Starting phenix.real_space_refine on Sun May 18 09:52:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9g_36986/05_2025/8k9g_36986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9g_36986/05_2025/8k9g_36986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k9g_36986/05_2025/8k9g_36986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9g_36986/05_2025/8k9g_36986.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9g_36986/05_2025/8k9g_36986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9g_36986/05_2025/8k9g_36986.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16759 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "G" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 8} Link IDs: {'rna2p': 20} Chain: "A" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3684 Classifications: {'peptide': 455} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3695 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 9.95, per 1000 atoms: 0.59 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: 4.32 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 5.94 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: 5.42 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4067 1.33 - 1.45: 3844 1.45 - 1.57: 9190 1.57 - 1.69: 176 1.69 - 1.81: 70 Bond restraints: 17347 Sorted by residual: bond pdb=" N VAL B 395 " pdb=" CA VAL B 395 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N THR F 11 " pdb=" CA THR F 11 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.26e+00 bond pdb=" N THR B 11 " pdb=" CA THR B 11 " ideal model delta sigma weight residual 1.462 1.490 -0.029 9.50e-03 1.11e+04 9.21e+00 bond pdb=" C THR B 11 " pdb=" N PRO B 12 " ideal model delta sigma weight residual 1.331 1.354 -0.023 7.90e-03 1.60e+04 8.25e+00 bond pdb=" C THR F 11 " pdb=" N PRO F 12 " ideal model delta sigma weight residual 1.332 1.355 -0.023 8.20e-03 1.49e+04 7.75e+00 ... (remaining 17342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 23275 2.35 - 4.69: 471 4.69 - 7.04: 65 7.04 - 9.38: 25 9.38 - 11.73: 10 Bond angle restraints: 23846 Sorted by residual: angle pdb=" N ASP B 386 " pdb=" CA ASP B 386 " pdb=" C ASP B 386 " ideal model delta sigma weight residual 111.71 105.69 6.02 1.15e+00 7.56e-01 2.74e+01 angle pdb=" CB ARG B 276 " pdb=" CG ARG B 276 " pdb=" CD ARG B 276 " ideal model delta sigma weight residual 111.30 122.10 -10.80 2.30e+00 1.89e-01 2.20e+01 angle pdb=" CA LYS B 280 " pdb=" CB LYS B 280 " pdb=" CG LYS B 280 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CA LYS F 400 " pdb=" CB LYS F 400 " pdb=" CG LYS F 400 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" CA LYS B 309 " pdb=" CB LYS B 309 " pdb=" CG LYS B 309 " ideal model delta sigma weight residual 114.10 123.00 -8.90 2.00e+00 2.50e-01 1.98e+01 ... (remaining 23841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8179 17.94 - 35.88: 1485 35.88 - 53.82: 534 53.82 - 71.77: 157 71.77 - 89.71: 33 Dihedral angle restraints: 10388 sinusoidal: 5059 harmonic: 5329 Sorted by residual: dihedral pdb=" C5' G G 5 " pdb=" C4' G G 5 " pdb=" C3' G G 5 " pdb=" O3' G G 5 " ideal model delta sinusoidal sigma weight residual 147.00 102.65 44.35 1 8.00e+00 1.56e-02 4.27e+01 dihedral pdb=" O4' G G 5 " pdb=" C4' G G 5 " pdb=" C3' G G 5 " pdb=" C2' G G 5 " ideal model delta sinusoidal sigma weight residual 24.00 -16.06 40.06 1 8.00e+00 1.56e-02 3.52e+01 dihedral pdb=" C3' G G 5 " pdb=" C4' G G 5 " pdb=" O4' G G 5 " pdb=" C1' G G 5 " ideal model delta sinusoidal sigma weight residual -2.00 33.77 -35.77 1 8.00e+00 1.56e-02 2.83e+01 ... (remaining 10385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2519 0.122 - 0.244: 87 0.244 - 0.366: 2 0.366 - 0.488: 2 0.488 - 0.610: 5 Chirality restraints: 2615 Sorted by residual: chirality pdb=" P DA H 36 " pdb=" OP1 DA H 36 " pdb=" OP2 DA H 36 " pdb=" O5' DA H 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" P DA H 31 " pdb=" OP1 DA H 31 " pdb=" OP2 DA H 31 " pdb=" O5' DA H 31 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" P DA D 36 " pdb=" OP1 DA D 36 " pdb=" OP2 DA D 36 " pdb=" O5' DA D 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 2612 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 15 " 0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ASP F 15 " -0.087 2.00e-02 2.50e+03 pdb=" O ASP F 15 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP F 16 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 272 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ALA F 272 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA F 272 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE F 273 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 276 " -0.240 9.50e-02 1.11e+02 1.07e-01 7.11e+00 pdb=" NE ARG F 276 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG F 276 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG F 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 276 " -0.008 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1578 2.74 - 3.28: 15893 3.28 - 3.82: 28524 3.82 - 4.36: 31846 4.36 - 4.90: 53629 Nonbonded interactions: 131470 Sorted by model distance: nonbonded pdb=" OG1 THR A 71 " pdb=" OE2 GLU B 426 " model vdw 2.201 3.040 nonbonded pdb=" NE1 TRP B 219 " pdb=" OE1 GLU B 398 " model vdw 2.220 3.120 nonbonded pdb=" O PRO A 404 " pdb=" OH TYR B 416 " model vdw 2.245 3.040 nonbonded pdb=" O3' DA D 36 " pdb=" NH2 ARG B 263 " model vdw 2.246 3.120 nonbonded pdb=" OG1 THR E 71 " pdb=" OE2 GLU F 426 " model vdw 2.250 3.040 ... (remaining 131465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 1 through 151 or resid 204 through 507)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.950 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17347 Z= 0.246 Angle : 0.852 11.726 23846 Z= 0.471 Chirality : 0.059 0.610 2615 Planarity : 0.006 0.107 2712 Dihedral : 21.185 89.707 6942 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.25 % Allowed : 35.10 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.002 TRP B 219 HIS 0.008 0.001 HIS A 251 PHE 0.039 0.002 PHE E 313 TYR 0.024 0.002 TYR F 154 ARG 0.013 0.001 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.17935 ( 555) hydrogen bonds : angle 7.99788 ( 1576) covalent geometry : bond 0.00477 (17347) covalent geometry : angle 0.85234 (23846) *********************** 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 : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.6470 (t80) outliers start: 4 outliers final: 2 residues processed: 161 average time/residue: 0.3328 time to fit residues: 77.8666 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 : 1.808 ------------------------------------------------------------------------------- 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 158 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 0.0370 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 151 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 262 GLN B 349 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 446 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063984 restraints weight = 128893.293| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 5.11 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17347 Z= 0.162 Angle : 0.624 9.143 23846 Z= 0.333 Chirality : 0.043 0.243 2615 Planarity : 0.004 0.061 2712 Dihedral : 18.811 88.331 3180 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.27 % Allowed : 32.70 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1799 helix: 0.02 (0.20), residues: 632 sheet: -0.44 (0.31), residues: 293 loop : -1.70 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 373 HIS 0.004 0.001 HIS E 329 PHE 0.016 0.001 PHE F 273 TYR 0.016 0.001 TYR F 154 ARG 0.004 0.000 ARG B 250 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 555) hydrogen bonds : angle 5.65856 ( 1576) covalent geometry : bond 0.00358 (17347) covalent geometry : angle 0.62436 (23846) *********************** 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 161 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9037 (mp0) REVERT: A 406 MET cc_start: 0.8973 (ppp) cc_final: 0.8756 (ppp) REVERT: A 435 MET cc_start: 0.9008 (tpp) cc_final: 0.8683 (tpp) REVERT: B 146 ASP cc_start: 0.8776 (t0) cc_final: 0.8539 (t0) REVERT: B 261 CYS cc_start: 0.9722 (OUTLIER) cc_final: 0.9446 (m) REVERT: B 287 MET cc_start: 0.9296 (tpp) cc_final: 0.8497 (tpt) REVERT: E 150 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.8819 (t80) REVERT: E 331 LYS cc_start: 0.9837 (tppt) cc_final: 0.9624 (tppt) REVERT: E 435 MET cc_start: 0.8677 (tpp) cc_final: 0.8468 (mmm) REVERT: F 92 MET cc_start: 0.9463 (ttp) cc_final: 0.9169 (ttt) REVERT: F 287 MET cc_start: 0.9137 (mmm) cc_final: 0.8287 (mmm) outliers start: 53 outliers final: 21 residues processed: 154 average time/residue: 0.3043 time to fit residues: 69.6030 Evaluate side-chains 112 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 389 ASN Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 133 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 ASN E 371 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.067853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058397 restraints weight = 131966.481| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 5.26 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17347 Z= 0.235 Angle : 0.670 9.525 23846 Z= 0.352 Chirality : 0.044 0.185 2615 Planarity : 0.005 0.052 2712 Dihedral : 18.992 98.810 3174 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.18 % Allowed : 30.29 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1799 helix: 0.22 (0.20), residues: 641 sheet: -0.55 (0.31), residues: 286 loop : -1.59 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 370 HIS 0.004 0.001 HIS B 340 PHE 0.015 0.002 PHE F 158 TYR 0.015 0.002 TYR E 346 ARG 0.005 0.001 ARG E 113 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 555) hydrogen bonds : angle 5.46276 ( 1576) covalent geometry : bond 0.00513 (17347) covalent geometry : angle 0.66951 (23846) *********************** 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 176 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 92 time to evaluate : 1.810 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: 0.9407 (OUTLIER) cc_final: 0.8920 (pp30) REVERT: A 134 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9062 (mp0) REVERT: A 225 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7575 (mtt90) REVERT: A 406 MET cc_start: 0.9039 (ppp) cc_final: 0.8812 (ppp) REVERT: B 36 ILE cc_start: 0.9148 (mm) cc_final: 0.8839 (mm) REVERT: B 287 MET cc_start: 0.9588 (tpp) cc_final: 0.9077 (tpp) REVERT: B 345 MET cc_start: 0.9372 (tmm) cc_final: 0.8989 (tmm) REVERT: E 504 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8501 (ptpp) REVERT: E 507 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7592 (mp) REVERT: F 4 LYS cc_start: 0.9122 (ttmm) cc_final: 0.8904 (tttm) REVERT: F 52 GLU cc_start: 0.9494 (OUTLIER) cc_final: 0.9181 (pm20) REVERT: F 92 MET cc_start: 0.9506 (ttp) cc_final: 0.9001 (ttp) REVERT: F 287 MET cc_start: 0.9231 (mmm) cc_final: 0.9011 (mmm) outliers start: 84 outliers final: 42 residues processed: 166 average time/residue: 0.3325 time to fit residues: 79.7182 Evaluate side-chains 131 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 225 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 415 SER 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 370 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 504 LYS Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 372 LYS Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.057491 restraints weight = 135839.445| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 5.28 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17347 Z= 0.228 Angle : 0.652 8.814 23846 Z= 0.341 Chirality : 0.043 0.186 2615 Planarity : 0.004 0.054 2712 Dihedral : 19.055 99.687 3174 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.44 % Allowed : 30.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1799 helix: 0.29 (0.21), residues: 643 sheet: -0.87 (0.32), residues: 283 loop : -1.52 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 370 HIS 0.030 0.002 HIS A 251 PHE 0.019 0.001 PHE F 158 TYR 0.017 0.002 TYR E 346 ARG 0.005 0.000 ARG E 113 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 555) hydrogen bonds : angle 5.40031 ( 1576) covalent geometry : bond 0.00498 (17347) covalent geometry : angle 0.65218 (23846) *********************** 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 156 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 84 time to evaluate : 1.835 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: 0.9424 (OUTLIER) cc_final: 0.9024 (pp30) REVERT: A 134 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9076 (mp0) REVERT: A 285 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5355 (m-80) REVERT: B 19 ARG cc_start: 0.9536 (OUTLIER) cc_final: 0.9330 (ttp80) REVERT: B 287 MET cc_start: 0.9580 (tpp) cc_final: 0.9058 (tpp) REVERT: B 345 MET cc_start: 0.9396 (tmm) cc_final: 0.9163 (tmm) REVERT: E 364 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.9110 (mpp-170) REVERT: F 52 GLU cc_start: 0.9486 (OUTLIER) cc_final: 0.9155 (pm20) REVERT: F 92 MET cc_start: 0.9530 (ttp) cc_final: 0.8947 (ttp) REVERT: F 186 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6954 (mmm-85) REVERT: F 287 MET cc_start: 0.9239 (mmm) cc_final: 0.8908 (mmm) outliers start: 72 outliers final: 39 residues processed: 146 average time/residue: 0.3265 time to fit residues: 70.4114 Evaluate side-chains 126 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 81 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 285 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 E residue 507 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 376 LYS Chi-restraints excluded: chain F residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 54 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 124 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057557 restraints weight = 131565.449| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 5.41 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17347 Z= 0.173 Angle : 0.606 8.880 23846 Z= 0.316 Chirality : 0.042 0.193 2615 Planarity : 0.004 0.051 2712 Dihedral : 19.068 99.305 3174 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.76 % Allowed : 30.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1799 helix: 0.44 (0.21), residues: 642 sheet: -0.70 (0.33), residues: 266 loop : -1.46 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 370 HIS 0.006 0.001 HIS A 251 PHE 0.013 0.001 PHE F 273 TYR 0.014 0.001 TYR E 346 ARG 0.003 0.000 ARG E 113 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 555) hydrogen bonds : angle 5.25647 ( 1576) covalent geometry : bond 0.00381 (17347) covalent geometry : angle 0.60585 (23846) *********************** 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 147 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 86 time to evaluate : 1.764 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: 0.9406 (OUTLIER) cc_final: 0.9039 (pp30) REVERT: A 134 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9049 (mp0) REVERT: A 216 GLU cc_start: 0.9508 (OUTLIER) cc_final: 0.9297 (mp0) REVERT: A 225 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7318 (mtt90) REVERT: B 19 ARG cc_start: 0.9491 (OUTLIER) cc_final: 0.8987 (ttt180) REVERT: B 287 MET cc_start: 0.9565 (tpp) cc_final: 0.9026 (tpp) REVERT: B 345 MET cc_start: 0.9415 (tmm) cc_final: 0.9131 (tmm) REVERT: E 112 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9261 (ptmm) REVERT: E 364 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.9163 (mpp-170) REVERT: F 52 GLU cc_start: 0.9469 (OUTLIER) cc_final: 0.9147 (pm20) REVERT: F 92 MET cc_start: 0.9501 (ttp) cc_final: 0.8842 (ttp) REVERT: F 186 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6917 (mmm-85) REVERT: F 378 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9218 (mm) outliers start: 61 outliers final: 38 residues processed: 139 average time/residue: 0.3150 time to fit residues: 64.2005 Evaluate side-chains 128 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 81 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 214 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 225 ARG 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 B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 285 TYR 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 432 THR Chi-restraints excluded: chain E residue 434 SER Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 200 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 349 ASN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057604 restraints weight = 135681.449| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 5.36 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17347 Z= 0.178 Angle : 0.608 10.220 23846 Z= 0.315 Chirality : 0.042 0.214 2615 Planarity : 0.004 0.050 2712 Dihedral : 19.043 98.814 3174 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.87 % Allowed : 29.73 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1799 helix: 0.50 (0.21), residues: 644 sheet: -0.75 (0.32), residues: 266 loop : -1.41 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 370 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE F 343 TYR 0.014 0.001 TYR E 346 ARG 0.004 0.000 ARG E 364 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 555) hydrogen bonds : angle 5.19250 ( 1576) covalent geometry : bond 0.00394 (17347) covalent geometry : angle 0.60824 (23846) *********************** 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 168 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 89 time to evaluate : 1.774 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: 0.9406 (OUTLIER) cc_final: 0.9040 (pp30) REVERT: A 134 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8982 (mp0) REVERT: A 216 GLU cc_start: 0.9517 (OUTLIER) cc_final: 0.9308 (mp0) REVERT: A 225 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7260 (mtt90) REVERT: A 285 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5535 (m-80) REVERT: B 19 ARG cc_start: 0.9532 (OUTLIER) cc_final: 0.9241 (ttt180) REVERT: B 181 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8818 (t80) REVERT: B 226 GLN cc_start: 0.9688 (OUTLIER) cc_final: 0.9183 (pm20) REVERT: B 287 MET cc_start: 0.9566 (tpp) cc_final: 0.9030 (tpp) REVERT: B 345 MET cc_start: 0.9444 (tmm) cc_final: 0.9119 (tmm) REVERT: E 112 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9294 (ptmm) REVERT: E 150 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8902 (t80) REVERT: E 364 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.9198 (mpp-170) REVERT: F 52 GLU cc_start: 0.9440 (OUTLIER) cc_final: 0.9127 (pm20) REVERT: F 92 MET cc_start: 0.9511 (ttp) cc_final: 0.8812 (ttp) REVERT: F 186 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6940 (mmm-85) REVERT: F 250 ARG cc_start: 0.9286 (tpm170) cc_final: 0.9082 (ttp80) REVERT: F 378 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9212 (mm) outliers start: 79 outliers final: 50 residues processed: 159 average time/residue: 0.3305 time to fit residues: 75.9868 Evaluate side-chains 148 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 85 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 216 GLU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 338 LEU 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 E residue 504 LYS Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 320 HIS Chi-restraints excluded: chain F residue 332 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 52 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN B 226 GLN B 357 GLN 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 = 0.3357 r_free = 0.3357 target = 0.069457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059871 restraints weight = 131898.394| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 5.38 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17347 Z= 0.116 Angle : 0.590 10.380 23846 Z= 0.304 Chirality : 0.043 0.245 2615 Planarity : 0.004 0.050 2712 Dihedral : 18.908 96.069 3174 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.71 % Allowed : 31.34 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1799 helix: 0.64 (0.21), residues: 643 sheet: -0.57 (0.33), residues: 257 loop : -1.32 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 370 HIS 0.005 0.001 HIS E 207 PHE 0.012 0.001 PHE F 343 TYR 0.010 0.001 TYR E 346 ARG 0.003 0.000 ARG E 113 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 555) hydrogen bonds : angle 5.01656 ( 1576) covalent geometry : bond 0.00262 (17347) covalent geometry : angle 0.58957 (23846) *********************** 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 142 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8980 (mp0) REVERT: A 225 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7253 (mtt90) REVERT: A 288 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8462 (pt) REVERT: A 302 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: B 19 ARG cc_start: 0.9496 (OUTLIER) cc_final: 0.9100 (ttt180) REVERT: B 181 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8742 (t80) REVERT: B 287 MET cc_start: 0.9505 (tpp) cc_final: 0.9060 (tpp) REVERT: B 345 MET cc_start: 0.9516 (tmm) cc_final: 0.9202 (tmm) REVERT: E 112 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9271 (ptmm) REVERT: E 150 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8871 (t80) REVERT: E 313 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7877 (p90) REVERT: F 33 TRP cc_start: 0.8851 (t60) cc_final: 0.7875 (t60) REVERT: F 52 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.8976 (pm20) REVERT: F 92 MET cc_start: 0.9567 (ttp) cc_final: 0.8998 (ttp) REVERT: F 287 MET cc_start: 0.8993 (mmm) cc_final: 0.8639 (mmm) REVERT: F 378 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9108 (mm) outliers start: 44 outliers final: 20 residues processed: 135 average time/residue: 0.3536 time to fit residues: 69.2534 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 : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 146 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS B 267 GLN B 349 ASN ** B 435 ASN ** 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 = 0.3322 r_free = 0.3322 target = 0.067931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058336 restraints weight = 130710.037| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 5.24 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17347 Z= 0.163 Angle : 0.601 12.111 23846 Z= 0.311 Chirality : 0.042 0.227 2615 Planarity : 0.004 0.050 2712 Dihedral : 18.940 94.724 3174 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.08 % Allowed : 30.97 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1799 helix: 0.70 (0.21), residues: 643 sheet: -0.52 (0.32), residues: 264 loop : -1.34 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 370 HIS 0.003 0.001 HIS E 207 PHE 0.012 0.001 PHE F 343 TYR 0.010 0.001 TYR E 346 ARG 0.007 0.000 ARG E 364 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 555) hydrogen bonds : angle 5.02791 ( 1576) covalent geometry : bond 0.00363 (17347) covalent geometry : angle 0.60072 (23846) *********************** 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 133 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 83 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8971 (mp0) REVERT: A 285 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.5573 (m-80) REVERT: B 19 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8964 (ttt180) REVERT: B 181 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8793 (t80) REVERT: B 287 MET cc_start: 0.9515 (tpp) cc_final: 0.9029 (tpp) REVERT: B 345 MET cc_start: 0.9507 (tmm) cc_final: 0.9187 (tmm) REVERT: E 112 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9317 (ptmm) REVERT: E 150 TYR cc_start: 0.9258 (OUTLIER) cc_final: 0.8903 (t80) REVERT: E 313 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7958 (p90) REVERT: E 485 LYS cc_start: 0.9309 (ptmm) cc_final: 0.8993 (tttt) REVERT: F 33 TRP cc_start: 0.8952 (t60) cc_final: 0.7966 (t60) REVERT: F 41 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8375 (ptpp) REVERT: F 52 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.8964 (pm20) REVERT: F 92 MET cc_start: 0.9536 (ttp) cc_final: 0.8847 (ttp) REVERT: F 287 MET cc_start: 0.9036 (mmm) cc_final: 0.8701 (mmm) REVERT: F 378 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9178 (mm) outliers start: 50 outliers final: 33 residues processed: 124 average time/residue: 0.3451 time to fit residues: 61.6127 Evaluate side-chains 124 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain E residue 432 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 41 LYS Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 332 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 170 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 114 optimal weight: 0.0060 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 302 GLN F 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060029 restraints weight = 131964.131| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 5.29 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17347 Z= 0.118 Angle : 0.587 13.678 23846 Z= 0.302 Chirality : 0.042 0.224 2615 Planarity : 0.004 0.048 2712 Dihedral : 18.848 94.200 3174 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.71 % Allowed : 31.34 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1799 helix: 0.70 (0.21), residues: 646 sheet: -0.55 (0.33), residues: 257 loop : -1.32 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 370 HIS 0.014 0.001 HIS A 251 PHE 0.012 0.001 PHE F 343 TYR 0.010 0.001 TYR F 293 ARG 0.003 0.000 ARG E 113 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 555) hydrogen bonds : angle 4.92787 ( 1576) covalent geometry : bond 0.00266 (17347) covalent geometry : angle 0.58704 (23846) *********************** 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 131 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8963 (mp0) REVERT: A 288 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8408 (pt) REVERT: A 302 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: B 19 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.8978 (ttt180) REVERT: B 181 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8763 (t80) REVERT: B 287 MET cc_start: 0.9469 (tpp) cc_final: 0.9020 (tpp) REVERT: B 345 MET cc_start: 0.9525 (tmm) cc_final: 0.9200 (tmm) REVERT: E 112 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9292 (ptmm) REVERT: E 150 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.8881 (t80) REVERT: E 313 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7867 (p90) REVERT: E 485 LYS cc_start: 0.9325 (ptmm) cc_final: 0.9022 (tttt) REVERT: F 33 TRP cc_start: 0.8755 (t60) cc_final: 0.7754 (t60) REVERT: F 52 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8917 (pm20) REVERT: F 92 MET cc_start: 0.9568 (ttp) cc_final: 0.8896 (ttp) REVERT: F 158 PHE cc_start: 0.8259 (t80) cc_final: 0.7987 (t80) REVERT: F 287 MET cc_start: 0.8983 (mmm) cc_final: 0.8633 (mmm) REVERT: F 378 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9120 (mm) outliers start: 44 outliers final: 26 residues processed: 124 average time/residue: 0.3307 time to fit residues: 59.6231 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 : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 302 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 313 PHE Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060421 restraints weight = 132941.191| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 5.35 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17347 Z= 0.114 Angle : 0.585 13.654 23846 Z= 0.301 Chirality : 0.042 0.220 2615 Planarity : 0.004 0.048 2712 Dihedral : 18.759 93.043 3174 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.97 % Allowed : 31.89 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1799 helix: 0.79 (0.21), residues: 646 sheet: -0.59 (0.33), residues: 269 loop : -1.35 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 370 HIS 0.020 0.001 HIS A 251 PHE 0.012 0.001 PHE F 343 TYR 0.009 0.001 TYR F 154 ARG 0.005 0.000 ARG E 364 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 555) hydrogen bonds : angle 4.86224 ( 1576) covalent geometry : bond 0.00257 (17347) covalent geometry : angle 0.58511 (23846) ********************** 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 119 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8954 (mp0) REVERT: A 288 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8365 (pt) REVERT: B 19 ARG cc_start: 0.9463 (OUTLIER) cc_final: 0.8922 (ttt180) REVERT: B 118 ILE cc_start: 0.8761 (tt) cc_final: 0.8462 (tp) REVERT: B 181 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8692 (t80) REVERT: B 287 MET cc_start: 0.9473 (tpp) cc_final: 0.9040 (tpp) REVERT: B 345 MET cc_start: 0.9530 (tmm) cc_final: 0.9203 (tmm) REVERT: E 112 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9297 (ptmm) REVERT: E 150 TYR cc_start: 0.9274 (OUTLIER) cc_final: 0.8833 (t80) REVERT: E 485 LYS cc_start: 0.9361 (ptmm) cc_final: 0.9068 (tttt) REVERT: F 33 TRP cc_start: 0.8709 (t60) cc_final: 0.7687 (t60) REVERT: F 52 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: F 92 MET cc_start: 0.9564 (ttp) cc_final: 0.8968 (ttp) REVERT: F 158 PHE cc_start: 0.8321 (t80) cc_final: 0.8077 (t80) REVERT: F 287 MET cc_start: 0.8956 (mmm) cc_final: 0.8609 (mmm) REVERT: F 378 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9137 (mm) outliers start: 32 outliers final: 23 residues processed: 114 average time/residue: 0.3329 time to fit residues: 55.6510 Evaluate side-chains 115 residues out of total 1623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 447 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 181 PHE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 370 TRP Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 133 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 0.5980 chunk 13 optimal weight: 0.0370 chunk 168 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** 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 = 0.3372 r_free = 0.3372 target = 0.069661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059983 restraints weight = 131124.536| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.30 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17347 Z= 0.120 Angle : 0.584 13.443 23846 Z= 0.299 Chirality : 0.042 0.219 2615 Planarity : 0.004 0.048 2712 Dihedral : 18.724 92.041 3174 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.22 % Allowed : 31.65 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1799 helix: 0.82 (0.21), residues: 646 sheet: -0.63 (0.33), residues: 274 loop : -1.32 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 370 HIS 0.004 0.001 HIS E 207 PHE 0.012 0.001 PHE F 343 TYR 0.009 0.001 TYR F 154 ARG 0.004 0.000 ARG E 364 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 555) hydrogen bonds : angle 4.85827 ( 1576) covalent geometry : bond 0.00272 (17347) covalent geometry : angle 0.58383 (23846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5910.51 seconds wall clock time: 104 minutes 17.37 seconds (6257.37 seconds total)