Starting phenix.real_space_refine on Thu Aug 6 18:57:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_36986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_36986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_36986.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_36986.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_36986.cif" model { file = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_36986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9g_36986/08_2026/8k9g_36986.cif" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 2.58, per 1000 atoms: 0.15 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: 0.86 Conformation dependent library (CDL) restraints added in 494.0 milliseconds 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: 1.58 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: 2.37 Time building geometry restraints manager: 1.14 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: 22962 2.35 - 4.69: 727 4.69 - 7.04: 122 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: 7853 17.94 - 35.88: 1529 35.88 - 53.82: 568 53.82 - 71.77: 216 71.77 - 89.71: 62 Dihedral angle restraints: 10228 sinusoidal: 4899 harmonic: 5329 Sorted by residual: dihedral pdb=" C4' A G 7 " pdb=" C3' A G 7 " pdb=" C2' A G 7 " pdb=" C1' A G 7 " ideal model delta sinusoidal sigma weight residual 36.34 -43.20 79.55 1 3.10e+00 1.04e-01 8.18e+02 dihedral pdb=" C4' G G 8 " pdb=" C3' G G 8 " pdb=" C2' G G 8 " pdb=" C1' G G 8 " ideal model delta sinusoidal sigma weight residual 36.34 -43.17 79.51 1 3.10e+00 1.04e-01 8.17e+02 dihedral pdb=" C4' G C 8 " pdb=" C3' G C 8 " pdb=" C2' G C 8 " pdb=" C1' G C 8 " ideal model delta sinusoidal sigma weight residual 36.34 -41.26 77.61 1 3.10e+00 1.04e-01 7.85e+02 ... (remaining 10225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 2448 0.150 - 0.300: 142 0.300 - 0.450: 19 0.450 - 0.600: 3 0.600 - 0.750: 3 Chirality restraints: 2615 Sorted by residual: chirality pdb=" P A G 7 " pdb=" OP1 A G 7 " pdb=" OP2 A G 7 " pdb=" O5' A G 7 " both_signs ideal model delta sigma weight residual True 2.17 -2.92 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" P G G 5 " pdb=" OP1 G G 5 " pdb=" OP2 G G 5 " pdb=" O5' G G 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.87 -0.69 2.00e-01 2.50e+01 1.20e+01 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 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.61e+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: 0.920 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.590 Find NCS groups from input model: 0.220 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 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= 0.301 Angle : 0.968 11.726 23846 Z= 0.543 Chirality : 0.084 0.750 2615 Planarity : 0.006 0.107 2712 Dihedral : 22.993 89.707 6782 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 are 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/Z covalent geometry : bond 0.00512 / 0.30 (17347) covalent geometry : angle 0.96759 / 0.54 (23846) hydrogen bonds : bond 0.17935 / 19.54 ( 555) hydrogen bonds : angle 7.99788 / 6.68 ( 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 : 0.545 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: 0.6469 (t80) outliers start: 4 outliers final: 2 residues processed: 161 average time/residue: 0.1277 time to fit residues: 30.1677 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 : 0.419 ------------------------------------------------------------------------------- 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... B 258 ASN B 349 ASN E 446 ASN F 314 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 = 0.3438 r_free = 0.3438 target = 0.074834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065549 restraints weight = 127381.981| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 5.24 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17347 Z= 0.242 Angle : 1.450 33.144 23846 Z= 0.607 Chirality : 0.140 1.638 2615 Planarity : 0.005 0.086 2712 Dihedral : 20.665 154.341 3020 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.27 % Allowed : 33.13 % Favored : 63.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.19), residues: 1799 helix: -0.23 (0.20), residues: 648 sheet: -0.69 (0.31), residues: 299 loop : -1.81 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 250 TYR 0.017 0.001 TYR F 154 PHE 0.014 0.001 PHE F 187 TRP 0.026 0.001 TRP B 373 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 (17347) covalent geometry : angle 1.45015 / 0.61 (23846) hydrogen bonds : bond 0.04518 / 4.92 ( 555) hydrogen bonds : angle 6.11719 / 5.10 ( 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 165 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9347 (mm-30) cc_final: 0.8987 (mp0) REVERT: A 406 MET cc_start: 0.8820 (ppp) cc_final: 0.8581 (ppp) REVERT: A 435 MET cc_start: 0.8843 (tpp) cc_final: 0.8555 (tpp) REVERT: B 92 MET cc_start: 0.9774 (mmm) cc_final: 0.9504 (mmm) REVERT: B 261 CYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9251 (m) REVERT: B 287 MET cc_start: 0.8842 (tpp) cc_final: 0.8363 (tpt) REVERT: B 438 GLU cc_start: 0.5469 (OUTLIER) cc_final: 0.5058 (pm20) REVERT: F 52 GLU cc_start: 0.9541 (OUTLIER) cc_final: 0.9241 (pm20) REVERT: F 92 MET cc_start: 0.9362 (ttp) cc_final: 0.8819 (ttp) REVERT: F 287 MET cc_start: 0.9030 (mmm) cc_final: 0.8499 (mmm) outliers start: 53 outliers final: 18 residues processed: 156 average time/residue: 0.1177 time to fit residues: 27.8921 Evaluate side-chains 113 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 128 LEU 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 B residue 438 GLU Chi-restraints excluded: chain E residue 283 LEU 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 153 LEU Chi-restraints excluded: chain F residue 188 HIS Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 364 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 24 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 371 ASN F 9 HIS F 340 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063294 restraints weight = 131808.560| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 5.32 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17347 Z= 0.208 Angle : 1.072 29.985 23846 Z= 0.465 Chirality : 0.090 1.225 2615 Planarity : 0.005 0.062 2712 Dihedral : 19.880 153.233 3014 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.21 % Allowed : 33.07 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 1799 helix: 0.20 (0.21), residues: 639 sheet: -0.57 (0.31), residues: 286 loop : -1.72 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 113 TYR 0.018 0.001 TYR F 154 PHE 0.023 0.001 PHE F 273 TRP 0.019 0.001 TRP E 370 HIS 0.005 0.001 HIS B 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (17347) covalent geometry : angle 1.07180 / 0.47 (23846) hydrogen bonds : bond 0.04099 / 4.22 ( 555) hydrogen bonds : angle 5.67503 / 4.74 ( 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 149 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 0.391 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: 0.9245 (mm-30) cc_final: 0.9023 (mp0) REVERT: A 406 MET cc_start: 0.8996 (ppp) cc_final: 0.8775 (ppp) REVERT: A 435 MET cc_start: 0.9134 (tpp) cc_final: 0.8792 (tpp) REVERT: B 261 CYS cc_start: 0.9681 (OUTLIER) cc_final: 0.9373 (m) REVERT: B 287 MET cc_start: 0.9285 (tpp) cc_final: 0.8876 (tpp) REVERT: B 345 MET cc_start: 0.9338 (tmm) cc_final: 0.9110 (tmm) REVERT: F 92 MET cc_start: 0.9505 (ttp) cc_final: 0.9015 (ttp) REVERT: F 287 MET cc_start: 0.8831 (mmm) cc_final: 0.8417 (mmm) outliers start: 52 outliers final: 25 residues processed: 143 average time/residue: 0.1266 time to fit residues: 26.6265 Evaluate side-chains 113 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 387 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 59 LYS 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 125 ILE 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 51 LYS Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.071380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062020 restraints weight = 131850.771| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 5.25 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17347 Z= 0.201 Angle : 0.924 18.658 23846 Z= 0.415 Chirality : 0.076 0.930 2615 Planarity : 0.004 0.052 2712 Dihedral : 19.902 160.508 3014 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.70 % Allowed : 32.02 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1799 helix: 0.37 (0.21), residues: 641 sheet: -0.50 (0.32), residues: 284 loop : -1.65 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 276 TYR 0.014 0.001 TYR E 346 PHE 0.020 0.001 PHE F 158 TRP 0.019 0.001 TRP E 370 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (17347) covalent geometry : angle 0.92381 / 0.41 (23846) hydrogen bonds : bond 0.03646 / 3.90 ( 555) hydrogen bonds : angle 5.43383 / 4.56 ( 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 147 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 87 time to evaluate : 0.416 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: 0.9395 (OUTLIER) cc_final: 0.9011 (pp30) REVERT: A 134 GLU cc_start: 0.9261 (mm-30) cc_final: 0.9011 (mp0) REVERT: A 406 MET cc_start: 0.9057 (ppp) cc_final: 0.8831 (ppp) REVERT: A 435 MET cc_start: 0.9332 (tpp) cc_final: 0.8962 (tpp) REVERT: B 261 CYS cc_start: 0.9706 (OUTLIER) cc_final: 0.9366 (m) REVERT: B 334 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8729 (p) REVERT: B 336 MET cc_start: 0.9563 (tpp) cc_final: 0.8799 (tpt) REVERT: B 345 MET cc_start: 0.9354 (tmm) cc_final: 0.9069 (tmm) REVERT: E 1 MET cc_start: 0.9470 (tpp) cc_final: 0.9265 (tpp) REVERT: E 331 LYS cc_start: 0.9724 (tppt) cc_final: 0.9458 (tppt) REVERT: E 364 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9086 (mpp-170) REVERT: F 52 GLU cc_start: 0.9554 (OUTLIER) cc_final: 0.9272 (pm20) REVERT: F 92 MET cc_start: 0.9535 (ttp) cc_final: 0.9045 (ttp) REVERT: F 287 MET cc_start: 0.8987 (mmm) cc_final: 0.8570 (mmm) outliers start: 60 outliers final: 31 residues processed: 139 average time/residue: 0.1218 time to fit residues: 25.0222 Evaluate side-chains 119 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 210 LEU 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 389 THR 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 59 LYS 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 334 VAL Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 288 ILE 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 113 VAL Chi-restraints excluded: chain F residue 153 LEU 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 428 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061157 restraints weight = 132808.818| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.30 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3041 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= 0.192 Angle : 0.860 18.591 23846 Z= 0.393 Chirality : 0.070 0.873 2615 Planarity : 0.004 0.052 2712 Dihedral : 19.749 170.718 3014 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.39 % Allowed : 32.02 % 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 are not related in a simple way. whole: -1.04 (0.20), residues: 1799 helix: 0.44 (0.21), residues: 644 sheet: -0.61 (0.32), residues: 279 loop : -1.59 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 201 TYR 0.015 0.001 TYR E 346 PHE 0.012 0.001 PHE F 273 TRP 0.021 0.001 TRP E 370 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (17347) covalent geometry : angle 0.86028 / 0.39 (23846) hydrogen bonds : bond 0.03553 / 3.73 ( 555) hydrogen bonds : angle 5.31383 / 4.49 ( 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 143 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 88 time to evaluate : 0.423 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: 0.9399 (OUTLIER) cc_final: 0.9012 (pp30) REVERT: A 134 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9031 (mp0) REVERT: A 406 MET cc_start: 0.9093 (ppp) cc_final: 0.8864 (ppp) REVERT: A 435 MET cc_start: 0.9268 (tpp) cc_final: 0.8840 (tpp) REVERT: B 19 ARG cc_start: 0.9512 (OUTLIER) cc_final: 0.9097 (ttt180) REVERT: B 334 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8791 (p) REVERT: B 336 MET cc_start: 0.9394 (tpp) cc_final: 0.8716 (tpt) REVERT: E 331 LYS cc_start: 0.9759 (tppt) cc_final: 0.9462 (tppt) REVERT: E 429 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (mp) REVERT: F 52 GLU cc_start: 0.9540 (OUTLIER) cc_final: 0.9250 (pm20) REVERT: F 92 MET cc_start: 0.9545 (ttp) cc_final: 0.9045 (ttp) REVERT: F 287 MET cc_start: 0.8982 (mmm) cc_final: 0.8601 (mmm) REVERT: F 414 MET cc_start: 0.9109 (mmm) cc_final: 0.8904 (mmm) outliers start: 55 outliers final: 32 residues processed: 135 average time/residue: 0.1366 time to fit residues: 27.4771 Evaluate side-chains 123 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 210 LEU 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 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 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 200 VAL 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 44 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 223 ILE 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 429 LEU Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain F residue 11 THR 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 428 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 163 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.060284 restraints weight = 132939.385| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 5.33 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17347 Z= 0.196 Angle : 0.831 19.366 23846 Z= 0.381 Chirality : 0.066 0.792 2615 Planarity : 0.004 0.050 2712 Dihedral : 19.828 172.241 3010 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.64 % Allowed : 31.40 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1799 helix: 0.54 (0.21), residues: 645 sheet: -0.73 (0.32), residues: 282 loop : -1.50 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 113 TYR 0.013 0.001 TYR E 346 PHE 0.011 0.001 PHE F 273 TRP 0.021 0.001 TRP E 370 HIS 0.004 0.001 HIS E 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (17347) covalent geometry : angle 0.83136 / 0.38 (23846) hydrogen bonds : bond 0.03450 / 3.64 ( 555) hydrogen bonds : angle 5.24377 / 4.47 ( 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 146 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 87 time to evaluate : 0.573 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 35 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.9002 (pp30) REVERT: A 134 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9043 (mp0) REVERT: B 19 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.9124 (ttt180) REVERT: B 334 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8827 (p) REVERT: B 345 MET cc_start: 0.9401 (tmm) cc_final: 0.9157 (tmm) REVERT: E 57 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8950 (pp) REVERT: E 331 LYS cc_start: 0.9795 (tppt) cc_final: 0.9532 (tppt) REVERT: F 52 GLU cc_start: 0.9545 (OUTLIER) cc_final: 0.9271 (pm20) REVERT: F 92 MET cc_start: 0.9532 (ttp) cc_final: 0.9034 (ttp) REVERT: F 378 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9305 (mm) outliers start: 59 outliers final: 36 residues processed: 140 average time/residue: 0.1542 time to fit residues: 31.8862 Evaluate side-chains 125 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 83 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 210 LEU 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 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 62 ILE 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 334 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER 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 148 TYR Chi-restraints excluded: chain E residue 288 ILE 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 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 113 VAL Chi-restraints excluded: chain F residue 153 LEU 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: 8.9990 chunk 89 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059704 restraints weight = 132811.770| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 5.27 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17347 Z= 0.204 Angle : 0.826 19.001 23846 Z= 0.380 Chirality : 0.065 0.783 2615 Planarity : 0.004 0.048 2712 Dihedral : 19.841 170.956 3010 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.89 % Allowed : 31.22 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.20), residues: 1799 helix: 0.55 (0.21), residues: 644 sheet: -0.73 (0.32), residues: 280 loop : -1.45 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 72 TYR 0.017 0.001 TYR E 346 PHE 0.009 0.001 PHE F 45 TRP 0.021 0.001 TRP E 370 HIS 0.023 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (17347) covalent geometry : angle 0.82598 / 0.38 (23846) hydrogen bonds : bond 0.03520 / 3.73 ( 555) hydrogen bonds : angle 5.25375 / 4.46 ( 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 147 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 84 time to evaluate : 0.676 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 35 GLN cc_start: 0.9407 (OUTLIER) cc_final: 0.9007 (pp30) REVERT: A 134 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9034 (mp0) REVERT: B 19 ARG cc_start: 0.9537 (OUTLIER) cc_final: 0.9056 (ttt180) REVERT: B 287 MET cc_start: 0.8813 (tpp) cc_final: 0.8376 (tpp) REVERT: B 334 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8870 (p) REVERT: B 345 MET cc_start: 0.9399 (tmm) cc_final: 0.9078 (tmm) REVERT: E 331 LYS cc_start: 0.9790 (tppt) cc_final: 0.9562 (tppt) REVERT: F 4 LYS cc_start: 0.9143 (ttmm) cc_final: 0.8864 (tttm) REVERT: F 52 GLU cc_start: 0.9519 (OUTLIER) cc_final: 0.9255 (pm20) REVERT: F 92 MET cc_start: 0.9541 (ttp) cc_final: 0.8992 (ttp) REVERT: F 287 MET cc_start: 0.8558 (mmm) cc_final: 0.7689 (mmm) REVERT: F 378 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9291 (mm) outliers start: 63 outliers final: 44 residues processed: 138 average time/residue: 0.1468 time to fit residues: 30.1444 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 : 0.617 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 433 LEU 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 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER 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 148 TYR Chi-restraints excluded: chain E residue 288 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 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 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 320 HIS 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 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: 0.0040 chunk 1 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 173 optimal weight: 0.4980 chunk 4 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 142 optimal weight: 0.0000 chunk 143 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** 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** F 434 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061682 restraints weight = 129973.619| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 5.24 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17347 Z= 0.136 Angle : 0.795 19.328 23846 Z= 0.366 Chirality : 0.064 0.791 2615 Planarity : 0.004 0.047 2712 Dihedral : 19.831 171.009 3010 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.78 % Allowed : 32.33 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.20), residues: 1799 helix: 0.64 (0.21), residues: 643 sheet: -0.58 (0.32), residues: 278 loop : -1.40 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 364 TYR 0.013 0.001 TYR E 346 PHE 0.013 0.001 PHE F 343 TRP 0.020 0.001 TRP E 370 HIS 0.003 0.001 HIS E 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (17347) covalent geometry : angle 0.79528 / 0.37 (23846) hydrogen bonds : bond 0.03308 / 3.44 ( 555) hydrogen bonds : angle 5.11755 / 4.38 ( 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 136 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 91 time to evaluate : 0.463 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: 0.9349 (OUTLIER) cc_final: 0.8960 (pp30) REVERT: A 134 GLU cc_start: 0.9304 (mm-30) cc_final: 0.9010 (mp0) REVERT: A 288 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8436 (pt) REVERT: B 19 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.9073 (ttt180) REVERT: B 287 MET cc_start: 0.8935 (tpp) cc_final: 0.8700 (tpp) REVERT: B 345 MET cc_start: 0.9413 (tmm) cc_final: 0.9052 (tmm) REVERT: E 57 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8806 (pp) REVERT: E 331 LYS cc_start: 0.9799 (tppt) cc_final: 0.9584 (tppt) REVERT: F 4 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8894 (tttm) REVERT: F 23 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9262 (mm) REVERT: F 52 GLU cc_start: 0.9512 (OUTLIER) cc_final: 0.9272 (pm20) REVERT: F 92 MET cc_start: 0.9522 (ttp) cc_final: 0.9008 (ttp) REVERT: F 378 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9168 (mm) outliers start: 45 outliers final: 25 residues processed: 131 average time/residue: 0.1458 time to fit residues: 28.2145 Evaluate side-chains 116 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 271 LEU 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 F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 332 SER 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: 5.9990 chunk 132 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.060538 restraints weight = 131477.508| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.22 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17347 Z= 0.171 Angle : 0.803 19.576 23846 Z= 0.369 Chirality : 0.062 0.767 2615 Planarity : 0.004 0.049 2712 Dihedral : 19.858 174.092 3010 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.16 % Allowed : 32.76 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1799 helix: 0.70 (0.21), residues: 644 sheet: -0.58 (0.32), residues: 290 loop : -1.41 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 364 TYR 0.019 0.001 TYR F 293 PHE 0.010 0.001 PHE E 30 TRP 0.021 0.001 TRP E 370 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (17347) covalent geometry : angle 0.80287 / 0.37 (23846) hydrogen bonds : bond 0.03414 / 3.59 ( 555) hydrogen bonds : angle 5.09442 / 4.34 ( 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 119 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.8970 (pp30) REVERT: A 134 GLU cc_start: 0.9298 (mm-30) cc_final: 0.9015 (mp0) REVERT: A 288 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8423 (pt) REVERT: B 19 ARG cc_start: 0.9520 (OUTLIER) cc_final: 0.9078 (ttt180) REVERT: B 287 MET cc_start: 0.9048 (tpp) cc_final: 0.8662 (tpp) REVERT: B 345 MET cc_start: 0.9450 (tmm) cc_final: 0.9076 (tmm) REVERT: E 331 LYS cc_start: 0.9792 (tppt) cc_final: 0.9578 (tppt) REVERT: F 4 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8840 (tttm) REVERT: F 52 GLU cc_start: 0.9495 (OUTLIER) cc_final: 0.9207 (pm20) REVERT: F 92 MET cc_start: 0.9534 (ttp) cc_final: 0.8997 (ttp) REVERT: F 378 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9208 (mm) outliers start: 35 outliers final: 23 residues processed: 116 average time/residue: 0.1302 time to fit residues: 22.5870 Evaluate side-chains 111 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 125 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 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 332 SER 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: 4.9990 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 142 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.070338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060886 restraints weight = 130389.636| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 5.19 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17347 Z= 0.150 Angle : 0.795 19.929 23846 Z= 0.366 Chirality : 0.062 0.742 2615 Planarity : 0.004 0.047 2712 Dihedral : 19.821 176.299 3010 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.16 % Allowed : 32.39 % 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 are not related in a simple way. whole: -0.76 (0.20), residues: 1799 helix: 0.68 (0.21), residues: 643 sheet: -0.67 (0.32), residues: 280 loop : -1.34 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 364 TYR 0.011 0.001 TYR E 346 PHE 0.012 0.001 PHE F 343 TRP 0.020 0.001 TRP E 370 HIS 0.003 0.001 HIS E 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (17347) covalent geometry : angle 0.79549 / 0.37 (23846) hydrogen bonds : bond 0.03324 / 3.46 ( 555) hydrogen bonds : angle 5.06888 / 4.33 ( 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 120 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7984 (tpt) cc_final: 0.7368 (tpt) REVERT: A 35 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8963 (pp30) REVERT: A 134 GLU cc_start: 0.9278 (mm-30) cc_final: 0.9009 (mp0) REVERT: A 288 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (pt) REVERT: B 19 ARG cc_start: 0.9499 (OUTLIER) cc_final: 0.9163 (ttt180) REVERT: B 287 MET cc_start: 0.9062 (tpp) cc_final: 0.8677 (tpp) REVERT: B 345 MET cc_start: 0.9440 (tmm) cc_final: 0.9055 (tmm) REVERT: E 331 LYS cc_start: 0.9790 (tppt) cc_final: 0.9583 (tppt) REVERT: E 371 ASN cc_start: 0.9829 (OUTLIER) cc_final: 0.9620 (p0) REVERT: F 4 LYS cc_start: 0.9109 (ttmm) cc_final: 0.8846 (tttm) REVERT: F 52 GLU cc_start: 0.9478 (OUTLIER) cc_final: 0.9193 (pm20) REVERT: F 92 MET cc_start: 0.9537 (ttp) cc_final: 0.8995 (ttp) REVERT: F 378 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9166 (mm) outliers start: 35 outliers final: 24 residues processed: 117 average time/residue: 0.1385 time to fit residues: 24.2353 Evaluate side-chains 113 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN 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 288 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 434 ASN 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 370 TRP Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 332 SER 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: 0.0000 chunk 100 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** 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 = 0.3378 r_free = 0.3378 target = 0.070518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060931 restraints weight = 131107.776| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 5.23 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17347 Z= 0.141 Angle : 0.798 20.039 23846 Z= 0.366 Chirality : 0.061 0.734 2615 Planarity : 0.004 0.048 2712 Dihedral : 19.823 177.360 3010 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.04 % Allowed : 32.70 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1799 helix: 0.64 (0.21), residues: 643 sheet: -0.64 (0.32), residues: 280 loop : -1.34 (0.21), residues: 876 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 0.013 0.001 PHE F 343 TRP 0.020 0.001 TRP E 370 HIS 0.021 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (17347) covalent geometry : angle 0.79796 / 0.37 (23846) hydrogen bonds : bond 0.03295 / 3.46 ( 555) hydrogen bonds : angle 5.10941 / 4.33 ( 1576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.46 seconds wall clock time: 45 minutes 18.05 seconds (2718.05 seconds total)