Starting phenix.real_space_refine on Thu Jul 31 18:35:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g75_51110/07_2025/9g75_51110.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g75_51110/07_2025/9g75_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_51110/07_2025/9g75_51110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g75_51110/07_2025/9g75_51110.map" model { file = "/net/cci-nas-00/data/ceres_data/9g75_51110/07_2025/9g75_51110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g75_51110/07_2025/9g75_51110.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.972 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'TYR:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG: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: 10.24, per 1000 atoms: 0.74 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: 3.64 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 5.18 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: 5.38 Time building geometry restraints manager: 4.28 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=" CA SER B 54 " pdb=" C SER B 54 " ideal model delta sigma weight residual 1.520 1.490 0.031 1.22e-02 6.72e+03 6.44e+00 bond pdb=" CA ASN A 253 " pdb=" C ASN A 253 " ideal model delta sigma weight residual 1.531 1.498 0.033 1.46e-02 4.69e+03 5.13e+00 bond pdb=" CA VAL B 312 " pdb=" C VAL B 312 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.28e-02 6.10e+03 4.97e+00 bond pdb=" CA SER C 431 " pdb=" C SER C 431 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.24e-02 6.50e+03 4.58e+00 bond pdb=" CA GLY B 314 " pdb=" C GLY B 314 " ideal model delta sigma weight residual 1.516 1.494 0.022 1.07e-02 8.73e+03 4.42e+00 ... (remaining 14192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 19143 1.89 - 3.77: 264 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=" N VAL C 345 " pdb=" CA VAL C 345 " pdb=" C VAL C 345 " ideal model delta sigma weight residual 107.77 113.77 -6.00 1.48e+00 4.57e-01 1.65e+01 angle pdb=" N VAL B 312 " pdb=" CA VAL B 312 " pdb=" C VAL B 312 " ideal model delta sigma weight residual 107.80 102.31 5.49 1.45e+00 4.76e-01 1.44e+01 angle pdb=" C SER B 313 " pdb=" CA SER B 313 " pdb=" CB SER B 313 " ideal model delta sigma weight residual 112.09 107.30 4.79 1.43e+00 4.89e-01 1.12e+01 angle pdb=" N ILE C 296 " pdb=" CA ILE C 296 " pdb=" C ILE C 296 " ideal model delta sigma weight residual 112.96 109.75 3.21 1.00e+00 1.00e+00 1.03e+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: 1709 0.044 - 0.088: 310 0.088 - 0.132: 113 0.132 - 0.176: 1 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=" CA ILE A 722 " pdb=" N ILE A 722 " pdb=" C ILE A 722 " pdb=" CB ILE A 722 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-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: 2.840 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.670 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 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 0.037 14197 Z= 0.158 Angle : 0.521 9.429 19429 Z= 0.305 Chirality : 0.038 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (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 TRP 0.009 0.001 TRP A 203 HIS 0.003 0.001 HIS A 783 PHE 0.011 0.001 PHE A1158 TYR 0.010 0.001 TYR B 167 ARG 0.003 0.000 ARG A1124 Details of bonding type rmsd hydrogen bonds : bond 0.22743 ( 652) hydrogen bonds : angle 7.93604 ( 1795) covalent geometry : bond 0.00283 (14197) covalent geometry : angle 0.52075 (19429) *********************** 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 : 1.520 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: 1.2333 time to fit residues: 399.0504 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 : 1.389 ------------------------------------------------------------------------------- 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 139 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 60 GLN 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 = 0.5045 r_free = 0.5045 target = 0.256871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.212086 restraints weight = 20092.450| |-----------------------------------------------------------------------------| r_work (start): 0.4669 rms_B_bonded: 2.29 r_work: 0.4466 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1879 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= 0.186 Angle : 0.606 8.728 19429 Z= 0.314 Chirality : 0.043 0.163 2134 Planarity : 0.005 0.048 2362 Dihedral : 14.904 177.033 2168 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.15 % Allowed : 11.75 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1603 helix: 0.47 (0.19), residues: 707 sheet: 0.04 (0.34), residues: 218 loop : 0.03 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 215 HIS 0.007 0.001 HIS A 783 PHE 0.019 0.002 PHE A 290 TYR 0.017 0.002 TYR A 461 ARG 0.006 0.001 ARG A 830 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 652) hydrogen bonds : angle 5.48643 ( 1795) covalent geometry : bond 0.00429 (14197) covalent geometry : angle 0.60626 (19429) *********************** 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 257 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.4982 (tt) REVERT: A 340 ASP cc_start: 0.6829 (m-30) cc_final: 0.6391 (m-30) REVERT: A 425 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7063 (mmm160) REVERT: A 476 GLU cc_start: 0.6337 (mp0) cc_final: 0.5583 (tm-30) REVERT: A 508 GLN cc_start: 0.5373 (tp40) cc_final: 0.5051 (pp30) REVERT: A 562 ASP cc_start: 0.7840 (m-30) cc_final: 0.7595 (m-30) REVERT: A 768 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.4214 (ttt90) REVERT: A 801 ARG cc_start: 0.6395 (mmt180) cc_final: 0.6077 (mmm160) REVERT: A 834 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6928 (tp30) REVERT: A 897 MET cc_start: 0.6707 (ttm) cc_final: 0.5925 (tmt) REVERT: A 1176 LYS cc_start: 0.7203 (mttp) cc_final: 0.6207 (tptt) REVERT: B 177 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7626 (mtpp) REVERT: C 125 GLU cc_start: 0.7223 (mm-30) cc_final: 0.7000 (mt-10) REVERT: C 154 LYS cc_start: 0.7982 (pttp) cc_final: 0.7770 (ptpt) REVERT: C 176 ARG cc_start: 0.6897 (mtt180) cc_final: 0.5813 (mtp-110) outliers start: 59 outliers final: 18 residues processed: 236 average time/residue: 1.0609 time to fit residues: 279.0162 Evaluate side-chains 192 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 768 ARG Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1040 GLU 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 209 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 113 optimal weight: 0.0980 chunk 67 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 60 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5113 r_free = 0.5113 target = 0.264900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.221628 restraints weight = 20138.910| |-----------------------------------------------------------------------------| r_work (start): 0.4754 rms_B_bonded: 2.26 r_work: 0.4554 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4604 r_free = 0.4604 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4604 r_free = 0.4604 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14197 Z= 0.126 Angle : 0.536 8.417 19429 Z= 0.276 Chirality : 0.040 0.151 2134 Planarity : 0.004 0.044 2362 Dihedral : 14.789 178.004 2166 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.96 % Allowed : 13.93 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1603 helix: 0.85 (0.20), residues: 713 sheet: -0.09 (0.33), residues: 224 loop : 0.17 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 215 HIS 0.004 0.001 HIS A 402 PHE 0.031 0.002 PHE C 216 TYR 0.014 0.001 TYR A 133 ARG 0.005 0.000 ARG A 830 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 652) hydrogen bonds : angle 4.96817 ( 1795) covalent geometry : bond 0.00280 (14197) covalent geometry : angle 0.53603 (19429) *********************** 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: 42 poor density : 195 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 340 ASP cc_start: 0.6775 (m-30) cc_final: 0.6305 (m-30) REVERT: A 476 GLU cc_start: 0.6192 (mp0) cc_final: 0.5445 (tm-30) REVERT: A 508 GLN cc_start: 0.5426 (tp40) cc_final: 0.5099 (pp30) REVERT: A 562 ASP cc_start: 0.7826 (m-30) cc_final: 0.7613 (m-30) REVERT: A 768 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.4138 (ttt90) REVERT: A 801 ARG cc_start: 0.6291 (mmt180) cc_final: 0.5979 (mmm160) REVERT: A 897 MET cc_start: 0.6562 (ttm) cc_final: 0.5802 (tmt) REVERT: A 1094 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5567 (mmt) REVERT: A 1125 TYR cc_start: 0.7783 (m-80) cc_final: 0.7572 (m-80) REVERT: A 1176 LYS cc_start: 0.7185 (mttp) cc_final: 0.6145 (tmtt) REVERT: B 370 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.5873 (mtp180) REVERT: B 399 LEU cc_start: 0.6207 (mt) cc_final: 0.5789 (mt) REVERT: C 125 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6906 (mt-10) REVERT: C 176 ARG cc_start: 0.6855 (mtt180) cc_final: 0.5781 (mtp-110) outliers start: 42 outliers final: 15 residues processed: 219 average time/residue: 1.0204 time to fit residues: 249.4806 Evaluate side-chains 188 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR 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 768 ARG 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 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain B residue 205 VAL 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 152 SER Chi-restraints excluded: chain C residue 345 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 54 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 97 optimal weight: 0.0000 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.264620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.219359 restraints weight = 22833.130| |-----------------------------------------------------------------------------| r_work (start): 0.4743 rms_B_bonded: 2.47 r_work: 0.4545 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4587 r_free = 0.4587 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4587 r_free = 0.4587 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14197 Z= 0.125 Angle : 0.537 8.214 19429 Z= 0.276 Chirality : 0.040 0.156 2134 Planarity : 0.004 0.045 2362 Dihedral : 14.766 177.945 2166 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.81 % Allowed : 15.90 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1603 helix: 0.97 (0.20), residues: 711 sheet: -0.19 (0.33), residues: 227 loop : 0.20 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 215 HIS 0.007 0.001 HIS B 287 PHE 0.023 0.001 PHE C 216 TYR 0.013 0.001 TYR A1125 ARG 0.003 0.000 ARG A 830 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 652) hydrogen bonds : angle 4.85023 ( 1795) covalent geometry : bond 0.00285 (14197) covalent geometry : angle 0.53700 (19429) *********************** 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 213 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.4998 (tt) REVERT: A 340 ASP cc_start: 0.6812 (m-30) cc_final: 0.6314 (m-30) REVERT: A 412 MET cc_start: 0.6195 (mtp) cc_final: 0.5828 (mtt) REVERT: A 476 GLU cc_start: 0.6181 (mp0) cc_final: 0.5425 (tm-30) REVERT: A 508 GLN cc_start: 0.5337 (tp40) cc_final: 0.5070 (pp30) REVERT: A 562 ASP cc_start: 0.7813 (m-30) cc_final: 0.7609 (m-30) REVERT: A 801 ARG cc_start: 0.6303 (mmt180) cc_final: 0.6003 (mmm160) REVERT: A 897 MET cc_start: 0.6529 (ttm) cc_final: 0.5787 (tmt) REVERT: A 1035 MET cc_start: 0.7735 (ppp) cc_final: 0.7345 (ppp) REVERT: A 1094 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5468 (mmt) REVERT: A 1176 LYS cc_start: 0.7206 (mttp) cc_final: 0.6215 (tmtt) REVERT: B 296 ILE cc_start: 0.6344 (OUTLIER) cc_final: 0.6122 (mt) REVERT: B 310 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 370 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5816 (mtp180) REVERT: B 399 LEU cc_start: 0.6240 (mt) cc_final: 0.5850 (mt) REVERT: C 125 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6915 (mt-10) REVERT: C 176 ARG cc_start: 0.6782 (mtt180) cc_final: 0.5749 (mtp-110) outliers start: 40 outliers final: 14 residues processed: 195 average time/residue: 1.0762 time to fit residues: 235.4924 Evaluate side-chains 181 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 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 1094 MET 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 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 164 optimal weight: 4.9990 chunk 117 optimal weight: 0.0030 chunk 151 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 370 ASN ** 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 = 0.5097 r_free = 0.5097 target = 0.263046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.219050 restraints weight = 24922.871| |-----------------------------------------------------------------------------| r_work (start): 0.4733 rms_B_bonded: 2.56 r_work: 0.4502 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4553 r_free = 0.4553 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4553 r_free = 0.4553 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14197 Z= 0.140 Angle : 0.539 8.008 19429 Z= 0.278 Chirality : 0.041 0.147 2134 Planarity : 0.004 0.044 2362 Dihedral : 14.780 178.063 2166 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.67 % Allowed : 16.54 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1603 helix: 1.05 (0.20), residues: 705 sheet: -0.26 (0.32), residues: 226 loop : 0.17 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 468 HIS 0.009 0.001 HIS B 287 PHE 0.022 0.002 PHE C 216 TYR 0.015 0.002 TYR A1125 ARG 0.005 0.000 ARG A 368 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 652) hydrogen bonds : angle 4.81720 ( 1795) covalent geometry : bond 0.00325 (14197) covalent geometry : angle 0.53883 (19429) *********************** 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 206 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.5037 (tt) REVERT: A 340 ASP cc_start: 0.6779 (m-30) cc_final: 0.6296 (m-30) REVERT: A 412 MET cc_start: 0.6149 (mtp) cc_final: 0.5809 (mtt) REVERT: A 476 GLU cc_start: 0.6163 (mp0) cc_final: 0.5372 (tm-30) REVERT: A 508 GLN cc_start: 0.5308 (tp40) cc_final: 0.5048 (pp30) REVERT: A 562 ASP cc_start: 0.7848 (m-30) cc_final: 0.7620 (m-30) REVERT: A 801 ARG cc_start: 0.6353 (mmt180) cc_final: 0.6027 (mmm160) REVERT: A 897 MET cc_start: 0.6564 (ttm) cc_final: 0.5827 (tmt) REVERT: A 1035 MET cc_start: 0.7758 (ppp) cc_final: 0.7372 (ppp) REVERT: A 1094 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5534 (mmt) REVERT: B 310 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8167 (mt) REVERT: B 370 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5842 (mtp180) REVERT: B 399 LEU cc_start: 0.6131 (mt) cc_final: 0.5755 (mt) REVERT: C 125 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6946 (mt-10) REVERT: C 176 ARG cc_start: 0.6814 (mtt180) cc_final: 0.5738 (mtp-110) outliers start: 38 outliers final: 19 residues processed: 191 average time/residue: 0.9762 time to fit residues: 210.3953 Evaluate side-chains 176 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL 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 251 ASP 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 158 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 119 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A1088 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.262778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.218150 restraints weight = 23900.954| |-----------------------------------------------------------------------------| r_work (start): 0.4722 rms_B_bonded: 2.57 r_work: 0.4503 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4557 r_free = 0.4557 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4557 r_free = 0.4557 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14197 Z= 0.138 Angle : 0.542 8.369 19429 Z= 0.279 Chirality : 0.041 0.194 2134 Planarity : 0.004 0.044 2362 Dihedral : 14.777 178.239 2166 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.39 % Allowed : 17.10 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1603 helix: 1.03 (0.20), residues: 704 sheet: -0.30 (0.32), residues: 237 loop : 0.23 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 468 HIS 0.010 0.001 HIS B 287 PHE 0.023 0.002 PHE C 216 TYR 0.012 0.002 TYR A1125 ARG 0.006 0.000 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 652) hydrogen bonds : angle 4.80894 ( 1795) covalent geometry : bond 0.00320 (14197) covalent geometry : angle 0.54235 (19429) *********************** 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 : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4961 (tt) REVERT: A 340 ASP cc_start: 0.6771 (m-30) cc_final: 0.6279 (m-30) REVERT: A 412 MET cc_start: 0.6120 (mtp) cc_final: 0.5780 (mtt) REVERT: A 476 GLU cc_start: 0.6116 (mp0) cc_final: 0.5338 (tm-30) REVERT: A 508 GLN cc_start: 0.5262 (tp40) cc_final: 0.5029 (pp30) REVERT: A 754 ASP cc_start: 0.7577 (m-30) cc_final: 0.7255 (m-30) REVERT: A 801 ARG cc_start: 0.6359 (mmt180) cc_final: 0.6045 (mmm160) REVERT: A 897 MET cc_start: 0.6531 (ttm) cc_final: 0.5814 (tmt) REVERT: A 1035 MET cc_start: 0.7766 (ppp) cc_final: 0.7337 (ppp) REVERT: B 204 ARG cc_start: 0.7317 (mtm180) cc_final: 0.7000 (mtm180) REVERT: B 296 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6126 (mt) REVERT: B 310 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8143 (mt) REVERT: B 370 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.5814 (mtp180) REVERT: B 399 LEU cc_start: 0.6087 (mt) cc_final: 0.5727 (mt) REVERT: C 125 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6983 (mt-10) REVERT: C 176 ARG cc_start: 0.6796 (mtt180) cc_final: 0.5693 (mtp-110) outliers start: 34 outliers final: 19 residues processed: 191 average time/residue: 1.0322 time to fit residues: 222.0053 Evaluate side-chains 182 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 863 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 899 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 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 251 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 0.5980 chunk 64 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.0470 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 370 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** B 383 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.264346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.220533 restraints weight = 19939.977| |-----------------------------------------------------------------------------| r_work (start): 0.4766 rms_B_bonded: 2.36 r_work: 0.4585 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4622 r_free = 0.4622 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4622 r_free = 0.4622 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14197 Z= 0.105 Angle : 0.512 9.121 19429 Z= 0.264 Chirality : 0.039 0.154 2134 Planarity : 0.004 0.045 2362 Dihedral : 14.673 178.604 2166 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.25 % Allowed : 17.73 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1603 helix: 1.29 (0.20), residues: 705 sheet: -0.30 (0.32), residues: 233 loop : 0.34 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 468 HIS 0.011 0.001 HIS B 287 PHE 0.023 0.001 PHE C 216 TYR 0.011 0.001 TYR A1125 ARG 0.003 0.000 ARG A 830 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 652) hydrogen bonds : angle 4.59272 ( 1795) covalent geometry : bond 0.00232 (14197) covalent geometry : angle 0.51246 (19429) *********************** 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 205 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5230 (OUTLIER) cc_final: 0.4819 (tt) REVERT: A 340 ASP cc_start: 0.6726 (m-30) cc_final: 0.6237 (m-30) REVERT: A 412 MET cc_start: 0.6023 (mtp) cc_final: 0.5651 (mtt) REVERT: A 508 GLN cc_start: 0.5327 (tp40) cc_final: 0.5113 (pp30) REVERT: A 754 ASP cc_start: 0.7543 (m-30) cc_final: 0.7186 (m-30) REVERT: A 801 ARG cc_start: 0.6313 (mmt180) cc_final: 0.5995 (mmm160) REVERT: A 897 MET cc_start: 0.6501 (ttm) cc_final: 0.5804 (tmt) REVERT: A 1035 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7474 (ppp) REVERT: A 1117 TYR cc_start: 0.7465 (m-80) cc_final: 0.7160 (m-80) REVERT: B 310 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 370 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5596 (mtp180) REVERT: B 399 LEU cc_start: 0.6074 (mt) cc_final: 0.5761 (mt) REVERT: C 125 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6935 (mt-10) REVERT: C 176 ARG cc_start: 0.6714 (mtt180) cc_final: 0.5662 (mtp-110) outliers start: 32 outliers final: 14 residues processed: 193 average time/residue: 0.9469 time to fit residues: 207.0170 Evaluate side-chains 173 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 414 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 827 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 B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL 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 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 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 83 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS B 383 ASN ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.265314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.220457 restraints weight = 21459.130| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 2.34 r_work: 0.4569 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4625 r_free = 0.4625 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4625 r_free = 0.4625 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14197 Z= 0.120 Angle : 0.544 11.885 19429 Z= 0.277 Chirality : 0.041 0.374 2134 Planarity : 0.004 0.044 2362 Dihedral : 14.700 178.506 2166 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.39 % Allowed : 18.86 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1603 helix: 1.25 (0.20), residues: 704 sheet: -0.25 (0.32), residues: 242 loop : 0.34 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 468 HIS 0.013 0.001 HIS B 287 PHE 0.023 0.001 PHE C 216 TYR 0.015 0.001 TYR A1125 ARG 0.008 0.000 ARG A 638 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 652) hydrogen bonds : angle 4.61756 ( 1795) covalent geometry : bond 0.00275 (14197) covalent geometry : angle 0.54365 (19429) *********************** 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 205 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.4922 (tt) REVERT: A 340 ASP cc_start: 0.6720 (m-30) cc_final: 0.6232 (m-30) REVERT: A 377 TYR cc_start: 0.6867 (m-10) cc_final: 0.6551 (m-10) REVERT: A 412 MET cc_start: 0.6170 (mtp) cc_final: 0.5831 (mtt) REVERT: A 754 ASP cc_start: 0.7550 (m-30) cc_final: 0.7195 (m-30) REVERT: A 801 ARG cc_start: 0.6319 (mmt180) cc_final: 0.6060 (mmm160) REVERT: A 897 MET cc_start: 0.6479 (ttm) cc_final: 0.5792 (tmt) REVERT: A 1035 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7478 (ppp) REVERT: A 1094 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5397 (mmt) REVERT: A 1117 TYR cc_start: 0.7524 (m-80) cc_final: 0.7215 (m-80) REVERT: A 1121 GLU cc_start: 0.5715 (pm20) cc_final: 0.5321 (pm20) REVERT: B 255 GLU cc_start: 0.7043 (pm20) cc_final: 0.6807 (mm-30) REVERT: B 310 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8053 (mt) REVERT: B 370 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.5537 (mtp180) REVERT: B 399 LEU cc_start: 0.6041 (mt) cc_final: 0.5724 (mt) REVERT: C 176 ARG cc_start: 0.6686 (mtt180) cc_final: 0.5642 (mtp-110) outliers start: 34 outliers final: 17 residues processed: 189 average time/residue: 0.9096 time to fit residues: 194.9834 Evaluate side-chains 183 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 827 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 B residue 56 THR Chi-restraints excluded: chain B residue 205 VAL 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 251 ASP Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.257772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.214555 restraints weight = 25120.041| |-----------------------------------------------------------------------------| r_work (start): 0.4713 rms_B_bonded: 2.64 r_work: 0.4472 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4511 r_free = 0.4511 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4511 r_free = 0.4511 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14197 Z= 0.194 Angle : 0.636 11.984 19429 Z= 0.320 Chirality : 0.044 0.461 2134 Planarity : 0.005 0.053 2362 Dihedral : 14.868 178.190 2166 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.39 % Allowed : 19.07 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1603 helix: 0.94 (0.20), residues: 705 sheet: -0.39 (0.33), residues: 235 loop : 0.06 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 468 HIS 0.007 0.001 HIS A 783 PHE 0.026 0.002 PHE A1158 TYR 0.020 0.002 TYR A 461 ARG 0.010 0.001 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 652) hydrogen bonds : angle 4.95069 ( 1795) covalent geometry : bond 0.00457 (14197) covalent geometry : angle 0.63581 (19429) *********************** 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 185 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.6869 (m-30) cc_final: 0.6351 (m-30) REVERT: A 412 MET cc_start: 0.6295 (mtp) cc_final: 0.5939 (mtt) REVERT: A 425 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6953 (mmm160) REVERT: A 577 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: A 754 ASP cc_start: 0.7632 (m-30) cc_final: 0.7306 (m-30) REVERT: A 897 MET cc_start: 0.6543 (ttm) cc_final: 0.5808 (tmt) REVERT: A 1035 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7459 (ppp) REVERT: A 1094 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.5588 (mmt) REVERT: A 1121 GLU cc_start: 0.5905 (pm20) cc_final: 0.5491 (pm20) REVERT: B 255 GLU cc_start: 0.7180 (pm20) cc_final: 0.6816 (mm-30) REVERT: B 310 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8170 (mt) REVERT: B 370 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5836 (mtp180) REVERT: B 399 LEU cc_start: 0.6180 (mt) cc_final: 0.5837 (mt) REVERT: C 176 ARG cc_start: 0.6808 (mtt180) cc_final: 0.5703 (mtp-110) outliers start: 34 outliers final: 16 residues processed: 173 average time/residue: 1.0002 time to fit residues: 194.1348 Evaluate side-chains 171 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 827 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 B residue 104 SER Chi-restraints excluded: chain B residue 205 VAL 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 251 ASP 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 1 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 370 ASN A 872 GLN A 884 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** 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 = 0.5033 r_free = 0.5033 target = 0.254351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.211391 restraints weight = 26186.110| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 2.70 r_work: 0.4441 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14197 Z= 0.250 Angle : 0.704 13.100 19429 Z= 0.357 Chirality : 0.047 0.464 2134 Planarity : 0.005 0.059 2362 Dihedral : 15.075 178.191 2166 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.60 % Allowed : 19.14 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1603 helix: 0.44 (0.19), residues: 710 sheet: -0.82 (0.32), residues: 234 loop : -0.30 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 468 HIS 0.011 0.002 HIS B 287 PHE 0.032 0.002 PHE A1158 TYR 0.023 0.003 TYR A1117 ARG 0.007 0.001 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 652) hydrogen bonds : angle 5.27704 ( 1795) covalent geometry : bond 0.00599 (14197) covalent geometry : angle 0.70376 (19429) ********************** 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 198 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.6938 (m-30) cc_final: 0.6435 (m-30) REVERT: A 412 MET cc_start: 0.6363 (mtp) cc_final: 0.5964 (mtt) REVERT: A 425 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7097 (mmm160) REVERT: A 577 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7980 (mtt) REVERT: A 754 ASP cc_start: 0.7694 (m-30) cc_final: 0.7379 (m-30) REVERT: A 897 MET cc_start: 0.6606 (ttm) cc_final: 0.5855 (tmt) REVERT: A 1035 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7440 (ppp) REVERT: A 1094 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5704 (mmt) REVERT: B 255 GLU cc_start: 0.7237 (pm20) cc_final: 0.6865 (mm-30) REVERT: B 310 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8253 (mt) REVERT: B 399 LEU cc_start: 0.5947 (mt) cc_final: 0.5550 (mt) REVERT: C 176 ARG cc_start: 0.6768 (mtt180) cc_final: 0.5718 (mtp-110) outliers start: 37 outliers final: 20 residues processed: 185 average time/residue: 1.0942 time to fit residues: 225.2892 Evaluate side-chains 181 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 414 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 827 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 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 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 251 ASP Chi-restraints excluded: chain C residue 274 ILE 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 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 370 ASN A 872 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 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 = 0.5071 r_free = 0.5071 target = 0.259362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.216633 restraints weight = 19443.508| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.17 r_work: 0.4532 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.4404 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4458 r_free = 0.4458 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 = 0.4458 r_free = 0.4458 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14197 Z= 0.140 Angle : 0.613 13.120 19429 Z= 0.309 Chirality : 0.043 0.417 2134 Planarity : 0.004 0.042 2362 Dihedral : 14.919 178.832 2166 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.76 % Allowed : 20.20 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1603 helix: 0.71 (0.20), residues: 711 sheet: -0.59 (0.33), residues: 231 loop : -0.13 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 468 HIS 0.014 0.001 HIS B 287 PHE 0.031 0.002 PHE A1158 TYR 0.023 0.002 TYR A 461 ARG 0.009 0.000 ARG C 370 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 652) hydrogen bonds : angle 4.94192 ( 1795) covalent geometry : bond 0.00325 (14197) covalent geometry : angle 0.61260 (19429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9869.31 seconds wall clock time: 168 minutes 40.96 seconds (10120.96 seconds total)