERT: F 52 GLU cc_start: 0.9469 (OUTLIER) cc_final: 0.9140 (pm20) REVERT: F 92 MET cc_start: 0.9542 (ttp) cc_final: 0.8910 (ttp) REVERT: F 287 MET cc_start: 0.9108 (mmm) cc_final: 0.8878 (mmm) REVERT: F 378 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9175 (mm) outliers start: 62 outliers final: 35 residues processed: 147 average time/residue: 0.1658 time to fit residues: 35.9528 Evaluate side-chains 131 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 88 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 187 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.057379 restraints weight = 134870.111| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 5.18 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17347 Z= 0.220 Angle : 0.645 12.852 23846 Z= 0.333 Chirality : 0.043 0.217 2615 Planarity : 0.004 0.051 2712 Dihedral : 19.050 97.759 3174 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.95 % Allowed : 30.48 % Favored : 65.58 % 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: -0.86 (0.20), residues: 1799 helix: 0.53 (0.21), residues: 643 sheet: -0.76 (0.33), residues: 254 loop : -1.32 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 364 TYR 0.014 0.001 TYR E 346 PHE 0.013 0.001 PHE F 343 TRP 0.025 0.001 TRP E 370 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00483 (17347) covalent geometry : angle 0.64513 (23846) hydrogen bonds : bond 0.03530 ( 555) hydrogen bonds : angle 5.19803 ( 1576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 86 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.9001 (pp30) REVERT: A 134 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8999 (mp0) REVERT: A 285 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5601 (m-80) REVERT: B 19 ARG cc_start: 0.9515 (OUTLIER) cc_final: 0.9160 (ttt180) REVERT: B 287 MET cc_start: 0.9539 (tpp) cc_final: 0.9020 (tpp) REVERT: B 345 MET cc_start: 0.9402 (tmm) cc_final: 0.9056 (tmm) REVERT: E 504 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8559 (ptpp) REVERT: F 52 GLU cc_start: 0.9444 (OUTLIER) cc_final: 0.9099 (pm20) REVERT: F 92 MET cc_start: 0.9491 (ttp) cc_final: 0.8842 (ttp) REVERT: F 250 ARG cc_start: 0.9297 (tpm170) cc_final: 0.9088 (ttp80) REVERT: F 287 MET cc_start: 0.9146 (mmm) cc_final: 0.8905 (mmm) REVERT: F 364 GLN cc_start: 0.5358 (OUTLIER) cc_final: 0.5067 (tp40) REVERT: F 378 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9265 (mm) outliers start: 64 outliers final: 42 residues processed: 141 average time/residue: 0.1714 time to fit residues: 35.5392 Evaluate side-chains 132 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 83 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 504 LYS Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 155 optimal weight: 0.0870 chunk 173 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 302 GLN B 226 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN F 314 GLN F 364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059669 restraints weight = 129508.350| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.35 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17347 Z= 0.119 Angle : 0.587 12.574 23846 Z= 0.303 Chirality : 0.042 0.242 2615 Planarity : 0.004 0.048 2712 Dihedral : 18.912 96.988 3174 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.22 % Allowed : 32.14 % Favored : 65.64 % 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: -0.72 (0.20), residues: 1799 helix: 0.64 (0.21), residues: 644 sheet: -0.50 (0.34), residues: 252 loop : -1.30 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 113 TYR 0.010 0.001 TYR E 346 PHE 0.012 0.001 PHE F 321 TRP 0.021 0.001 TRP E 370 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00272 (17347) covalent geometry : angle 0.58673 (23846) hydrogen bonds : bond 0.03066 ( 555) hydrogen bonds : angle 4.96426 ( 1576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8973 (mp0) REVERT: A 302 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: B 19 ARG cc_start: 0.9492 (OUTLIER) cc_final: 0.8991 (ttt180) REVERT: B 135 PHE cc_start: 0.8296 (m-10) cc_final: 0.8082 (m-80) REVERT: B 287 MET cc_start: 0.9507 (tpp) cc_final: 0.9041 (tpp) REVERT: B 345 MET cc_start: 0.9413 (tmm) cc_final: 0.9025 (tmm) REVERT: F 33 TRP cc_start: 0.8841 (t60) cc_final: 0.7853 (t60) REVERT: F 52 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9022 (pm20) REVERT: F 92 MET cc_start: 0.9550 (ttp) cc_final: 0.8928 (ttp) REVERT: F 158 PHE cc_start: 0.8223 (t80) cc_final: 0.8011 (t80) REVERT: F 287 MET cc_start: 0.9117 (mmm) cc_final: 0.8884 (mmm) REVERT: F 378 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9117 (mm) outliers start: 36 outliers final: 25 residues processed: 124 average time/residue: 0.1695 time to fit residues: 30.9318 Evaluate side-chains 118 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 160 optimal weight: 6.9990 chunk 132 optimal weight: 0.0980 chunk 57 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057529 restraints weight = 134575.090| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 5.36 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17347 Z= 0.231 Angle : 0.653 13.948 23846 Z= 0.338 Chirality : 0.043 0.231 2615 Planarity : 0.004 0.049 2712 Dihedral : 19.060 94.579 3174 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.59 % Allowed : 31.65 % Favored : 65.76 % 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: -0.82 (0.20), residues: 1799 helix: 0.60 (0.21), residues: 644 sheet: -0.82 (0.32), residues: 265 loop : -1.30 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 364 TYR 0.012 0.001 TYR E 346 PHE 0.012 0.001 PHE F 343 TRP 0.022 0.001 TRP E 370 HIS 0.013 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00505 (17347) covalent geometry : angle 0.65307 (23846) hydrogen bonds : bond 0.03462 ( 555) hydrogen bonds : angle 5.13254 ( 1576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8979 (mp0) REVERT: A 216 GLU cc_start: 0.9506 (OUTLIER) cc_final: 0.9297 (mp0) REVERT: A 285 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5462 (m-80) REVERT: B 19 ARG cc_start: 0.9493 (OUTLIER) cc_final: 0.9043 (ttt180) REVERT: B 287 MET cc_start: 0.9523 (tpp) cc_final: 0.9065 (tpp) REVERT: B 345 MET cc_start: 0.9433 (tmm) cc_final: 0.9033 (tmm) REVERT: E 504 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8728 (ptpp) REVERT: F 33 TRP cc_start: 0.8943 (t60) cc_final: 0.8034 (t60) REVERT: F 52 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.8986 (pm20) REVERT: F 92 MET cc_start: 0.9523 (ttp) cc_final: 0.8816 (ttp) REVERT: F 287 MET cc_start: 0.9128 (mmm) cc_final: 0.8908 (mmm) REVERT: F 378 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9207 (mm) outliers start: 42 outliers final: 34 residues processed: 120 average time/residue: 0.1713 time to fit residues: 30.2195 Evaluate side-chains 122 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 82 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 504 LYS Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 150 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 163 optimal weight: 0.3980 chunk 184 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 349 ASN E 18 GLN F 364 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.070179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060561 restraints weight = 131870.993| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 5.37 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17347 Z= 0.117 Angle : 0.604 13.184 23846 Z= 0.310 Chirality : 0.042 0.224 2615 Planarity : 0.004 0.047 2712 Dihedral : 18.858 94.274 3174 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.73 % Allowed : 32.57 % Favored : 65.70 % 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: -0.72 (0.20), residues: 1799 helix: 0.68 (0.21), residues: 644 sheet: -0.69 (0.33), residues: 259 loop : -1.26 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 364 TYR 0.010 0.001 TYR A 397 PHE 0.019 0.001 PHE F 321 TRP 0.021 0.001 TRP E 370 HIS 0.022 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00262 (17347) covalent geometry : angle 0.60418 (23846) hydrogen bonds : bond 0.03035 ( 555) hydrogen bonds : angle 4.90679 ( 1576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8958 (mp0) REVERT: B 1 MET cc_start: 0.8493 (ptp) cc_final: 0.8224 (pmm) REVERT: B 19 ARG cc_start: 0.9464 (OUTLIER) cc_final: 0.9105 (ttt180) REVERT: B 135 PHE cc_start: 0.8233 (m-10) cc_final: 0.8016 (m-80) REVERT: B 287 MET cc_start: 0.9440 (tpp) cc_final: 0.9001 (tpp) REVERT: B 345 MET cc_start: 0.9432 (tmm) cc_final: 0.8997 (tmm) REVERT: F 33 TRP cc_start: 0.8726 (t60) cc_final: 0.7781 (t60) REVERT: F 52 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8935 (pm20) REVERT: F 92 MET cc_start: 0.9560 (ttp) cc_final: 0.8977 (ttp) REVERT: F 158 PHE cc_start: 0.8306 (t80) cc_final: 0.8070 (t80) REVERT: F 378 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9144 (mm) outliers start: 28 outliers final: 23 residues processed: 117 average time/residue: 0.1704 time to fit residues: 29.1570 Evaluate side-chains 114 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 156 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 123 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060303 restraints weight = 130107.567| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 5.39 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 17347 Z= 0.169 Angle : 0.925 59.197 23846 Z= 0.547 Chirality : 0.048 0.916 2615 Planarity : 0.004 0.090 2712 Dihedral : 18.860 94.271 3174 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.85 % Allowed : 32.33 % Favored : 65.82 % Cbeta Deviations : 0.12 % 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: -0.72 (0.20), residues: 1799 helix: 0.68 (0.21), residues: 644 sheet: -0.69 (0.33), residues: 259 loop : -1.27 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 364 TYR 0.013 0.001 TYR F 293 PHE 0.017 0.001 PHE F 321 TRP 0.021 0.001 TRP E 370 HIS 0.015 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00347 (17347) covalent geometry : angle 0.92529 (23846) hydrogen bonds : bond 0.03044 ( 555) hydrogen bonds : angle 4.91064 ( 1576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2858.57 seconds wall clock time: 50 minutes 41.79 seconds (3041.79 seconds total)