Starting phenix.real_space_refine on Tue Nov 18 14:15:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g77_51114/11_2025/9g77_51114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g77_51114/11_2025/9g77_51114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g77_51114/11_2025/9g77_51114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g77_51114/11_2025/9g77_51114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g77_51114/11_2025/9g77_51114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g77_51114/11_2025/9g77_51114.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.183 sd= 0.910 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 44 5.49 5 S 77 5.16 5 C 9253 2.51 5 N 2610 2.21 5 O 2804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14790 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7599 Classifications: {'peptide': 953} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 62, 'TRANS': 890} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 397, 3161 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 378} 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: 397, 3161 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 378} 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: 3198 Chain: "C" Number of atoms: 3129 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 3119 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 373} 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: 392, 3119 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 373} 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: 3180 Chain: "P" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 438 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 402 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' CA': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS B 161 " occ=0.49 ... (18 atoms not shown) pdb=" NE2BHIS B 161 " occ=0.51 residue: pdb=" N AARG B 231 " occ=0.59 ... (20 atoms not shown) pdb=" NH2BARG B 231 " occ=0.41 residue: pdb=" N AHIS B 287 " occ=0.83 ... (18 atoms not shown) pdb=" NE2BHIS B 287 " occ=0.17 residue: pdb=" N AHIS C 161 " occ=0.46 ... (18 atoms not shown) pdb=" NE2BHIS C 161 " occ=0.54 Time building chain proxies: 4.52, per 1000 atoms: 0.31 Number of scatterers: 14790 At special positions: 0 Unit cell: (99.825, 127.05, 140.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 77 16.00 P 44 15.00 O 2804 8.00 N 2610 7.00 C 9253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 757.6 milliseconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 14 sheets defined 48.9% alpha, 13.1% beta 18 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.503A pdb=" N GLN A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.552A pdb=" N HIS A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.635A pdb=" N ALA A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 260 through 261 No H-bonds generated for 'chain 'A' and resid 260 through 261' Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.731A pdb=" N LEU A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.504A pdb=" N MET A 330 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 3.773A 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 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 402 through 413 removed outlier: 4.031A pdb=" N LEU A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 453 removed outlier: 3.666A pdb=" N ARG A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.596A pdb=" N SER A 457 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 460 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR A 461 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 533 removed outlier: 3.640A pdb=" N LEU A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.880A pdb=" N ASP A 538 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.692A pdb=" N LYS A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 629 through 644 Processing helix chain 'A' and resid 748 through 754 Processing helix chain 'A' and resid 765 through 776 removed outlier: 3.536A pdb=" N LEU A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 788 removed outlier: 5.885A pdb=" N LYS A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.680A pdb=" N THR A 804 " --> pdb=" O PRO A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 871 through 886 Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 908 through 918 removed outlier: 3.642A pdb=" N VAL A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 934 Processing helix chain 'A' and resid 936 through 948 Processing helix chain 'A' and resid 952 through 966 Processing helix chain 'A' and resid 1032 through 1044 Processing helix chain 'A' and resid 1058 through 1061 Processing helix chain 'A' and resid 1062 through 1067 Processing helix chain 'A' and resid 1071 through 1101 removed outlier: 3.519A pdb=" N ASN A1076 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1146 Processing helix chain 'A' and resid 1152 through 1156 removed outlier: 3.534A pdb=" N VAL A1155 " --> pdb=" O PRO A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.714A pdb=" N ARG A1187 " --> pdb=" O GLY A1183 " (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 56 through 60 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 74 through 93 Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 137 through 149 removed outlier: 3.607A pdb=" N LEU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.753A pdb=" N HIS B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 221 through 240 removed outlier: 4.148A pdb=" N PHE B 240 " --> pdb=" O TRP B 236 " (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 316 through 328 removed outlier: 3.539A pdb=" N PHE B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 removed outlier: 3.559A pdb=" N LEU B 369 " --> pdb=" O PRO B 365 " (cutoff:3.500A) 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 420 through 425 Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.535A pdb=" N GLY C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 93 Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.709A pdb=" N ILE C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 151 removed outlier: 3.560A pdb=" N LEU C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 166 removed outlier: 3.566A pdb=" N ALA C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 221 through 240 removed outlier: 4.016A pdb=" N PHE C 240 " --> pdb=" O TRP C 236 " (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 removed outlier: 3.577A pdb=" N PHE C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 384 removed outlier: 3.793A pdb=" N LEU C 369 " --> pdb=" O PRO C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 418 through 424 removed outlier: 3.515A pdb=" N LEU C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 170 removed outlier: 6.988A pdb=" N GLU A 183 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 179 removed outlier: 6.541A pdb=" N LEU A 178 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 420 removed outlier: 3.571A pdb=" N VAL A 792 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 586 through 588 Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 6.822A pdb=" N ARG A1116 " --> pdb=" O CYS A1108 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A1196 " --> pdb=" O VAL A1161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 6.074A pdb=" N PHE B 100 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE B 185 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 274 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU B 275 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LYS B 259 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA9, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.747A pdb=" N GLY C 153 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 299 Processing sheet with id=AB2, first strand: chain 'B' and resid 387 through 389 removed outlier: 6.915A pdb=" N VAL B 357 " --> pdb=" O TRP B 388 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ALA B 358 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL B 417 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 360 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.092A pdb=" N PHE C 100 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ILE C 185 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL C 309 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 274 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS C 271 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE C 267 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS C 259 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AB5, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.651A pdb=" N VAL C 357 " --> pdb=" O TRP C 388 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA C 358 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL C 417 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP C 360 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET C 436 " --> pdb=" O SER C 431 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4493 1.34 - 1.45: 2550 1.45 - 1.57: 7993 1.57 - 1.69: 85 1.69 - 1.81: 120 Bond restraints: 15241 Sorted by residual: bond pdb=" O1A DCP A1301 " pdb=" PA DCP A1301 " ideal model delta sigma weight residual 1.477 1.510 -0.033 1.00e-02 1.00e+04 1.06e+01 bond pdb=" C6 DCP A1301 " pdb=" N1 DCP A1301 " ideal model delta sigma weight residual 1.375 1.336 0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" C4 DCP A1301 " pdb=" C5 DCP A1301 " ideal model delta sigma weight residual 1.426 1.390 0.036 1.20e-02 6.94e+03 8.97e+00 bond pdb=" O1B DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 1.477 1.510 -0.033 1.10e-02 8.26e+03 8.78e+00 bond pdb=" CA GLU C 379 " pdb=" C GLU C 379 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.26e-02 6.30e+03 8.10e+00 ... (remaining 15236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 20822 3.84 - 7.67: 29 7.67 - 11.51: 0 11.51 - 15.35: 0 15.35 - 19.18: 2 Bond angle restraints: 20853 Sorted by residual: angle pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 139.87 120.69 19.18 1.00e+00 1.00e+00 3.68e+02 angle pdb=" PA DCP A1301 " pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 136.83 120.55 16.28 1.00e+00 1.00e+00 2.65e+02 angle pdb=" N PHE C 52 " pdb=" CA PHE C 52 " pdb=" C PHE C 52 " ideal model delta sigma weight residual 112.04 104.46 7.58 1.44e+00 4.82e-01 2.77e+01 angle pdb=" N TYR A1125 " pdb=" CA TYR A1125 " pdb=" C TYR A1125 " ideal model delta sigma weight residual 112.45 106.25 6.20 1.39e+00 5.18e-01 1.99e+01 angle pdb=" N ASN C 378 " pdb=" CA ASN C 378 " pdb=" C ASN C 378 " ideal model delta sigma weight residual 111.82 106.76 5.06 1.16e+00 7.43e-01 1.90e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 8341 16.31 - 32.62: 435 32.62 - 48.93: 149 48.93 - 65.24: 65 65.24 - 81.56: 4 Dihedral angle restraints: 8994 sinusoidal: 3950 harmonic: 5044 Sorted by residual: dihedral pdb=" CA GLY B 364 " pdb=" C GLY B 364 " pdb=" N PRO B 365 " pdb=" CA PRO B 365 " ideal model delta harmonic sigma weight residual 0.00 20.80 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" N ASP C 116 " pdb=" CA ASP C 116 " pdb=" CB ASP C 116 " pdb=" CG ASP C 116 " ideal model delta sinusoidal sigma weight residual -60.00 -114.98 54.98 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA ARG C 432 " pdb=" CB ARG C 432 " pdb=" CG ARG C 432 " pdb=" CD ARG C 432 " ideal model delta sinusoidal sigma weight residual -60.00 -114.95 54.95 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 8991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1901 0.049 - 0.098: 293 0.098 - 0.147: 67 0.147 - 0.196: 1 0.196 - 0.245: 1 Chirality restraints: 2263 Sorted by residual: chirality pdb=" CA HIS C 51 " pdb=" N HIS C 51 " pdb=" C HIS C 51 " pdb=" CB HIS C 51 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE A 919 " pdb=" N ILE A 919 " pdb=" C ILE A 919 " pdb=" CB ILE A 919 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ILE A1163 " pdb=" N ILE A1163 " pdb=" C ILE A1163 " pdb=" CB ILE A1163 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 2260 not shown) Planarity restraints: 2543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 115 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C GLY A 115 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY A 115 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY A 116 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 370 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.24e+00 pdb=" C ARG C 370 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG C 370 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C 371 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 50 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C ARG C 50 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG C 50 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS C 51 " 0.011 2.00e-02 2.50e+03 ... (remaining 2540 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1276 2.74 - 3.28: 14310 3.28 - 3.82: 25571 3.82 - 4.36: 30281 4.36 - 4.90: 51375 Nonbonded interactions: 122813 Sorted by model distance: nonbonded pdb=" O LEU C 121 " pdb=" OG SER C 152 " model vdw 2.201 3.040 nonbonded pdb=" O LEU B 65 " pdb=" NH1 ARG B 72 " model vdw 2.222 3.120 nonbonded pdb=" O LYS A 751 " pdb=" OG1 THR A 756 " model vdw 2.282 3.040 nonbonded pdb=" NH1 ARG A 529 " pdb=" OE1 GLU B 368 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR A 159 " pdb=" OG SER A 205 " model vdw 2.287 3.040 ... (remaining 122808 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 230 or resid 232 through 286 or resid 288 through 328 or resid 343 through 45 \ 8)) selection = (chain 'C' and (resid 42 through 160 or resid 162 through 230 or resid 232 throu \ gh 286 or resid 288 through 458)) } 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=0.17 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 0.042 15241 Z= 0.206 Angle : 0.560 19.182 20853 Z= 0.367 Chirality : 0.038 0.245 2263 Planarity : 0.003 0.035 2543 Dihedral : 12.154 81.556 5734 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.40 % Allowed : 2.64 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1728 helix: 1.71 (0.19), residues: 744 sheet: 0.39 (0.33), residues: 263 loop : 0.24 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 370 TYR 0.009 0.001 TYR A1086 PHE 0.010 0.001 PHE A 927 TRP 0.006 0.001 TRP A1077 HIS 0.005 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00307 (15241) covalent geometry : angle 0.56042 (20853) hydrogen bonds : bond 0.16658 ( 714) hydrogen bonds : angle 6.96082 ( 2001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 325 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.6929 (tt0) cc_final: 0.6474 (tp30) REVERT: A 142 GLU cc_start: 0.7335 (pp20) cc_final: 0.6987 (mp0) REVERT: A 364 MET cc_start: 0.6021 (tpp) cc_final: 0.5809 (tpt) REVERT: A 439 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7356 (mtp180) REVERT: A 589 ASP cc_start: 0.7587 (t0) cc_final: 0.7032 (t0) REVERT: A 726 TRP cc_start: 0.8188 (m-90) cc_final: 0.7787 (m-90) REVERT: A 808 SER cc_start: 0.7991 (t) cc_final: 0.7778 (m) REVERT: A 855 MET cc_start: 0.6307 (mmm) cc_final: 0.6106 (mmm) REVERT: A 1056 CYS cc_start: 0.6458 (m) cc_final: 0.6105 (m) REVERT: B 56 THR cc_start: 0.8913 (p) cc_final: 0.8694 (p) REVERT: B 58 GLN cc_start: 0.8394 (mp10) cc_final: 0.7984 (mp-120) REVERT: B 79 GLU cc_start: 0.7764 (tp30) cc_final: 0.7438 (mm-30) REVERT: B 122 VAL cc_start: 0.8347 (m) cc_final: 0.8140 (p) REVERT: B 316 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7838 (t) REVERT: B 329 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7439 (pp30) REVERT: B 402 LEU cc_start: 0.8831 (tp) cc_final: 0.8331 (tp) REVERT: B 439 MET cc_start: 0.8341 (mmt) cc_final: 0.7938 (mmt) REVERT: C 79 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7382 (mm-30) REVERT: C 119 PHE cc_start: 0.8297 (m-80) cc_final: 0.7994 (m-10) REVERT: C 299 ARG cc_start: 0.5785 (mtm110) cc_final: 0.5545 (ptp90) REVERT: C 405 LYS cc_start: 0.7476 (ttpt) cc_final: 0.7240 (tttp) outliers start: 6 outliers final: 2 residues processed: 330 average time/residue: 0.6432 time to fit residues: 232.2166 Evaluate side-chains 196 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 329 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0570 chunk 149 optimal weight: 4.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS A 253 ASN A 550 HIS A 718 ASN A 781 ASN A 961 GLN B 98 GLN B 113 GLN B 224 GLN B 374 GLN B 383 ASN C 113 GLN C 253 GLN C 371 GLN C 383 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.152909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123133 restraints weight = 61720.367| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 5.59 r_work: 0.3372 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15241 Z= 0.125 Angle : 0.534 12.278 20853 Z= 0.275 Chirality : 0.040 0.160 2263 Planarity : 0.004 0.039 2543 Dihedral : 13.866 70.750 2365 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.75 % Favored : 98.19 % Rotamer: Outliers : 2.38 % Allowed : 11.55 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1728 helix: 1.96 (0.19), residues: 779 sheet: 0.48 (0.33), residues: 247 loop : 0.48 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 801 TYR 0.024 0.002 TYR B 406 PHE 0.023 0.002 PHE A 939 TRP 0.014 0.001 TRP C 215 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00272 (15241) covalent geometry : angle 0.53408 (20853) hydrogen bonds : bond 0.03744 ( 714) hydrogen bonds : angle 4.86395 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7585 (pp20) cc_final: 0.7079 (mp0) REVERT: A 172 ILE cc_start: 0.8335 (pt) cc_final: 0.8065 (mm) REVERT: A 589 ASP cc_start: 0.8308 (t0) cc_final: 0.7778 (t0) REVERT: A 961 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: A 1131 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 79 GLU cc_start: 0.8170 (tp30) cc_final: 0.7893 (mm-30) REVERT: B 258 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.4844 (mtp85) REVERT: B 259 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8227 (pttt) REVERT: B 316 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.8010 (t) REVERT: B 361 VAL cc_start: 0.7667 (t) cc_final: 0.7364 (m) REVERT: C 49 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6999 (ptp-170) REVERT: C 79 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7588 (mm-30) REVERT: C 119 PHE cc_start: 0.8517 (m-80) cc_final: 0.8218 (m-10) REVERT: C 299 ARG cc_start: 0.5756 (mtm110) cc_final: 0.5545 (ptp90) REVERT: C 405 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7614 (tttp) REVERT: C 436 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.5898 (mpt) outliers start: 36 outliers final: 9 residues processed: 228 average time/residue: 0.6081 time to fit residues: 152.4034 Evaluate side-chains 190 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 961 GLN Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 3 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 527 HIS A 531 GLN A 718 ASN A 758 GLN B 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.147171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117217 restraints weight = 60536.033| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 5.62 r_work: 0.3250 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15241 Z= 0.228 Angle : 0.615 11.617 20853 Z= 0.313 Chirality : 0.044 0.169 2263 Planarity : 0.005 0.056 2543 Dihedral : 13.978 66.417 2357 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.92 % Favored : 98.02 % Rotamer: Outliers : 3.23 % Allowed : 12.34 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1728 helix: 1.70 (0.19), residues: 771 sheet: 0.25 (0.32), residues: 242 loop : 0.30 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 439 TYR 0.025 0.002 TYR A1086 PHE 0.030 0.003 PHE A 386 TRP 0.018 0.002 TRP A 588 HIS 0.008 0.002 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00539 (15241) covalent geometry : angle 0.61527 (20853) hydrogen bonds : bond 0.04090 ( 714) hydrogen bonds : angle 4.92130 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7827 (pp20) cc_final: 0.7382 (mp0) REVERT: A 360 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7791 (p) REVERT: A 522 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7657 (mtt90) REVERT: A 589 ASP cc_start: 0.8332 (t0) cc_final: 0.7846 (t0) REVERT: A 961 GLN cc_start: 0.8247 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 1044 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.5963 (mpp) REVERT: B 53 PHE cc_start: 0.7925 (m-10) cc_final: 0.7297 (m-10) REVERT: B 79 GLU cc_start: 0.8304 (tp30) cc_final: 0.7943 (mm-30) REVERT: B 122 VAL cc_start: 0.8310 (m) cc_final: 0.7872 (p) REVERT: B 204 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6967 (mtm-85) REVERT: B 258 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.5181 (mtp85) REVERT: C 48 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.5754 (tmm160) REVERT: C 49 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7123 (ptp-170) REVERT: C 119 PHE cc_start: 0.8550 (m-80) cc_final: 0.8348 (m-80) REVERT: C 299 ARG cc_start: 0.6010 (mtm110) cc_final: 0.5551 (ptp90) REVERT: C 378 ASN cc_start: 0.7845 (t0) cc_final: 0.7164 (m110) REVERT: C 405 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7661 (tttp) REVERT: C 436 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6139 (mpt) outliers start: 49 outliers final: 18 residues processed: 239 average time/residue: 0.6587 time to fit residues: 171.8714 Evaluate side-chains 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 116 optimal weight: 0.5980 chunk 69 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 130 optimal weight: 0.0470 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 531 GLN A 718 ASN B 107 GLN C 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.149887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.120868 restraints weight = 63683.231| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 5.82 r_work: 0.3298 rms_B_bonded: 5.61 restraints_weight: 2.0000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15241 Z= 0.112 Angle : 0.521 11.275 20853 Z= 0.265 Chirality : 0.040 0.254 2263 Planarity : 0.004 0.061 2543 Dihedral : 13.834 67.134 2357 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.75 % Favored : 98.19 % Rotamer: Outliers : 2.31 % Allowed : 14.32 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1728 helix: 1.96 (0.19), residues: 777 sheet: 0.15 (0.31), residues: 248 loop : 0.41 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 209 TYR 0.017 0.001 TYR B 264 PHE 0.028 0.002 PHE A 386 TRP 0.019 0.001 TRP A 726 HIS 0.003 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00245 (15241) covalent geometry : angle 0.52113 (20853) hydrogen bonds : bond 0.03147 ( 714) hydrogen bonds : angle 4.62325 ( 2001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7789 (pp20) cc_final: 0.7332 (mp0) REVERT: A 360 VAL cc_start: 0.8124 (t) cc_final: 0.7855 (p) REVERT: A 476 GLU cc_start: 0.8382 (mp0) cc_final: 0.8062 (mp0) REVERT: A 589 ASP cc_start: 0.8315 (t0) cc_final: 0.7825 (t0) REVERT: A 961 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 79 GLU cc_start: 0.8278 (tp30) cc_final: 0.7991 (mm-30) REVERT: B 122 VAL cc_start: 0.8262 (m) cc_final: 0.7818 (p) REVERT: B 258 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.5120 (mtp85) REVERT: C 119 PHE cc_start: 0.8514 (m-80) cc_final: 0.8228 (m-10) REVERT: C 299 ARG cc_start: 0.5989 (mtm110) cc_final: 0.5614 (ptp90) REVERT: C 378 ASN cc_start: 0.7724 (t0) cc_final: 0.7068 (m110) REVERT: C 405 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7638 (tttp) REVERT: C 436 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6280 (mpt) outliers start: 35 outliers final: 14 residues processed: 215 average time/residue: 0.6456 time to fit residues: 152.0007 Evaluate side-chains 189 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 128 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN B 107 GLN B 190 HIS C 58 GLN C 169 ASN C 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.149333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.119391 restraints weight = 56143.872| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 5.27 r_work: 0.3308 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15241 Z= 0.122 Angle : 0.519 10.828 20853 Z= 0.263 Chirality : 0.040 0.197 2263 Planarity : 0.005 0.084 2543 Dihedral : 13.772 66.988 2356 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.57 % Allowed : 14.79 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.20), residues: 1728 helix: 1.99 (0.19), residues: 779 sheet: 0.16 (0.31), residues: 246 loop : 0.43 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 439 TYR 0.014 0.001 TYR B 264 PHE 0.030 0.002 PHE A 386 TRP 0.023 0.001 TRP A 726 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00279 (15241) covalent geometry : angle 0.51914 (20853) hydrogen bonds : bond 0.03136 ( 714) hydrogen bonds : angle 4.59921 ( 2001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7761 (pp20) cc_final: 0.7358 (mp0) REVERT: A 360 VAL cc_start: 0.8151 (t) cc_final: 0.7901 (p) REVERT: A 476 GLU cc_start: 0.8295 (mp0) cc_final: 0.7961 (mp0) REVERT: A 589 ASP cc_start: 0.8297 (t0) cc_final: 0.7820 (t0) REVERT: A 961 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 1044 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.5946 (mpp) REVERT: B 79 GLU cc_start: 0.8226 (tp30) cc_final: 0.7942 (mm-30) REVERT: B 122 VAL cc_start: 0.8230 (m) cc_final: 0.7783 (p) REVERT: B 258 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.5118 (mtp85) REVERT: C 49 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7142 (ptp-170) REVERT: C 299 ARG cc_start: 0.5988 (mtm110) cc_final: 0.5636 (ptp90) REVERT: C 378 ASN cc_start: 0.7746 (t0) cc_final: 0.7067 (m110) REVERT: C 406 TYR cc_start: 0.7689 (m-10) cc_final: 0.7440 (m-10) REVERT: C 436 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6309 (mpt) outliers start: 39 outliers final: 20 residues processed: 213 average time/residue: 0.6196 time to fit residues: 145.2693 Evaluate side-chains 198 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 75 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 108 optimal weight: 0.0030 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 961 GLN B 107 GLN C 232 HIS C 403 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.147655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117204 restraints weight = 61183.722| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 5.60 r_work: 0.3279 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15241 Z= 0.174 Angle : 0.557 10.749 20853 Z= 0.282 Chirality : 0.041 0.178 2263 Planarity : 0.005 0.074 2543 Dihedral : 13.809 65.398 2356 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.04 % Allowed : 14.72 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 1728 helix: 1.84 (0.19), residues: 779 sheet: 0.07 (0.31), residues: 239 loop : 0.35 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 209 TYR 0.015 0.002 TYR A 265 PHE 0.032 0.002 PHE A 386 TRP 0.027 0.002 TRP A 726 HIS 0.006 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00414 (15241) covalent geometry : angle 0.55737 (20853) hydrogen bonds : bond 0.03476 ( 714) hydrogen bonds : angle 4.72282 ( 2001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7828 (pp20) cc_final: 0.7462 (mp0) REVERT: A 360 VAL cc_start: 0.8150 (t) cc_final: 0.7921 (p) REVERT: A 476 GLU cc_start: 0.8309 (mp0) cc_final: 0.7983 (mp0) REVERT: A 589 ASP cc_start: 0.8341 (t0) cc_final: 0.7876 (t0) REVERT: A 633 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6430 (mm) REVERT: A 932 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 961 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: A 1035 MET cc_start: 0.6547 (tmm) cc_final: 0.6342 (ptt) REVERT: A 1044 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.5984 (mpp) REVERT: B 79 GLU cc_start: 0.8214 (tp30) cc_final: 0.7905 (mm-30) REVERT: B 258 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7429 (mpp80) REVERT: B 378 ASN cc_start: 0.8465 (t0) cc_final: 0.8253 (t0) REVERT: C 49 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7165 (ptp-170) REVERT: C 79 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: C 299 ARG cc_start: 0.5971 (mtm110) cc_final: 0.5577 (ptp90) REVERT: C 378 ASN cc_start: 0.7829 (t0) cc_final: 0.7127 (m110) REVERT: C 406 TYR cc_start: 0.7751 (m-10) cc_final: 0.7538 (m-10) REVERT: C 436 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6306 (mpt) outliers start: 46 outliers final: 26 residues processed: 208 average time/residue: 0.6075 time to fit residues: 139.1783 Evaluate side-chains 201 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 961 GLN Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 80 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 26 optimal weight: 0.0030 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS A 93 HIS B 107 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.118596 restraints weight = 57065.637| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 5.33 r_work: 0.3315 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15241 Z= 0.120 Angle : 0.521 10.569 20853 Z= 0.266 Chirality : 0.040 0.232 2263 Planarity : 0.004 0.088 2543 Dihedral : 13.769 65.184 2356 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.77 % Allowed : 14.65 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1728 helix: 2.02 (0.19), residues: 772 sheet: 0.04 (0.31), residues: 236 loop : 0.39 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 209 TYR 0.018 0.001 TYR A 933 PHE 0.033 0.002 PHE A 386 TRP 0.032 0.001 TRP A 726 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00271 (15241) covalent geometry : angle 0.52122 (20853) hydrogen bonds : bond 0.03136 ( 714) hydrogen bonds : angle 4.61109 ( 2001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7800 (pp20) cc_final: 0.7463 (mp0) REVERT: A 360 VAL cc_start: 0.8192 (t) cc_final: 0.7960 (p) REVERT: A 476 GLU cc_start: 0.8297 (mp0) cc_final: 0.7973 (mp0) REVERT: A 589 ASP cc_start: 0.8298 (t0) cc_final: 0.7830 (t0) REVERT: A 633 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6473 (mm) REVERT: A 932 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7736 (mp) REVERT: A 961 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 1204 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8427 (mp) REVERT: B 79 GLU cc_start: 0.8197 (tp30) cc_final: 0.7922 (mm-30) REVERT: B 258 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7482 (mpp80) REVERT: C 49 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7168 (ptp-170) REVERT: C 299 ARG cc_start: 0.5933 (mtm110) cc_final: 0.5548 (ptp90) REVERT: C 378 ASN cc_start: 0.7768 (t0) cc_final: 0.7085 (m110) REVERT: C 406 TYR cc_start: 0.7769 (m-10) cc_final: 0.7541 (m-10) REVERT: C 436 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6312 (mpt) outliers start: 42 outliers final: 24 residues processed: 206 average time/residue: 0.6145 time to fit residues: 139.3343 Evaluate side-chains 199 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 718 ASN B 107 GLN B 428 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS C 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.146248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115424 restraints weight = 62291.954| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 5.61 r_work: 0.3236 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15241 Z= 0.215 Angle : 0.595 10.588 20853 Z= 0.302 Chirality : 0.043 0.220 2263 Planarity : 0.005 0.096 2543 Dihedral : 13.867 62.827 2356 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.84 % Allowed : 14.72 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1728 helix: 1.73 (0.19), residues: 772 sheet: 0.17 (0.31), residues: 242 loop : 0.24 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 209 TYR 0.018 0.002 TYR A1086 PHE 0.036 0.002 PHE A 290 TRP 0.038 0.002 TRP A 726 HIS 0.007 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00516 (15241) covalent geometry : angle 0.59452 (20853) hydrogen bonds : bond 0.03760 ( 714) hydrogen bonds : angle 4.79503 ( 2001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7986 (pp20) cc_final: 0.7596 (mp0) REVERT: A 292 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6802 (ttm-80) REVERT: A 476 GLU cc_start: 0.8306 (mp0) cc_final: 0.7959 (mp0) REVERT: A 589 ASP cc_start: 0.8368 (t0) cc_final: 0.7897 (t0) REVERT: A 633 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6447 (mm) REVERT: B 79 GLU cc_start: 0.8249 (tp30) cc_final: 0.7920 (mm-30) REVERT: B 96 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7900 (mpt180) REVERT: B 258 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7431 (mpp80) REVERT: C 49 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7175 (ptp-170) REVERT: C 79 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 299 ARG cc_start: 0.6011 (mtm110) cc_final: 0.5584 (ptp90) REVERT: C 378 ASN cc_start: 0.7859 (t0) cc_final: 0.7128 (m110) REVERT: C 436 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6325 (mpt) outliers start: 43 outliers final: 26 residues processed: 209 average time/residue: 0.6375 time to fit residues: 146.3239 Evaluate side-chains 204 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN ** C 58 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 = 0.4090 r_free = 0.4090 target = 0.148299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.117894 restraints weight = 59413.863| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 5.46 r_work: 0.3295 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15241 Z= 0.131 Angle : 0.537 10.502 20853 Z= 0.275 Chirality : 0.040 0.202 2263 Planarity : 0.005 0.093 2543 Dihedral : 13.806 62.993 2356 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.24 % Allowed : 15.91 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1728 helix: 1.92 (0.19), residues: 772 sheet: 0.12 (0.32), residues: 234 loop : 0.31 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 209 TYR 0.015 0.002 TYR B 264 PHE 0.044 0.002 PHE A 290 TRP 0.034 0.001 TRP A 726 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00299 (15241) covalent geometry : angle 0.53716 (20853) hydrogen bonds : bond 0.03242 ( 714) hydrogen bonds : angle 4.65116 ( 2001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7811 (pp20) cc_final: 0.7517 (mp0) REVERT: A 292 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6785 (ttm-80) REVERT: A 365 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7226 (ptm160) REVERT: A 476 GLU cc_start: 0.8282 (mp0) cc_final: 0.7962 (mp0) REVERT: A 589 ASP cc_start: 0.8325 (t0) cc_final: 0.7860 (OUTLIER) REVERT: A 932 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 961 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 1035 MET cc_start: 0.6665 (tmm) cc_final: 0.6393 (ptt) REVERT: B 79 GLU cc_start: 0.8211 (tp30) cc_final: 0.7895 (mm-30) REVERT: C 48 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.5753 (tmm160) REVERT: C 49 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7231 (ptp-170) REVERT: C 299 ARG cc_start: 0.6026 (mtm110) cc_final: 0.5643 (ptp90) REVERT: C 378 ASN cc_start: 0.7824 (t0) cc_final: 0.7130 (m110) REVERT: C 436 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6320 (mpt) outliers start: 34 outliers final: 25 residues processed: 197 average time/residue: 0.6358 time to fit residues: 137.6025 Evaluate side-chains 197 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 92 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 chunk 155 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 GLN B 107 GLN C 58 GLN C 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.147792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.117720 restraints weight = 66267.210| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 5.55 r_work: 0.3264 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15241 Z= 0.143 Angle : 0.545 10.500 20853 Z= 0.279 Chirality : 0.041 0.196 2263 Planarity : 0.005 0.091 2543 Dihedral : 13.811 62.785 2356 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.11 % Allowed : 16.17 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1728 helix: 1.95 (0.19), residues: 773 sheet: 0.12 (0.32), residues: 234 loop : 0.30 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 209 TYR 0.014 0.002 TYR B 264 PHE 0.036 0.002 PHE A 386 TRP 0.037 0.001 TRP A 726 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00336 (15241) covalent geometry : angle 0.54467 (20853) hydrogen bonds : bond 0.03284 ( 714) hydrogen bonds : angle 4.62563 ( 2001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7798 (pp20) cc_final: 0.7524 (mp0) REVERT: A 292 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6782 (ttm-80) REVERT: A 476 GLU cc_start: 0.8338 (mp0) cc_final: 0.8017 (mp0) REVERT: A 589 ASP cc_start: 0.8375 (t0) cc_final: 0.7932 (OUTLIER) REVERT: A 932 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7780 (mp) REVERT: A 961 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: A 1035 MET cc_start: 0.6698 (tmm) cc_final: 0.6414 (ptt) REVERT: B 79 GLU cc_start: 0.8234 (tp30) cc_final: 0.7891 (mm-30) REVERT: B 175 ASN cc_start: 0.8341 (m-40) cc_final: 0.8038 (t0) REVERT: C 48 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.5752 (tmm160) REVERT: C 49 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7228 (ptp-170) REVERT: C 299 ARG cc_start: 0.6016 (mtm110) cc_final: 0.5627 (ptp90) REVERT: C 371 GLN cc_start: 0.7498 (tp-100) cc_final: 0.7296 (tp-100) REVERT: C 378 ASN cc_start: 0.7860 (t0) cc_final: 0.7133 (m110) REVERT: C 436 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6406 (mpt) outliers start: 32 outliers final: 23 residues processed: 190 average time/residue: 0.6151 time to fit residues: 128.4779 Evaluate side-chains 193 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 961 GLN Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 436 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.148179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118083 restraints weight = 55041.165| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 5.15 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15241 Z= 0.136 Angle : 0.544 10.453 20853 Z= 0.278 Chirality : 0.041 0.195 2263 Planarity : 0.005 0.093 2543 Dihedral : 13.817 62.781 2356 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.78 % Allowed : 16.57 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1728 helix: 1.96 (0.19), residues: 773 sheet: 0.09 (0.32), residues: 231 loop : 0.31 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 209 TYR 0.015 0.002 TYR B 264 PHE 0.036 0.002 PHE A 386 TRP 0.035 0.001 TRP A 726 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd covalent geometry : bond 0.00318 (15241) covalent geometry : angle 0.54401 (20853) hydrogen bonds : bond 0.03245 ( 714) hydrogen bonds : angle 4.61511 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6760.43 seconds wall clock time: 115 minutes 34.86 seconds (6934.86 seconds total)