Starting phenix.real_space_refine on Fri Jul 3 15:08:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g77_51114/07_2026/9g77_51114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g77_51114/07_2026/9g77_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_51114/07_2026/9g77_51114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g77_51114/07_2026/9g77_51114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g77_51114/07_2026/9g77_51114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g77_51114/07_2026/9g77_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 4.33, per 1000 atoms: 0.29 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: 1.25 Conformation dependent library (CDL) restraints added in 859.0 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: 1.77 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: 3.17 Time building geometry restraints manager: 1.65 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=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 1.746 1.609 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 1.672 1.609 0.063 2.00e-02 2.50e+03 9.99e+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 bond pdb=" C3' DG P 11 " pdb=" C2' DG P 11 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.04e+00 bond pdb=" C1' DT T 19 " pdb=" N1 DT T 19 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.54e+00 ... (remaining 15236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 20625 2.33 - 4.66: 211 4.66 - 6.99: 15 6.99 - 9.33: 1 9.33 - 11.66: 1 Bond angle restraints: 20853 Sorted by residual: 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=" O4' DG P 20 " pdb=" C4' DG P 20 " pdb=" C3' DG P 20 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+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 angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 8318 15.74 - 31.47: 452 31.47 - 47.21: 152 47.21 - 62.94: 76 62.94 - 78.68: 3 Dihedral angle restraints: 9001 sinusoidal: 3957 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 8998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1863 0.049 - 0.098: 329 0.098 - 0.147: 68 0.147 - 0.196: 1 0.196 - 0.245: 2 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=" C1' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" N1 DCP A1301 " pdb=" O4' DCP A1301 " both_signs ideal model delta sigma weight residual False 2.25 2.46 -0.22 2.00e-01 2.50e+01 1.16e+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 ... (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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.920 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 0.137 15241 Z= 0.247 Angle : 0.543 11.657 20853 Z= 0.352 Chirality : 0.039 0.245 2263 Planarity : 0.003 0.035 2543 Dihedral : 12.125 78.677 5741 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/Z covalent geometry : bond 0.00346 / 0.25 (15241) covalent geometry : angle 0.54299 / 0.35 (20853) hydrogen bonds : bond 0.16658 / 11.22 ( 714) hydrogen bonds : angle 6.96082 / 4.79 ( 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 : 0.566 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: 0.7355 (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: 0.7786 (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: 0.5722 time to fit residues: 207.3885 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 : 0.549 ------------------------------------------------------------------------------- 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... A 253 ASN A 390 GLN A 550 HIS A 718 ASN A 781 ASN A 961 GLN B 98 GLN B 113 GLN B 374 GLN B 383 ASN C 253 GLN C 371 GLN C 383 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.153335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.123521 restraints weight = 61893.777| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 5.52 r_work: 0.3376 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (16 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1719 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= 0.133 Angle : 0.564 12.117 20853 Z= 0.296 Chirality : 0.041 0.179 2263 Planarity : 0.004 0.044 2543 Dihedral : 13.823 64.746 2372 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.92 % Favored : 98.02 % Rotamer: Outliers : 2.38 % Allowed : 11.62 % Favored : 86.01 % 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: 1.55 (0.21), residues: 1728 helix: 1.89 (0.19), residues: 779 sheet: 0.33 (0.32), residues: 258 loop : 0.44 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 439 TYR 0.025 0.001 TYR B 406 PHE 0.021 0.002 PHE B 180 TRP 0.014 0.001 TRP C 215 HIS 0.005 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (15241) covalent geometry : angle 0.56418 / 0.30 (20853) hydrogen bonds : bond 0.04421 / 3.11 ( 714) hydrogen bonds : angle 5.03220 / 3.53 ( 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 244 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7518 (pp20) cc_final: 0.7015 (mp0) REVERT: A 172 ILE cc_start: 0.8371 (pt) cc_final: 0.8113 (mm) REVERT: A 188 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: A 589 ASP cc_start: 0.8259 (t0) cc_final: 0.7741 (t0) REVERT: A 801 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7430 (mpp-170) REVERT: A 961 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: A 1131 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 79 GLU cc_start: 0.8180 (tp30) cc_final: 0.7878 (mm-30) REVERT: B 258 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.4765 (mtp85) REVERT: B 361 VAL cc_start: 0.7645 (t) cc_final: 0.7304 (m) REVERT: C 49 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6977 (ptp-170) REVERT: C 79 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7596 (mm-30) REVERT: C 119 PHE cc_start: 0.8511 (m-80) cc_final: 0.8172 (m-10) REVERT: C 436 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.5949 (mpt) outliers start: 36 outliers final: 10 residues processed: 230 average time/residue: 0.5739 time to fit residues: 145.1490 Evaluate side-chains 188 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 188 GLU 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 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 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: 0.7980 chunk 138 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 91 optimal weight: 0.0270 chunk 168 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 HIS A 527 HIS A 531 GLN A 718 ASN B 58 GLN C 113 GLN C 371 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.152542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.122518 restraints weight = 61223.276| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 5.54 r_work: 0.3360 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15241 Z= 0.127 Angle : 0.524 11.278 20853 Z= 0.276 Chirality : 0.040 0.163 2263 Planarity : 0.004 0.063 2543 Dihedral : 13.875 64.822 2366 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % Rotamer: Outliers : 2.31 % Allowed : 12.94 % Favored : 84.75 % 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: 1.99 (0.19), residues: 781 sheet: 0.38 (0.32), residues: 250 loop : 0.48 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.016 0.001 TYR B 264 PHE 0.027 0.002 PHE B 180 TRP 0.017 0.001 TRP C 215 HIS 0.005 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (15241) covalent geometry : angle 0.52449 / 0.28 (20853) hydrogen bonds : bond 0.03727 / 2.56 ( 714) hydrogen bonds : angle 4.80483 / 3.37 ( 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 222 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7539 (ppt-90) REVERT: A 142 GLU cc_start: 0.7568 (pp20) cc_final: 0.7040 (mp0) REVERT: A 172 ILE cc_start: 0.8357 (pt) cc_final: 0.8090 (mm) REVERT: A 290 PHE cc_start: 0.7324 (t80) cc_final: 0.7076 (t80) REVERT: A 589 ASP cc_start: 0.8318 (t0) cc_final: 0.7786 (t0) REVERT: A 961 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7833 (pp30) REVERT: A 1035 MET cc_start: 0.6682 (ttp) cc_final: 0.6292 (ptt) REVERT: B 79 GLU cc_start: 0.8174 (tp30) cc_final: 0.7878 (mm-30) REVERT: B 258 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.4928 (mtp85) REVERT: B 259 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (pttt) REVERT: B 361 VAL cc_start: 0.7694 (t) cc_final: 0.7398 (m) REVERT: C 49 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7022 (ptp-170) REVERT: C 79 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7633 (mm-30) REVERT: C 119 PHE cc_start: 0.8513 (m-80) cc_final: 0.8206 (m-10) REVERT: C 378 ASN cc_start: 0.7684 (t0) cc_final: 0.7033 (m110) REVERT: C 436 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.5958 (mpt) outliers start: 35 outliers final: 14 residues processed: 209 average time/residue: 0.5269 time to fit residues: 121.5139 Evaluate side-chains 192 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 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 561 LEU Chi-restraints excluded: chain A residue 628 CYS 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 961 GLN 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 360 ASP 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 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: 0.7980 chunk 69 optimal weight: 0.0040 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN C 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.123068 restraints weight = 64049.549| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 5.96 r_work: 0.3336 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2337 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= 0.119 Angle : 0.514 10.970 20853 Z= 0.270 Chirality : 0.040 0.139 2263 Planarity : 0.004 0.060 2543 Dihedral : 13.901 64.337 2363 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.52 % Favored : 98.43 % Rotamer: Outliers : 2.51 % Allowed : 13.47 % Favored : 84.03 % 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: 1.64 (0.21), residues: 1728 helix: 1.95 (0.19), residues: 789 sheet: 0.35 (0.32), residues: 250 loop : 0.50 (0.25), residues: 689 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 0.026 0.002 PHE B 180 TRP 0.021 0.001 TRP A 726 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (15241) covalent geometry : angle 0.51415 / 0.27 (20853) hydrogen bonds : bond 0.03360 / 2.29 ( 714) hydrogen bonds : angle 4.64799 / 3.27 ( 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 222 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7667 (pp20) cc_final: 0.7176 (mp0) REVERT: A 172 ILE cc_start: 0.8329 (pt) cc_final: 0.8046 (mm) REVERT: A 589 ASP cc_start: 0.8286 (t0) cc_final: 0.7780 (t0) REVERT: A 961 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: A 1035 MET cc_start: 0.6723 (ttp) cc_final: 0.6363 (ptt) REVERT: B 79 GLU cc_start: 0.8194 (tp30) cc_final: 0.7893 (mm-30) REVERT: B 224 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: B 258 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.4988 (mtp85) REVERT: B 259 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8313 (pttt) REVERT: B 361 VAL cc_start: 0.7909 (t) cc_final: 0.7615 (m) REVERT: C 119 PHE cc_start: 0.8512 (m-80) cc_final: 0.8188 (m-10) REVERT: C 378 ASN cc_start: 0.7662 (t0) cc_final: 0.6985 (m110) REVERT: C 406 TYR cc_start: 0.7679 (m-10) cc_final: 0.7441 (m-10) REVERT: C 436 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6060 (mpt) outliers start: 38 outliers final: 11 residues processed: 214 average time/residue: 0.5960 time to fit residues: 140.0734 Evaluate side-chains 182 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 414 VAL 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 961 GLN Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 420 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 128 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 69 optimal weight: 0.0270 chunk 120 optimal weight: 0.0770 chunk 86 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN A 758 GLN A 961 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 = 0.4137 r_free = 0.4137 target = 0.151794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.122685 restraints weight = 56481.008| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 5.42 r_work: 0.3359 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15241 Z= 0.110 Angle : 0.501 10.699 20853 Z= 0.263 Chirality : 0.039 0.211 2263 Planarity : 0.004 0.058 2543 Dihedral : 13.877 63.796 2363 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.37 % Rotamer: Outliers : 2.18 % Allowed : 14.52 % Favored : 83.30 % 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: 1.71 (0.21), residues: 1728 helix: 2.05 (0.19), residues: 788 sheet: 0.39 (0.32), residues: 246 loop : 0.48 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 801 TYR 0.016 0.001 TYR B 264 PHE 0.027 0.002 PHE A 386 TRP 0.025 0.001 TRP A 726 HIS 0.003 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (15241) covalent geometry : angle 0.50120 / 0.26 (20853) hydrogen bonds : bond 0.03187 / 2.16 ( 714) hydrogen bonds : angle 4.58345 / 3.22 ( 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 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7683 (pp20) cc_final: 0.7204 (mp0) REVERT: A 172 ILE cc_start: 0.8337 (pt) cc_final: 0.8059 (mm) REVERT: A 589 ASP cc_start: 0.8258 (t0) cc_final: 0.7739 (t0) REVERT: A 961 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: A 1035 MET cc_start: 0.6765 (ttp) cc_final: 0.6331 (ptt) REVERT: A 1131 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 79 GLU cc_start: 0.8143 (tp30) cc_final: 0.7869 (mm-30) REVERT: B 204 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7056 (mtm-85) REVERT: B 259 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8309 (pttt) REVERT: B 361 VAL cc_start: 0.7800 (t) cc_final: 0.7535 (m) REVERT: C 58 GLN cc_start: 0.8346 (mp10) cc_final: 0.8140 (mp10) REVERT: C 119 PHE cc_start: 0.8463 (m-80) cc_final: 0.8138 (m-10) REVERT: C 378 ASN cc_start: 0.7653 (t0) cc_final: 0.6979 (m110) REVERT: C 393 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6395 (mm-30) REVERT: C 406 TYR cc_start: 0.7712 (m-10) cc_final: 0.7321 (m-10) REVERT: C 436 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6233 (mpt) outliers start: 33 outliers final: 15 residues processed: 200 average time/residue: 0.5517 time to fit residues: 121.6553 Evaluate side-chains 187 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 561 LEU Chi-restraints excluded: chain A residue 562 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 966 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 420 THR 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 393 GLU 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: 7.9990 chunk 100 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 718 ASN A1080 GLN C 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.148939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.119800 restraints weight = 61220.583| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 5.72 r_work: 0.3284 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 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 = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15241 Z= 0.186 Angle : 0.565 10.725 20853 Z= 0.293 Chirality : 0.042 0.168 2263 Planarity : 0.005 0.065 2543 Dihedral : 13.932 63.296 2363 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.81 % 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: 1.51 (0.20), residues: 1728 helix: 1.88 (0.19), residues: 784 sheet: 0.24 (0.31), residues: 246 loop : 0.40 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 209 TYR 0.018 0.002 TYR A1086 PHE 0.030 0.002 PHE A 386 TRP 0.030 0.002 TRP A 726 HIS 0.054 0.002 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (15241) covalent geometry : angle 0.56530 / 0.29 (20853) hydrogen bonds : bond 0.03677 / 2.45 ( 714) hydrogen bonds : angle 4.69207 / 3.29 ( 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 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7809 (pp20) cc_final: 0.7327 (mp0) REVERT: A 360 VAL cc_start: 0.8110 (t) cc_final: 0.7848 (p) REVERT: A 589 ASP cc_start: 0.8335 (t0) cc_final: 0.7839 (t0) REVERT: A 961 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7840 (pp30) REVERT: A 1035 MET cc_start: 0.6873 (ttp) cc_final: 0.6442 (ptt) REVERT: A 1204 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 79 GLU cc_start: 0.8293 (tp30) cc_final: 0.7992 (mm-30) REVERT: B 204 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7093 (mtm-85) REVERT: B 258 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.5197 (mtp85) REVERT: B 259 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8435 (pttt) REVERT: B 361 VAL cc_start: 0.8120 (t) cc_final: 0.7881 (m) REVERT: C 49 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7003 (ptp-170) REVERT: C 79 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: C 346 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (mp) REVERT: C 378 ASN cc_start: 0.7780 (t0) cc_final: 0.7117 (m110) REVERT: C 393 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6391 (mm-30) REVERT: C 406 TYR cc_start: 0.7747 (m-10) cc_final: 0.7507 (m-10) REVERT: C 436 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6219 (mpt) outliers start: 39 outliers final: 17 residues processed: 200 average time/residue: 0.5151 time to fit residues: 113.2329 Evaluate side-chains 190 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 562 ASP Chi-restraints excluded: chain A residue 740 VAL 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 961 GLN Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 258 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 420 THR 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 345 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 393 GLU 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: 0.8980 chunk 109 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN A 961 GLN B 107 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 = 0.4112 r_free = 0.4112 target = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.120886 restraints weight = 57051.385| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 5.33 r_work: 0.3318 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 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 = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2857 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= 0.127 Angle : 0.519 10.463 20853 Z= 0.272 Chirality : 0.040 0.149 2263 Planarity : 0.004 0.057 2543 Dihedral : 13.898 62.968 2363 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % Rotamer: Outliers : 2.51 % Allowed : 14.79 % Favored : 82.71 % 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: 1.61 (0.20), residues: 1728 helix: 2.02 (0.19), residues: 777 sheet: 0.28 (0.31), residues: 239 loop : 0.40 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 209 TYR 0.014 0.001 TYR B 406 PHE 0.031 0.002 PHE A 386 TRP 0.036 0.001 TRP A 726 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15241) covalent geometry : angle 0.51937 / 0.27 (20853) hydrogen bonds : bond 0.03305 / 2.22 ( 714) hydrogen bonds : angle 4.61726 / 3.24 ( 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 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7778 (pp20) cc_final: 0.7328 (mp0) REVERT: A 282 MET cc_start: 0.7978 (tpt) cc_final: 0.7648 (mmt) REVERT: A 360 VAL cc_start: 0.8073 (t) cc_final: 0.7824 (p) REVERT: A 589 ASP cc_start: 0.8317 (t0) cc_final: 0.7813 (t0) REVERT: A 961 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: A 1035 MET cc_start: 0.6776 (ttp) cc_final: 0.6327 (ptt) REVERT: A 1044 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.5830 (mpp) REVERT: A 1204 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8399 (mp) REVERT: B 79 GLU cc_start: 0.8228 (tp30) cc_final: 0.7909 (mm-30) REVERT: B 204 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6994 (mtm-85) REVERT: B 259 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8412 (pttt) REVERT: B 361 VAL cc_start: 0.8050 (t) cc_final: 0.7834 (m) REVERT: C 49 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7001 (ptp-170) REVERT: C 79 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: C 346 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 378 ASN cc_start: 0.7715 (t0) cc_final: 0.7020 (m110) REVERT: C 393 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6396 (mm-30) REVERT: C 406 TYR cc_start: 0.7676 (m-10) cc_final: 0.7451 (m-10) REVERT: C 436 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6182 (mpt) outliers start: 38 outliers final: 18 residues processed: 197 average time/residue: 0.6063 time to fit residues: 131.5026 Evaluate side-chains 196 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 794 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 919 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 A residue 1204 LEU Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 259 LYS 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 345 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 393 GLU 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: 0.7980 chunk 10 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 127 optimal weight: 0.0030 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN B 107 GLN C 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.149902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.121018 restraints weight = 63132.569| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 5.83 r_work: 0.3294 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2958 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= 0.125 Angle : 0.523 10.426 20853 Z= 0.275 Chirality : 0.040 0.251 2263 Planarity : 0.004 0.069 2543 Dihedral : 13.880 62.455 2363 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.86 % Favored : 98.08 % Rotamer: Outliers : 2.38 % Allowed : 15.45 % Favored : 82.18 % 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: 1.64 (0.20), residues: 1728 helix: 2.05 (0.19), residues: 774 sheet: 0.33 (0.31), residues: 237 loop : 0.40 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 578 TYR 0.014 0.001 TYR A1086 PHE 0.046 0.002 PHE A 386 TRP 0.040 0.001 TRP A 726 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (15241) covalent geometry : angle 0.52334 / 0.28 (20853) hydrogen bonds : bond 0.03288 / 2.21 ( 714) hydrogen bonds : angle 4.60220 / 3.23 ( 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 209 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7804 (pp20) cc_final: 0.7348 (mp0) REVERT: A 282 MET cc_start: 0.7997 (tpt) cc_final: 0.7789 (mmt) REVERT: A 360 VAL cc_start: 0.8169 (t) cc_final: 0.7912 (p) REVERT: A 386 PHE cc_start: 0.8290 (t80) cc_final: 0.8089 (t80) REVERT: A 589 ASP cc_start: 0.8342 (t0) cc_final: 0.7853 (t0) REVERT: A 932 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 1035 MET cc_start: 0.6832 (ttp) cc_final: 0.6362 (ptt) REVERT: A 1044 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.5915 (mpp) REVERT: B 79 GLU cc_start: 0.8276 (tp30) cc_final: 0.7982 (mm-30) REVERT: B 119 PHE cc_start: 0.7520 (m-80) cc_final: 0.7259 (m-80) REVERT: B 204 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7039 (mtm-85) REVERT: B 361 VAL cc_start: 0.8081 (t) cc_final: 0.7843 (m) REVERT: B 378 ASN cc_start: 0.8477 (t0) cc_final: 0.8258 (t0) REVERT: C 79 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: C 346 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8014 (mp) REVERT: C 378 ASN cc_start: 0.7767 (t0) cc_final: 0.7088 (m110) REVERT: C 393 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6371 (mm-30) REVERT: C 406 TYR cc_start: 0.7772 (m-10) cc_final: 0.7566 (m-10) REVERT: C 436 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6298 (mpt) outliers start: 36 outliers final: 20 residues processed: 198 average time/residue: 0.5796 time to fit residues: 126.5585 Evaluate side-chains 195 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 794 LEU Chi-restraints excluded: chain A residue 827 THR 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 1044 MET Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain B residue 204 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 79 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 393 GLU 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: 0.9980 chunk 12 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 GLN B 107 GLN B 190 HIS C 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.149306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.119872 restraints weight = 59657.101| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 5.49 r_work: 0.3301 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 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 = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15241 Z= 0.138 Angle : 0.545 13.694 20853 Z= 0.282 Chirality : 0.041 0.224 2263 Planarity : 0.005 0.084 2543 Dihedral : 13.878 61.922 2363 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.31 % Rotamer: Outliers : 2.18 % Allowed : 16.04 % Favored : 81.78 % 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: 1.60 (0.20), residues: 1728 helix: 2.04 (0.19), residues: 773 sheet: 0.34 (0.31), residues: 243 loop : 0.35 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 209 TYR 0.017 0.002 TYR A1086 PHE 0.039 0.002 PHE A 386 TRP 0.038 0.001 TRP A 726 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15241) covalent geometry : angle 0.54547 / 0.28 (20853) hydrogen bonds : bond 0.03346 / 2.24 ( 714) hydrogen bonds : angle 4.61991 / 3.25 ( 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 210 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7796 (pp20) cc_final: 0.7377 (mp0) REVERT: A 360 VAL cc_start: 0.8121 (t) cc_final: 0.7897 (p) REVERT: A 386 PHE cc_start: 0.8264 (t80) cc_final: 0.8055 (t80) REVERT: A 589 ASP cc_start: 0.8334 (t0) cc_final: 0.7839 (t0) REVERT: A 932 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 961 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: A 1035 MET cc_start: 0.6818 (ttp) cc_final: 0.6343 (ptt) REVERT: B 79 GLU cc_start: 0.8251 (tp30) cc_final: 0.7955 (mm-30) REVERT: B 119 PHE cc_start: 0.7492 (m-80) cc_final: 0.7198 (m-80) REVERT: B 361 VAL cc_start: 0.8092 (t) cc_final: 0.7890 (m) REVERT: B 378 ASN cc_start: 0.8467 (t0) cc_final: 0.8253 (t0) REVERT: C 48 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.5608 (tmm160) REVERT: C 49 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7030 (ptp-170) REVERT: C 79 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: C 346 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8029 (mp) REVERT: C 378 ASN cc_start: 0.7792 (t0) cc_final: 0.7093 (m110) REVERT: C 436 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6305 (mpt) outliers start: 33 outliers final: 19 residues processed: 198 average time/residue: 0.5827 time to fit residues: 126.8627 Evaluate side-chains 193 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 363 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 562 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 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 261 SER 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 79 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 346 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 92 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 961 GLN C 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.149163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.120244 restraints weight = 66312.492| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 5.94 r_work: 0.3277 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3134 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= 0.139 Angle : 0.547 10.403 20853 Z= 0.284 Chirality : 0.041 0.227 2263 Planarity : 0.005 0.095 2543 Dihedral : 13.879 61.692 2363 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.86 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 16.04 % Favored : 81.91 % 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: 1.60 (0.20), residues: 1728 helix: 2.05 (0.19), residues: 773 sheet: 0.31 (0.31), residues: 243 loop : 0.35 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 801 TYR 0.017 0.002 TYR C 406 PHE 0.039 0.002 PHE A 386 TRP 0.038 0.001 TRP A 726 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15241) covalent geometry : angle 0.54653 / 0.28 (20853) hydrogen bonds : bond 0.03363 / 2.26 ( 714) hydrogen bonds : angle 4.61692 / 3.25 ( 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 204 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.7816 (pp20) cc_final: 0.7397 (mp0) REVERT: A 360 VAL cc_start: 0.8122 (t) cc_final: 0.7905 (p) REVERT: A 386 PHE cc_start: 0.8283 (t80) cc_final: 0.8066 (t80) REVERT: A 589 ASP cc_start: 0.8383 (t0) cc_final: 0.7898 (t0) REVERT: A 932 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7786 (mp) REVERT: A 1035 MET cc_start: 0.6798 (ttp) cc_final: 0.6322 (ptt) REVERT: A 1044 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.5917 (mpp) REVERT: B 79 GLU cc_start: 0.8292 (tp30) cc_final: 0.7989 (mm-30) REVERT: B 361 VAL cc_start: 0.8107 (t) cc_final: 0.7898 (m) REVERT: B 378 ASN cc_start: 0.8489 (t0) cc_final: 0.8265 (t0) REVERT: C 48 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.5612 (tmm160) REVERT: C 49 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7045 (ptp-170) REVERT: C 79 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: C 346 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8011 (mp) REVERT: C 378 ASN cc_start: 0.7804 (t0) cc_final: 0.7087 (m110) REVERT: C 436 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6311 (mpt) outliers start: 31 outliers final: 20 residues processed: 195 average time/residue: 0.6011 time to fit residues: 129.1195 Evaluate side-chains 197 residues out of total 1510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 363 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 740 VAL 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 932 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain B residue 56 THR 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 48 ARG 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 345 VAL Chi-restraints excluded: chain C residue 346 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 110 optimal weight: 0.0470 chunk 119 optimal weight: 0.0020 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.150614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.121072 restraints weight = 55244.425| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 5.23 r_work: 0.3335 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15241 Z= 0.108 Angle : 0.519 10.235 20853 Z= 0.272 Chirality : 0.040 0.210 2263 Planarity : 0.004 0.100 2543 Dihedral : 13.838 61.229 2363 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.69 % Favored : 98.25 % Rotamer: Outliers : 1.72 % Allowed : 16.83 % Favored : 81.45 % 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: 1.74 (0.20), residues: 1728 helix: 2.18 (0.19), residues: 772 sheet: 0.37 (0.32), 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 0.022 0.001 TYR B 264 PHE 0.037 0.002 PHE A 386 TRP 0.038 0.001 TRP A 726 HIS 0.003 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (15241) covalent geometry : angle 0.51942 / 0.27 (20853) hydrogen bonds : bond 0.03105 / 2.09 ( 714) hydrogen bonds : angle 4.52261 / 3.17 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6205.57 seconds wall clock time: 106 minutes 8.43 seconds (6368.43 seconds total)