Starting phenix.real_space_refine on Thu Aug 6 05:23:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g75_51110/08_2026/9g75_51110.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g75_51110/08_2026/9g75_51110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g75_51110/08_2026/9g75_51110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g75_51110/08_2026/9g75_51110.map" model { file = "/net/cci-nas-00/data/ceres_data/9g75_51110/08_2026/9g75_51110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g75_51110/08_2026/9g75_51110.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.972 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 38 5.49 5 S 72 5.16 5 C 8655 2.51 5 N 2411 2.21 5 O 2604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13780 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6755 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 60, 'TRANS': 789} Chain breaks: 10 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3127 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3118 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 391, 3108 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 391, 3108 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3169 Chain: "P" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 397 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "T" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 383 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS C 161 " occ=0.69 ... (18 atoms not shown) pdb=" NE2BHIS C 161 " occ=0.31 Time building chain proxies: 3.61, per 1000 atoms: 0.26 Number of scatterers: 13780 At special positions: 0 Unit cell: (100.65, 103.125, 145.2, 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 72 16.00 P 38 15.00 O 2604 8.00 N 2411 7.00 C 8655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 872.0 milliseconds 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 15 sheets defined 47.3% alpha, 14.3% beta 19 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.636A pdb=" N GLN A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.752A pdb=" N LEU A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.542A pdb=" N VAL A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.693A pdb=" N LEU A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.593A pdb=" N GLN A 264 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 265 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 266' Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.753A pdb=" N SER A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.503A pdb=" N ASP A 331 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 370 through 400 removed outlier: 4.071A pdb=" N GLN A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 402 through 413 removed outlier: 4.057A pdb=" N LEU A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 451 removed outlier: 3.642A pdb=" N ARG A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.919A pdb=" N LYS A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 532 removed outlier: 3.745A pdb=" N LEU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.654A pdb=" N THR A 537 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 538 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 540 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.509A pdb=" N LEU A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 754 Processing helix chain 'A' and resid 766 through 787 removed outlier: 3.586A pdb=" N LEU A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE A 778 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TRP A 779 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LYS A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 removed outlier: 4.582A pdb=" N LYS A 853 " --> pdb=" O SER A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 885 removed outlier: 3.547A pdb=" N HIS A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 removed outlier: 3.742A pdb=" N GLN A 900 " --> pdb=" O TRP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1044 Processing helix chain 'A' and resid 1070 through 1101 removed outlier: 3.803A pdb=" N VAL A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1146 removed outlier: 3.702A pdb=" N LEU A1146 " --> pdb=" O PHE A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1188 removed outlier: 3.900A pdb=" N ARG A1186 " --> pdb=" O THR A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.595A pdb=" N GLY B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 93 removed outlier: 3.703A pdb=" N GLU B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 137 through 152 removed outlier: 3.960A pdb=" N VAL B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.677A pdb=" N ASP B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 241 removed outlier: 4.644A pdb=" N SER B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.606A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 444 through 457 removed outlier: 3.519A pdb=" N SER B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.512A pdb=" N LEU C 60 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.524A pdb=" N GLY C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 93 removed outlier: 3.747A pdb=" N GLU C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 133 Processing helix chain 'C' and resid 137 through 151 removed outlier: 3.655A pdb=" N LEU C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.744A pdb=" N VAL C 174 " --> pdb=" O CYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.992A pdb=" N PHE C 240 " --> pdb=" O TRP C 236 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 365 through 383 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 418 through 424 removed outlier: 3.976A pdb=" N LEU C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 458 removed outlier: 4.363A pdb=" N ARG C 446 " --> pdb=" O ILE C 442 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 161 removed outlier: 3.582A pdb=" N GLY A 157 " --> pdb=" O CYS A 207 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 207 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 203 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN A 247 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 275 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL A 249 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 419 removed outlier: 4.239A pdb=" N TYR A 815 " --> pdb=" O LEU A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 588 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.000A pdb=" N ARG A1116 " --> pdb=" O CYS A1108 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A1196 " --> pdb=" O VAL A1161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 5.877A pdb=" N PHE B 100 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE B 185 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 309 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 276 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 274 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 275 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYS B 259 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 359 removed outlier: 6.797A pdb=" N VAL B 357 " --> pdb=" O TRP B 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 413 through 416 removed outlier: 3.644A pdb=" N ARG B 430 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.201A pdb=" N PHE C 100 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE C 185 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 309 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE C 274 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS C 271 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE C 267 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS C 259 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AB5, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AB6, first strand: chain 'C' and resid 387 through 389 removed outlier: 7.201A pdb=" N TRP C 388 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 357 " --> pdb=" O TRP C 388 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS C 356 " --> pdb=" O PHE C 413 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 415 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA C 358 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C 417 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP C 360 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 428 " --> pdb=" O LEU C 416 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3902 1.33 - 1.45: 2562 1.45 - 1.57: 7547 1.57 - 1.69: 74 1.69 - 1.81: 112 Bond restraints: 14197 Sorted by residual: bond pdb=" C1' DC T 18 " pdb=" N1 DC T 18 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C3' DC P 15 " pdb=" C2' DC P 15 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DG T 16 " pdb=" C2' DG T 16 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG T 31 " pdb=" C2' DG T 31 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.45e+00 bond pdb=" C3' DG P 23 " pdb=" C2' DG P 23 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.18e+00 ... (remaining 14192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 19098 1.89 - 3.77: 309 3.77 - 5.66: 20 5.66 - 7.54: 1 7.54 - 9.43: 1 Bond angle restraints: 19429 Sorted by residual: angle pdb=" N SER B 313 " pdb=" CA SER B 313 " pdb=" C SER B 313 " ideal model delta sigma weight residual 107.67 117.10 -9.43 2.09e+00 2.29e-01 2.04e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT T 19 " pdb=" C4 DT T 19 " pdb=" O4 DT T 19 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 ... (remaining 19424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 8188 35.70 - 71.39: 177 71.39 - 107.09: 1 107.09 - 142.78: 0 142.78 - 178.48: 2 Dihedral angle restraints: 8368 sinusoidal: 3639 harmonic: 4729 Sorted by residual: dihedral pdb=" C4' DG T 31 " pdb=" C3' DG T 31 " pdb=" O3' DG T 31 " pdb=" P DA T 32 " ideal model delta sinusoidal sigma weight residual -140.00 38.48 -178.48 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG P 8 " pdb=" C3' DG P 8 " pdb=" O3' DG P 8 " pdb=" P DT P 9 " ideal model delta sinusoidal sigma weight residual 220.00 64.77 155.23 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" CA HIS C 51 " pdb=" C HIS C 51 " pdb=" N PHE C 52 " pdb=" CA PHE C 52 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 8365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1662 0.044 - 0.088: 340 0.088 - 0.132: 129 0.132 - 0.176: 2 0.176 - 0.219: 1 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CA VAL B 312 " pdb=" N VAL B 312 " pdb=" C VAL B 312 " pdb=" CB VAL B 312 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 198 " pdb=" N ILE A 198 " pdb=" C ILE A 198 " pdb=" CB ILE A 198 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" P DT P 9 " pdb=" OP1 DT P 9 " pdb=" OP2 DT P 9 " pdb=" O5' DT P 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 2131 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1177 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A1178 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1178 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1178 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 53 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C PHE B 53 " -0.022 2.00e-02 2.50e+03 pdb=" O PHE B 53 " 0.009 2.00e-02 2.50e+03 pdb=" N SER B 54 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 806 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO A 807 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 807 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 807 " -0.018 5.00e-02 4.00e+02 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1315 2.74 - 3.28: 13466 3.28 - 3.82: 23163 3.82 - 4.36: 28523 4.36 - 4.90: 47975 Nonbonded interactions: 114442 Sorted by model distance: nonbonded pdb=" O ALA C 63 " pdb=" OG SER C 67 " model vdw 2.203 3.040 nonbonded pdb=" O LEU C 148 " pdb=" OG SER C 152 " model vdw 2.216 3.040 nonbonded pdb=" O LEU B 65 " pdb=" NH1 ARG B 72 " model vdw 2.233 3.120 nonbonded pdb=" O GLY B 162 " pdb=" ND1 HIS B 166 " model vdw 2.239 3.120 nonbonded pdb=" O ASN A 773 " pdb=" OG SER A 777 " model vdw 2.246 3.040 ... (remaining 114437 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 'B' and (resid 42 through 160 or resid 162 through 192 or resid 204 throu \ gh 328 or resid 344 through 457)) selection = (chain 'C' and (resid 42 through 160 or resid 162 through 457)) } 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=0.31 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: 3.590 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.060 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.003 0.050 14197 Z= 0.234 Angle : 0.546 9.429 19429 Z= 0.359 Chirality : 0.040 0.219 2134 Planarity : 0.004 0.038 2362 Dihedral : 13.133 178.481 5302 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.35 % Allowed : 4.08 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1603 helix: 0.22 (0.20), residues: 671 sheet: -0.13 (0.33), residues: 245 loop : 0.27 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1124 TYR 0.010 0.001 TYR B 167 PHE 0.011 0.001 PHE A1158 TRP 0.009 0.001 TRP A 203 HIS 0.003 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.23 (14197) covalent geometry : angle 0.54599 / 0.36 (19429) hydrogen bonds : bond 0.22743 / 14.99 ( 652) hydrogen bonds : angle 7.93604 / 5.50 ( 1795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 291 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.6739 (m-30) cc_final: 0.6319 (m-30) REVERT: A 476 GLU cc_start: 0.6187 (mp0) cc_final: 0.5572 (tm-30) REVERT: A 508 GLN cc_start: 0.5482 (tp40) cc_final: 0.5129 (pp30) REVERT: A 562 ASP cc_start: 0.7833 (m-30) cc_final: 0.7626 (m-30) REVERT: A 836 THR cc_start: 0.6899 (m) cc_final: 0.6422 (p) REVERT: A 897 MET cc_start: 0.6416 (ttm) cc_final: 0.6062 (tmt) REVERT: A 1176 LYS cc_start: 0.7195 (mttp) cc_final: 0.6412 (tptt) REVERT: A 1199 TYR cc_start: 0.6428 (m-80) cc_final: 0.6014 (m-80) REVERT: B 399 LEU cc_start: 0.6497 (mt) cc_final: 0.5813 (mt) outliers start: 5 outliers final: 1 residues processed: 295 average time/residue: 0.5500 time to fit residues: 178.0689 Evaluate side-chains 181 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 ASN A 60 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS B 378 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.256999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.214038 restraints weight = 19621.469| |-----------------------------------------------------------------------------| r_work (start): 0.4693 rms_B_bonded: 2.19 r_work: 0.4498 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4554 r_free = 0.4554 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14197 Z= 0.160 Angle : 0.595 9.748 19429 Z= 0.315 Chirality : 0.043 0.217 2134 Planarity : 0.005 0.043 2362 Dihedral : 14.972 174.327 2168 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.52 % Allowed : 11.82 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1603 helix: 0.56 (0.19), residues: 706 sheet: -0.01 (0.34), residues: 227 loop : 0.24 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 830 TYR 0.018 0.002 TYR A 461 PHE 0.020 0.002 PHE C 180 TRP 0.033 0.001 TRP C 215 HIS 0.005 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (14197) covalent geometry : angle 0.59541 / 0.31 (19429) hydrogen bonds : bond 0.05615 / 3.60 ( 652) hydrogen bonds : angle 5.70649 / 3.95 ( 1795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7202 (mt) cc_final: 0.6992 (mm) REVERT: A 230 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.4887 (tt) REVERT: A 340 ASP cc_start: 0.6758 (m-30) cc_final: 0.6333 (m-30) REVERT: A 448 LEU cc_start: 0.8042 (mt) cc_final: 0.7800 (mt) REVERT: A 476 GLU cc_start: 0.6278 (mp0) cc_final: 0.5526 (tm-30) REVERT: A 508 GLN cc_start: 0.5396 (tp40) cc_final: 0.5098 (pp30) REVERT: A 562 ASP cc_start: 0.7836 (m-30) cc_final: 0.7620 (m-30) REVERT: A 768 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.4132 (ttt90) REVERT: A 897 MET cc_start: 0.6734 (ttm) cc_final: 0.5960 (tmt) REVERT: A 1094 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5507 (mmt) REVERT: A 1176 LYS cc_start: 0.7309 (mttp) cc_final: 0.6380 (tptt) outliers start: 50 outliers final: 13 residues processed: 230 average time/residue: 0.4004 time to fit residues: 103.4490 Evaluate side-chains 195 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 768 ARG Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 109 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 ASN A 60 GLN A 117 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN ** C 184 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 = 0.5050 r_free = 0.5050 target = 0.257795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.211409 restraints weight = 18443.032| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 2.61 r_work: 0.4477 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4533 r_free = 0.4533 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4533 r_free = 0.4533 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14197 Z= 0.169 Angle : 0.588 9.944 19429 Z= 0.306 Chirality : 0.043 0.227 2134 Planarity : 0.005 0.044 2362 Dihedral : 15.103 174.503 2168 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 13.30 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1603 helix: 0.63 (0.19), residues: 710 sheet: -0.23 (0.33), residues: 220 loop : 0.14 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 446 TYR 0.011 0.002 TYR A1125 PHE 0.012 0.002 PHE A 290 TRP 0.029 0.001 TRP C 215 HIS 0.006 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (14197) covalent geometry : angle 0.58767 / 0.31 (19429) hydrogen bonds : bond 0.04699 / 3.02 ( 652) hydrogen bonds : angle 5.35857 / 3.70 ( 1795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.4757 (tp) REVERT: A 340 ASP cc_start: 0.6807 (m-30) cc_final: 0.6344 (m-30) REVERT: A 425 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7051 (mmm160) REVERT: A 476 GLU cc_start: 0.6313 (mp0) cc_final: 0.5535 (tm-30) REVERT: A 508 GLN cc_start: 0.5376 (tp40) cc_final: 0.5069 (pp30) REVERT: A 562 ASP cc_start: 0.7777 (m-30) cc_final: 0.7557 (m-30) REVERT: A 751 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6949 (tppt) REVERT: A 897 MET cc_start: 0.6705 (ttm) cc_final: 0.5913 (tmt) REVERT: A 1094 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5534 (mmt) REVERT: A 1176 LYS cc_start: 0.7247 (mttp) cc_final: 0.6245 (tptt) REVERT: C 125 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7022 (mt-10) REVERT: C 176 ARG cc_start: 0.6903 (mtt180) cc_final: 0.5806 (mtp-110) REVERT: C 370 ARG cc_start: 0.7579 (mtt-85) cc_final: 0.7321 (mmt90) outliers start: 46 outliers final: 20 residues processed: 218 average time/residue: 0.4573 time to fit residues: 111.6196 Evaluate side-chains 195 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 60 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.257082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.214323 restraints weight = 25597.487| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 2.67 r_work: 0.4460 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4508 r_free = 0.4508 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4508 r_free = 0.4508 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14197 Z= 0.137 Angle : 0.555 9.517 19429 Z= 0.290 Chirality : 0.042 0.228 2134 Planarity : 0.004 0.045 2362 Dihedral : 15.141 174.560 2168 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.38 % Allowed : 14.50 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1603 helix: 0.83 (0.19), residues: 708 sheet: -0.23 (0.32), residues: 226 loop : 0.16 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 370 TYR 0.013 0.002 TYR A1125 PHE 0.027 0.002 PHE C 216 TRP 0.029 0.001 TRP A 468 HIS 0.009 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14197) covalent geometry : angle 0.55531 / 0.29 (19429) hydrogen bonds : bond 0.04167 / 2.66 ( 652) hydrogen bonds : angle 5.12555 / 3.53 ( 1795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.6891 (m-30) cc_final: 0.6432 (m-30) REVERT: A 425 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7031 (mmm160) REVERT: A 476 GLU cc_start: 0.6272 (mp0) cc_final: 0.5534 (tm-30) REVERT: A 508 GLN cc_start: 0.5372 (tp40) cc_final: 0.5050 (pp30) REVERT: A 562 ASP cc_start: 0.7823 (m-30) cc_final: 0.7610 (m-30) REVERT: A 897 MET cc_start: 0.6730 (ttm) cc_final: 0.5952 (tmt) REVERT: A 1035 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7343 (ppp) REVERT: A 1094 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5647 (mmt) REVERT: A 1176 LYS cc_start: 0.7282 (mttp) cc_final: 0.6300 (tmtt) REVERT: A 1204 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6552 (mp) REVERT: B 296 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.6351 (mt) REVERT: B 370 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5983 (mtp180) REVERT: C 125 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6994 (mt-10) outliers start: 48 outliers final: 20 residues processed: 208 average time/residue: 0.4836 time to fit residues: 112.5084 Evaluate side-chains 198 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 161 optimal weight: 0.0270 chunk 5 optimal weight: 7.9990 chunk 156 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.259466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.215698 restraints weight = 26284.053| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 2.73 r_work: 0.4472 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4519 r_free = 0.4519 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14197 Z= 0.162 Angle : 0.571 9.264 19429 Z= 0.296 Chirality : 0.042 0.229 2134 Planarity : 0.004 0.046 2362 Dihedral : 15.190 174.473 2166 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.73 % Allowed : 14.92 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1603 helix: 0.81 (0.20), residues: 707 sheet: -0.38 (0.32), residues: 224 loop : 0.04 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 370 TYR 0.013 0.002 TYR C 265 PHE 0.024 0.002 PHE C 216 TRP 0.030 0.001 TRP C 215 HIS 0.006 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14197) covalent geometry : angle 0.57103 / 0.30 (19429) hydrogen bonds : bond 0.04123 / 2.63 ( 652) hydrogen bonds : angle 5.06732 / 3.49 ( 1795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4975 (tt) REVERT: A 340 ASP cc_start: 0.6876 (m-30) cc_final: 0.6394 (m-30) REVERT: A 425 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6982 (mmm160) REVERT: A 476 GLU cc_start: 0.6246 (mp0) cc_final: 0.5503 (tm-30) REVERT: A 508 GLN cc_start: 0.5309 (tp40) cc_final: 0.4965 (pp30) REVERT: A 562 ASP cc_start: 0.7820 (m-30) cc_final: 0.7595 (m-30) REVERT: A 897 MET cc_start: 0.6708 (ttm) cc_final: 0.5909 (tmt) REVERT: A 1035 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7288 (ppp) REVERT: A 1094 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5532 (mmt) REVERT: A 1176 LYS cc_start: 0.7225 (mttp) cc_final: 0.6220 (tmtt) REVERT: A 1180 ASN cc_start: 0.7059 (OUTLIER) cc_final: 0.6854 (t0) REVERT: B 296 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6256 (mt) REVERT: B 310 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 370 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5937 (mtp180) REVERT: B 399 LEU cc_start: 0.6255 (mt) cc_final: 0.5826 (mt) REVERT: C 125 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6879 (mt-10) REVERT: C 176 ARG cc_start: 0.6859 (mtt180) cc_final: 0.5739 (mtp-110) outliers start: 53 outliers final: 22 residues processed: 206 average time/residue: 0.5041 time to fit residues: 115.6458 Evaluate side-chains 190 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain A residue 1180 ASN Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 0.4980 chunk 64 optimal weight: 0.0170 chunk 138 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.263639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.220371 restraints weight = 29741.928| |-----------------------------------------------------------------------------| r_work (start): 0.4764 rms_B_bonded: 3.48 r_work: 0.4493 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4535 r_free = 0.4535 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4535 r_free = 0.4535 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14197 Z= 0.123 Angle : 0.550 9.969 19429 Z= 0.284 Chirality : 0.042 0.229 2134 Planarity : 0.004 0.047 2362 Dihedral : 15.179 174.768 2166 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.39 % Allowed : 16.75 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1603 helix: 0.94 (0.20), residues: 710 sheet: -0.29 (0.32), residues: 222 loop : 0.08 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 370 TYR 0.021 0.001 TYR A1125 PHE 0.023 0.001 PHE C 216 TRP 0.034 0.001 TRP C 215 HIS 0.005 0.001 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (14197) covalent geometry : angle 0.54997 / 0.28 (19429) hydrogen bonds : bond 0.03837 / 2.44 ( 652) hydrogen bonds : angle 4.94053 / 3.41 ( 1795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5056 (tt) REVERT: A 340 ASP cc_start: 0.6838 (m-30) cc_final: 0.6370 (m-30) REVERT: A 476 GLU cc_start: 0.6143 (mp0) cc_final: 0.5384 (tm-30) REVERT: A 508 GLN cc_start: 0.5315 (tp40) cc_final: 0.5027 (pp30) REVERT: A 562 ASP cc_start: 0.7777 (m-30) cc_final: 0.7556 (m-30) REVERT: A 897 MET cc_start: 0.6632 (ttm) cc_final: 0.5850 (tmt) REVERT: A 1035 MET cc_start: 0.7740 (ppp) cc_final: 0.7344 (ppp) REVERT: A 1094 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5626 (mmt) REVERT: A 1176 LYS cc_start: 0.7269 (mttp) cc_final: 0.6261 (tmtt) REVERT: B 296 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.6192 (mt) REVERT: B 310 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8154 (mt) REVERT: B 370 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5849 (mtp180) REVERT: B 399 LEU cc_start: 0.6296 (mt) cc_final: 0.5900 (mt) REVERT: C 125 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6905 (mt-10) REVERT: C 176 ARG cc_start: 0.6832 (mtt180) cc_final: 0.5758 (mtp-110) outliers start: 34 outliers final: 18 residues processed: 193 average time/residue: 0.4243 time to fit residues: 92.4789 Evaluate side-chains 185 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.258818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.214195 restraints weight = 24123.619| |-----------------------------------------------------------------------------| r_work (start): 0.4700 rms_B_bonded: 2.60 r_work: 0.4473 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4529 r_free = 0.4529 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4529 r_free = 0.4529 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14197 Z= 0.201 Angle : 0.622 7.686 19429 Z= 0.320 Chirality : 0.044 0.227 2134 Planarity : 0.005 0.057 2362 Dihedral : 15.275 174.240 2166 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.89 % Allowed : 16.40 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1603 helix: 0.67 (0.19), residues: 708 sheet: -0.49 (0.32), residues: 225 loop : -0.10 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 430 TYR 0.018 0.002 TYR A1125 PHE 0.024 0.002 PHE C 216 TRP 0.039 0.002 TRP A 468 HIS 0.007 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (14197) covalent geometry : angle 0.62214 / 0.32 (19429) hydrogen bonds : bond 0.04219 / 2.72 ( 652) hydrogen bonds : angle 5.10423 / 3.52 ( 1795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4889 (tt) REVERT: A 340 ASP cc_start: 0.6868 (m-30) cc_final: 0.6398 (m-30) REVERT: A 425 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7047 (mmm160) REVERT: A 476 GLU cc_start: 0.6207 (mp0) cc_final: 0.5439 (tm-30) REVERT: A 508 GLN cc_start: 0.5310 (tp40) cc_final: 0.5051 (pp30) REVERT: A 562 ASP cc_start: 0.7859 (m-30) cc_final: 0.7614 (m-30) REVERT: A 801 ARG cc_start: 0.6298 (mmt180) cc_final: 0.6029 (mmm160) REVERT: A 897 MET cc_start: 0.6656 (ttm) cc_final: 0.5872 (tmt) REVERT: A 1035 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7287 (ppp) REVERT: A 1094 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5585 (mmt) REVERT: B 296 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6252 (mt) REVERT: B 310 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8191 (mt) REVERT: B 370 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5929 (mtp180) REVERT: B 399 LEU cc_start: 0.6213 (mt) cc_final: 0.5800 (mt) REVERT: C 125 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6883 (mt-10) REVERT: C 176 ARG cc_start: 0.6857 (mtt180) cc_final: 0.5776 (mtp-110) outliers start: 41 outliers final: 21 residues processed: 192 average time/residue: 0.4352 time to fit residues: 93.6993 Evaluate side-chains 183 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A1135 ASN ** C 184 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 = 0.5068 r_free = 0.5068 target = 0.259499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.216515 restraints weight = 28265.949| |-----------------------------------------------------------------------------| r_work (start): 0.4734 rms_B_bonded: 2.88 r_work: 0.4480 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4527 r_free = 0.4527 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4527 r_free = 0.4527 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14197 Z= 0.130 Angle : 0.567 10.034 19429 Z= 0.292 Chirality : 0.042 0.229 2134 Planarity : 0.004 0.046 2362 Dihedral : 15.245 174.969 2166 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.25 % Allowed : 18.16 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1603 helix: 0.81 (0.20), residues: 708 sheet: -0.52 (0.32), residues: 221 loop : 0.01 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 638 TYR 0.016 0.002 TYR A1125 PHE 0.024 0.002 PHE C 216 TRP 0.048 0.001 TRP A 468 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (14197) covalent geometry : angle 0.56688 / 0.29 (19429) hydrogen bonds : bond 0.03790 / 2.41 ( 652) hydrogen bonds : angle 4.93478 / 3.42 ( 1795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.7333 (Cg_exo) REVERT: A 230 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.4893 (tt) REVERT: A 340 ASP cc_start: 0.6854 (m-30) cc_final: 0.6361 (m-30) REVERT: A 476 GLU cc_start: 0.6127 (mp0) cc_final: 0.5308 (tm-30) REVERT: A 508 GLN cc_start: 0.5261 (tp40) cc_final: 0.4956 (pp30) REVERT: A 562 ASP cc_start: 0.7821 (m-30) cc_final: 0.7585 (m-30) REVERT: A 897 MET cc_start: 0.6658 (ttm) cc_final: 0.5875 (tmt) REVERT: A 1035 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7301 (ppp) REVERT: A 1094 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5627 (mmt) REVERT: B 296 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.6204 (mt) REVERT: B 310 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 399 LEU cc_start: 0.6162 (mt) cc_final: 0.5778 (mt) REVERT: C 125 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6854 (mt-10) REVERT: C 176 ARG cc_start: 0.6853 (mtt180) cc_final: 0.5765 (mtp-110) outliers start: 32 outliers final: 19 residues processed: 186 average time/residue: 0.3857 time to fit residues: 81.0026 Evaluate side-chains 183 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.256321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.211450 restraints weight = 22525.242| |-----------------------------------------------------------------------------| r_work (start): 0.4690 rms_B_bonded: 2.38 r_work: 0.4478 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4529 r_free = 0.4529 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4529 r_free = 0.4529 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14197 Z= 0.197 Angle : 0.627 10.249 19429 Z= 0.321 Chirality : 0.044 0.228 2134 Planarity : 0.005 0.053 2362 Dihedral : 15.301 174.596 2166 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.46 % Allowed : 18.51 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1603 helix: 0.62 (0.20), residues: 709 sheet: -0.65 (0.32), residues: 224 loop : -0.11 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 430 TYR 0.015 0.002 TYR A1125 PHE 0.025 0.002 PHE A1158 TRP 0.054 0.002 TRP A 468 HIS 0.007 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (14197) covalent geometry : angle 0.62657 / 0.32 (19429) hydrogen bonds : bond 0.04086 / 2.63 ( 652) hydrogen bonds : angle 5.05767 / 3.51 ( 1795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.6452 (OUTLIER) cc_final: 0.6251 (pp) REVERT: A 340 ASP cc_start: 0.6882 (m-30) cc_final: 0.6407 (m-30) REVERT: A 425 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7021 (mmm160) REVERT: A 476 GLU cc_start: 0.6142 (mp0) cc_final: 0.5375 (tm-30) REVERT: A 508 GLN cc_start: 0.5162 (tp40) cc_final: 0.4942 (pp30) REVERT: A 562 ASP cc_start: 0.7868 (m-30) cc_final: 0.7620 (m-30) REVERT: A 897 MET cc_start: 0.6639 (ttm) cc_final: 0.5868 (tmt) REVERT: A 1035 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7304 (ppp) REVERT: A 1094 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5627 (mmt) REVERT: B 296 ILE cc_start: 0.6437 (OUTLIER) cc_final: 0.6176 (mt) REVERT: B 310 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8212 (mt) REVERT: B 399 LEU cc_start: 0.6132 (mt) cc_final: 0.5752 (mt) REVERT: C 125 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6901 (mt-10) REVERT: C 176 ARG cc_start: 0.6869 (mtt180) cc_final: 0.5799 (mtp-110) outliers start: 35 outliers final: 19 residues processed: 183 average time/residue: 0.4066 time to fit residues: 83.1419 Evaluate side-chains 180 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 69 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 0.4980 chunk 141 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.263096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.219289 restraints weight = 24052.998| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 2.57 r_work: 0.4526 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4567 r_free = 0.4567 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4567 r_free = 0.4567 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14197 Z= 0.122 Angle : 0.579 10.874 19429 Z= 0.296 Chirality : 0.042 0.229 2134 Planarity : 0.004 0.048 2362 Dihedral : 15.249 175.385 2166 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.62 % Allowed : 19.28 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1603 helix: 0.85 (0.20), residues: 708 sheet: -0.51 (0.33), residues: 221 loop : 0.02 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 370 TYR 0.013 0.001 TYR A 461 PHE 0.027 0.002 PHE A1158 TRP 0.063 0.002 TRP A 468 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14197) covalent geometry : angle 0.57918 / 0.30 (19429) hydrogen bonds : bond 0.03704 / 2.34 ( 652) hydrogen bonds : angle 4.86867 / 3.38 ( 1795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5113 (tt) REVERT: A 340 ASP cc_start: 0.6806 (m-30) cc_final: 0.6302 (m-30) REVERT: A 508 GLN cc_start: 0.5241 (tp40) cc_final: 0.5010 (pp30) REVERT: A 897 MET cc_start: 0.6568 (ttm) cc_final: 0.5831 (tmt) REVERT: A 1035 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7399 (ppp) REVERT: A 1094 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5613 (mmt) REVERT: B 296 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.6135 (mt) REVERT: B 310 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 399 LEU cc_start: 0.6019 (mt) cc_final: 0.5686 (mt) REVERT: C 125 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6886 (mt-10) outliers start: 23 outliers final: 16 residues processed: 177 average time/residue: 0.3730 time to fit residues: 74.2746 Evaluate side-chains 176 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1035 MET Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 40.0000 chunk 97 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS C 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.257961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.214430 restraints weight = 29685.600| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 3.67 r_work: 0.4421 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4464 r_free = 0.4464 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14197 Z= 0.228 Angle : 0.658 12.212 19429 Z= 0.337 Chirality : 0.045 0.228 2134 Planarity : 0.005 0.056 2362 Dihedral : 15.340 174.709 2166 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.97 % Allowed : 19.63 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1603 helix: 0.59 (0.20), residues: 705 sheet: -0.59 (0.33), residues: 223 loop : -0.18 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 430 TYR 0.017 0.002 TYR C 265 PHE 0.031 0.002 PHE A1158 TRP 0.057 0.002 TRP A 468 HIS 0.008 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (14197) covalent geometry : angle 0.65838 / 0.34 (19429) hydrogen bonds : bond 0.04166 / 2.69 ( 652) hydrogen bonds : angle 5.11032 / 3.55 ( 1795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.50 seconds wall clock time: 70 minutes 39.17 seconds (4239.17 seconds total)