Starting phenix.real_space_refine on Thu Feb 5 08:31:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v6e_64799/02_2026/9v6e_64799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v6e_64799/02_2026/9v6e_64799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v6e_64799/02_2026/9v6e_64799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v6e_64799/02_2026/9v6e_64799.map" model { file = "/net/cci-nas-00/data/ceres_data/9v6e_64799/02_2026/9v6e_64799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v6e_64799/02_2026/9v6e_64799.cif" } resolution = 3.19 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= -0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 9982 2.51 5 N 2757 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15625 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 7085 Classifications: {'peptide': 1120} Incomplete info: {'truncation_to_alanine': 535} Link IDs: {'PTRANS': 66, 'TRANS': 1053} Chain breaks: 24 Unresolved non-hydrogen bonds: 1977 Unresolved non-hydrogen angles: 2517 Unresolved non-hydrogen dihedrals: 1620 Unresolved non-hydrogen chiralities: 181 Planarities with less than four sites: {'GLN:plan1': 35, 'HIS:plan': 26, 'ARG:plan': 63, 'PHE:plan': 26, 'GLU:plan': 45, 'ASP:plan': 34, 'TRP:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 13} Unresolved non-hydrogen planarities: 1195 Chain: "B" Number of atoms: 2825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2825 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 13, 'TRANS': 367} Chain breaks: 4 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 5, 'GLN:plan1': 5, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2893 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 3 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 9, 'ARG:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 156 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2822 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 378 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 15, 'ARG:plan': 6, 'TRP:plan': 1, 'HIS:plan': 5, 'ASN:plan1': 5, 'GLN:plan1': 4, 'PHE:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 230 Time building chain proxies: 3.64, per 1000 atoms: 0.23 Number of scatterers: 15625 At special positions: 0 Unit cell: (123.25, 170.85, 299.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2838 8.00 N 2757 7.00 C 9982 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: 1.53 Conformation dependent library (CDL) restraints added in 818.0 milliseconds 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4334 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 26 sheets defined 35.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 1716 through 1729 Processing helix chain 'A' and resid 1748 through 1763 removed outlier: 4.620A pdb=" N THR A1754 " --> pdb=" O GLU A1750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A1755 " --> pdb=" O ARG A1751 " (cutoff:3.500A) Processing helix chain 'A' and resid 1943 through 1979 removed outlier: 3.711A pdb=" N GLU A1947 " --> pdb=" O GLY A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 1996 Processing helix chain 'A' and resid 2024 through 2029 Processing helix chain 'A' and resid 2061 through 2072 Processing helix chain 'A' and resid 2170 through 2175 Processing helix chain 'A' and resid 2175 through 2199 Processing helix chain 'A' and resid 2204 through 2212 removed outlier: 3.808A pdb=" N ILE A2211 " --> pdb=" O ASP A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2227 through 2232 Proline residue: A2232 - end of helix Processing helix chain 'A' and resid 2233 through 2245 Processing helix chain 'A' and resid 2366 through 2390 Processing helix chain 'A' and resid 2505 through 2510 Processing helix chain 'A' and resid 2519 through 2525 removed outlier: 3.563A pdb=" N ARG A2524 " --> pdb=" O PRO A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2526 through 2528 No H-bonds generated for 'chain 'A' and resid 2526 through 2528' Processing helix chain 'A' and resid 2532 through 2537 Processing helix chain 'A' and resid 2550 through 2552 No H-bonds generated for 'chain 'A' and resid 2550 through 2552' Processing helix chain 'A' and resid 2553 through 2568 Processing helix chain 'A' and resid 2614 through 2620 removed outlier: 4.087A pdb=" N ARG A2620 " --> pdb=" O LEU A2616 " (cutoff:3.500A) Processing helix chain 'A' and resid 2667 through 2700 removed outlier: 3.509A pdb=" N LEU A2700 " --> pdb=" O LEU A2696 " (cutoff:3.500A) Processing helix chain 'A' and resid 2720 through 2724 removed outlier: 4.155A pdb=" N LEU A2724 " --> pdb=" O PRO A2721 " (cutoff:3.500A) Processing helix chain 'A' and resid 2728 through 2735 Processing helix chain 'A' and resid 2763 through 2767 Processing helix chain 'A' and resid 2789 through 2806 removed outlier: 4.146A pdb=" N GLU A2804 " --> pdb=" O ILE A2800 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A2805 " --> pdb=" O LYS A2801 " (cutoff:3.500A) Processing helix chain 'A' and resid 2807 through 2823 removed outlier: 3.683A pdb=" N GLN A2811 " --> pdb=" O GLU A2807 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP A2821 " --> pdb=" O LEU A2817 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN A2823 " --> pdb=" O VAL A2819 " (cutoff:3.500A) Processing helix chain 'A' and resid 2833 through 2843 removed outlier: 3.613A pdb=" N LEU A2837 " --> pdb=" O SER A2833 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A2838 " --> pdb=" O ALA A2834 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A2839 " --> pdb=" O GLY A2835 " (cutoff:3.500A) Processing helix chain 'A' and resid 2907 through 2926 Processing helix chain 'A' and resid 3026 through 3034 Processing helix chain 'A' and resid 3043 through 3059 Processing helix chain 'A' and resid 3070 through 3082 Processing helix chain 'A' and resid 3106 through 3117 Processing helix chain 'A' and resid 3249 through 3284 removed outlier: 3.846A pdb=" N ARG A3274 " --> pdb=" O GLY A3270 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG A3275 " --> pdb=" O GLY A3271 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A3276 " --> pdb=" O HIS A3272 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3311 removed outlier: 3.838A pdb=" N GLU A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU A3306 " --> pdb=" O ALA A3302 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A3307 " --> pdb=" O GLU A3303 " (cutoff:3.500A) Processing helix chain 'A' and resid 3316 through 3320 Processing helix chain 'A' and resid 3321 through 3329 removed outlier: 4.330A pdb=" N CYS A3325 " --> pdb=" O GLN A3322 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A3326 " --> pdb=" O LEU A3323 " (cutoff:3.500A) Processing helix chain 'A' and resid 3330 through 3345 Processing helix chain 'A' and resid 3409 through 3432 removed outlier: 4.270A pdb=" N THR A3422 " --> pdb=" O SER A3418 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A3423 " --> pdb=" O VAL A3419 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.654A pdb=" N THR B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 401 through 411 removed outlier: 3.848A pdb=" N HIS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 431 Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.813A pdb=" N THR C 195 " --> pdb=" O PRO C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 398 through 418 removed outlier: 3.521A pdb=" N LEU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.633A pdb=" N ILE D 27 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 removed outlier: 4.062A pdb=" N ASN D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 Processing helix chain 'D' and resid 89 through 105 removed outlier: 4.060A pdb=" N SER D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 98 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 151 removed outlier: 4.224A pdb=" N THR D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 180 through 206 Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.537A pdb=" N THR D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 273 removed outlier: 3.753A pdb=" N LEU D 256 " --> pdb=" O PRO D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 280 removed outlier: 4.135A pdb=" N GLN D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 296 through 306 removed outlier: 4.293A pdb=" N ARG D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 removed outlier: 3.589A pdb=" N ASP D 344 " --> pdb=" O LYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 366 removed outlier: 3.522A pdb=" N VAL D 364 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 372 through 377 removed outlier: 3.639A pdb=" N SER D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 416 Processing helix chain 'D' and resid 417 through 432 removed outlier: 3.516A pdb=" N SER D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 438 removed outlier: 4.107A pdb=" N PHE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1736 through 1742 removed outlier: 4.557A pdb=" N LEU A1919 " --> pdb=" O VAL A1781 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2040 through 2047 Processing sheet with id=AA3, first strand: chain 'A' and resid 2221 through 2225 Processing sheet with id=AA4, first strand: chain 'A' and resid 2279 through 2280 Processing sheet with id=AA5, first strand: chain 'A' and resid 2649 through 2650 Processing sheet with id=AA6, first strand: chain 'A' and resid 2653 through 2655 Processing sheet with id=AA7, first strand: chain 'A' and resid 2845 through 2852 removed outlier: 6.031A pdb=" N LEU A2846 " --> pdb=" O ALA A3009 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA A3009 " --> pdb=" O LEU A2846 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A2993 " --> pdb=" O PHE A3008 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A2994 " --> pdb=" O LEU A2983 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3092 through 3101 removed outlier: 3.692A pdb=" N SER A3166 " --> pdb=" O VAL A3194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A3126 " --> pdb=" O ALA A3140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3314 through 3315 removed outlier: 3.586A pdb=" N THR A3388 " --> pdb=" O LEU A3375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3352 through 3353 Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.003A pdb=" N LYS B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 356 " --> pdb=" O CYS B 368 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 352 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AB4, first strand: chain 'B' and resid 65 through 71 removed outlier: 4.331A pdb=" N TRP B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE B 119 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.876A pdb=" N SER B 133 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 143 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 152 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 176 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA B 154 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 190 removed outlier: 4.321A pdb=" N LEU B 198 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.618A pdb=" N THR B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU B 285 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER B 300 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 287 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AB9, first strand: chain 'C' and resid 14 through 21 removed outlier: 6.880A pdb=" N ILE C 392 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE C 19 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL C 390 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 389 " --> pdb=" O SER C 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 41 through 44 removed outlier: 4.240A pdb=" N VAL C 50 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 79 through 87 removed outlier: 6.796A pdb=" N THR C 100 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE C 83 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY C 98 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR C 85 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 96 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 101 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 146 through 153 removed outlier: 8.842A pdb=" N THR C 159 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU C 175 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 161 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR C 173 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 172 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.731A pdb=" N TRP C 203 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS C 230 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 240 " --> pdb=" O HIS C 230 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP C 232 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL C 238 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 252 through 256 Processing sheet with id=AC6, first strand: chain 'C' and resid 310 through 316 removed outlier: 3.621A pdb=" N ALA C 329 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS C 339 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU C 356 " --> pdb=" O LYS C 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 315 through 317 removed outlier: 6.935A pdb=" N PHE D 402 " --> pdb=" O PRO D 398 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 391 through 393 820 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5190 1.34 - 1.46: 2981 1.46 - 1.58: 7709 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 15950 Sorted by residual: bond pdb=" CB PRO C 348 " pdb=" CG PRO C 348 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.14e+00 bond pdb=" C LEU A2817 " pdb=" N PHE A2818 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.35e-02 5.49e+03 1.94e+00 bond pdb=" C GLN A2708 " pdb=" N LEU A2709 " ideal model delta sigma weight residual 1.332 1.314 0.019 1.40e-02 5.10e+03 1.82e+00 bond pdb=" CA PHE A2552 " pdb=" C PHE A2552 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.72e-02 3.38e+03 1.72e+00 bond pdb=" CA PHE A2632 " pdb=" CB PHE A2632 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.48e+00 ... (remaining 15945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 21703 2.94 - 5.88: 149 5.88 - 8.82: 17 8.82 - 11.76: 2 11.76 - 14.70: 2 Bond angle restraints: 21873 Sorted by residual: angle pdb=" CB MET B 291 " pdb=" CG MET B 291 " pdb=" SD MET B 291 " ideal model delta sigma weight residual 112.70 127.40 -14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" N GLN A2527 " pdb=" CA GLN A2527 " pdb=" C GLN A2527 " ideal model delta sigma weight residual 114.64 107.20 7.44 1.52e+00 4.33e-01 2.39e+01 angle pdb=" CA MET B 291 " pdb=" CB MET B 291 " pdb=" CG MET B 291 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" C ASP B 417 " pdb=" N LEU B 418 " pdb=" CA LEU B 418 " ideal model delta sigma weight residual 121.80 131.72 -9.92 2.44e+00 1.68e-01 1.65e+01 angle pdb=" N VAL D 118 " pdb=" CA VAL D 118 " pdb=" C VAL D 118 " ideal model delta sigma weight residual 111.48 107.79 3.69 9.40e-01 1.13e+00 1.54e+01 ... (remaining 21868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8334 17.83 - 35.66: 800 35.66 - 53.50: 165 53.50 - 71.33: 29 71.33 - 89.16: 13 Dihedral angle restraints: 9341 sinusoidal: 2694 harmonic: 6647 Sorted by residual: dihedral pdb=" CA SER D 23 " pdb=" C SER D 23 " pdb=" N HIS D 24 " pdb=" CA HIS D 24 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA MET B 291 " pdb=" C MET B 291 " pdb=" N GLU B 292 " pdb=" CA GLU B 292 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE A2632 " pdb=" C PHE A2632 " pdb=" N GLU A2633 " pdb=" CA GLU A2633 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1955 0.041 - 0.083: 485 0.083 - 0.124: 177 0.124 - 0.166: 8 0.166 - 0.207: 2 Chirality restraints: 2627 Sorted by residual: chirality pdb=" CA PRO C 348 " pdb=" N PRO C 348 " pdb=" C PRO C 348 " pdb=" CB PRO C 348 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO A2593 " pdb=" N PRO A2593 " pdb=" C PRO A2593 " pdb=" CB PRO A2593 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE D 407 " pdb=" N ILE D 407 " pdb=" C ILE D 407 " pdb=" CB ILE D 407 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 2624 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 347 " -0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO C 348 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 146 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C MET D 146 " -0.036 2.00e-02 2.50e+03 pdb=" O MET D 146 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR D 147 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 90 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 91 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " 0.030 5.00e-02 4.00e+02 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 545 2.71 - 3.26: 15370 3.26 - 3.80: 25029 3.80 - 4.35: 27987 4.35 - 4.90: 48723 Nonbonded interactions: 117654 Sorted by model distance: nonbonded pdb=" O PHE D 22 " pdb=" OG SER D 23 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR B 332 " pdb=" OH TYR B 371 " model vdw 2.162 3.040 nonbonded pdb=" O ASP D 374 " pdb=" OG SER D 377 " model vdw 2.177 3.040 nonbonded pdb=" O TYR A2923 " pdb=" OG SER A2926 " model vdw 2.200 3.040 nonbonded pdb=" O LYS D 145 " pdb=" OG1 THR D 148 " model vdw 2.208 3.040 ... (remaining 117649 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 33.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.004 0.073 15950 Z= 0.161 Angle : 0.643 14.703 21873 Z= 0.332 Chirality : 0.041 0.207 2627 Planarity : 0.005 0.097 2871 Dihedral : 15.396 89.161 5007 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.05 % Favored : 92.63 % Rotamer: Outliers : 0.16 % Allowed : 27.36 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 2226 helix: 1.91 (0.21), residues: 726 sheet: -0.51 (0.21), residues: 632 loop : -1.81 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 320 TYR 0.017 0.001 TYR D 143 PHE 0.025 0.001 PHE A2632 TRP 0.013 0.001 TRP A2684 HIS 0.005 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00359 (15950) covalent geometry : angle 0.64321 (21873) hydrogen bonds : bond 0.14636 ( 820) hydrogen bonds : angle 6.08358 ( 2283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.488 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.0882 time to fit residues: 8.6887 Evaluate side-chains 52 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2796 GLN ** A3091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3421 ASN B 320 HIS ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.067728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.048171 restraints weight = 131886.393| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 6.09 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 15950 Z= 0.240 Angle : 0.660 11.940 21873 Z= 0.335 Chirality : 0.042 0.234 2627 Planarity : 0.005 0.096 2871 Dihedral : 4.382 20.065 2366 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.95 % Favored : 91.69 % Rotamer: Outliers : 4.32 % Allowed : 24.24 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.19), residues: 2226 helix: 1.78 (0.20), residues: 746 sheet: -0.68 (0.21), residues: 637 loop : -1.93 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 288 TYR 0.015 0.002 TYR D 143 PHE 0.027 0.002 PHE A2632 TRP 0.012 0.001 TRP A2684 HIS 0.005 0.001 HIS A3122 Details of bonding type rmsd covalent geometry : bond 0.00539 (15950) covalent geometry : angle 0.65995 (21873) hydrogen bonds : bond 0.03852 ( 820) hydrogen bonds : angle 4.95464 ( 2283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 50 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 2711 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: A 3123 MET cc_start: 0.8399 (mmp) cc_final: 0.8071 (mmp) REVERT: C 22 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6966 (m-10) REVERT: D 259 MET cc_start: 0.9069 (mmp) cc_final: 0.8831 (mmp) outliers start: 54 outliers final: 21 residues processed: 103 average time/residue: 0.1079 time to fit residues: 18.6173 Evaluate side-chains 73 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3004 CYS Chi-restraints excluded: chain A residue 3037 ARG Chi-restraints excluded: chain A residue 3122 HIS Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 221 CYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 298 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 98 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 50.0000 chunk 179 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 0.0370 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 133 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.068668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.049461 restraints weight = 131365.120| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 6.55 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15950 Z= 0.116 Angle : 0.584 11.936 21873 Z= 0.293 Chirality : 0.041 0.219 2627 Planarity : 0.005 0.094 2871 Dihedral : 4.064 19.330 2366 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.02 % Favored : 93.71 % Rotamer: Outliers : 2.64 % Allowed : 25.36 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 2226 helix: 1.96 (0.20), residues: 750 sheet: -0.46 (0.21), residues: 615 loop : -1.87 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 288 TYR 0.012 0.001 TYR D 143 PHE 0.023 0.001 PHE A2632 TRP 0.015 0.001 TRP A2684 HIS 0.007 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00274 (15950) covalent geometry : angle 0.58449 (21873) hydrogen bonds : bond 0.03106 ( 820) hydrogen bonds : angle 4.55110 ( 2283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.698 Fit side-chains REVERT: A 2711 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: A 3341 LEU cc_start: 0.9751 (tt) cc_final: 0.9425 (pp) REVERT: B 323 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8489 (m) REVERT: C 22 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: D 259 MET cc_start: 0.9119 (mmp) cc_final: 0.8826 (mmp) outliers start: 33 outliers final: 17 residues processed: 83 average time/residue: 0.1018 time to fit residues: 14.6563 Evaluate side-chains 70 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 110 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3091 ASN D 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.068420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.048754 restraints weight = 130460.972| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 6.36 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15950 Z= 0.139 Angle : 0.575 11.338 21873 Z= 0.287 Chirality : 0.041 0.207 2627 Planarity : 0.005 0.092 2871 Dihedral : 3.986 18.619 2366 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.65 % Favored : 93.08 % Rotamer: Outliers : 3.76 % Allowed : 25.04 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 2226 helix: 2.06 (0.20), residues: 748 sheet: -0.46 (0.21), residues: 626 loop : -1.83 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 279 TYR 0.011 0.001 TYR D 143 PHE 0.022 0.001 PHE A2632 TRP 0.013 0.001 TRP A2684 HIS 0.006 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00324 (15950) covalent geometry : angle 0.57482 (21873) hydrogen bonds : bond 0.02998 ( 820) hydrogen bonds : angle 4.40752 ( 2283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 50 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 2530 MET cc_start: 0.9057 (tmm) cc_final: 0.8531 (tmm) REVERT: A 2711 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: A 3341 LEU cc_start: 0.9759 (tt) cc_final: 0.9491 (pp) REVERT: B 323 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8536 (m) REVERT: C 22 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.6790 (m-10) REVERT: D 259 MET cc_start: 0.9170 (mmp) cc_final: 0.8943 (mmp) outliers start: 47 outliers final: 29 residues processed: 95 average time/residue: 0.0928 time to fit residues: 15.1476 Evaluate side-chains 81 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 49 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3104 LEU Chi-restraints excluded: chain A residue 3122 HIS Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3319 ILE Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain A residue 3429 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 191 optimal weight: 0.0050 chunk 202 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 115 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.068818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.049246 restraints weight = 130044.863| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 6.04 r_work: 0.3213 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15950 Z= 0.109 Angle : 0.555 11.052 21873 Z= 0.276 Chirality : 0.041 0.207 2627 Planarity : 0.005 0.090 2871 Dihedral : 3.851 17.773 2366 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.66 % Favored : 94.07 % Rotamer: Outliers : 3.44 % Allowed : 25.44 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 2226 helix: 2.12 (0.20), residues: 754 sheet: -0.32 (0.21), residues: 617 loop : -1.76 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3392 TYR 0.009 0.001 TYR D 143 PHE 0.021 0.001 PHE A2632 TRP 0.038 0.001 TRP D 207 HIS 0.006 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00263 (15950) covalent geometry : angle 0.55478 (21873) hydrogen bonds : bond 0.02767 ( 820) hydrogen bonds : angle 4.24648 ( 2283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 51 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 2530 MET cc_start: 0.9132 (tmm) cc_final: 0.8644 (tmm) REVERT: A 2711 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6579 (m-80) REVERT: A 3341 LEU cc_start: 0.9739 (tt) cc_final: 0.9487 (pp) REVERT: A 3391 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8685 (p90) REVERT: B 323 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8750 (m) REVERT: B 408 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7842 (tt) REVERT: C 22 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7219 (m-10) REVERT: D 259 MET cc_start: 0.9178 (mmp) cc_final: 0.8913 (mmp) outliers start: 43 outliers final: 26 residues processed: 92 average time/residue: 0.1082 time to fit residues: 16.7436 Evaluate side-chains 80 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain A residue 3429 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 142 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3007 GLN B 115 GLN B 426 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.065193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.047155 restraints weight = 142887.230| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 5.96 r_work: 0.3150 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 15950 Z= 0.327 Angle : 0.726 10.333 21873 Z= 0.363 Chirality : 0.044 0.208 2627 Planarity : 0.005 0.089 2871 Dihedral : 4.416 22.550 2366 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.27 % Favored : 91.51 % Rotamer: Outliers : 5.44 % Allowed : 24.24 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.18), residues: 2226 helix: 1.85 (0.19), residues: 745 sheet: -0.78 (0.21), residues: 634 loop : -1.93 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A3037 TYR 0.018 0.002 TYR B 48 PHE 0.029 0.002 PHE A2632 TRP 0.027 0.002 TRP D 207 HIS 0.011 0.002 HIS A2848 Details of bonding type rmsd covalent geometry : bond 0.00732 (15950) covalent geometry : angle 0.72632 (21873) hydrogen bonds : bond 0.03799 ( 820) hydrogen bonds : angle 4.73912 ( 2283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 48 time to evaluate : 0.620 Fit side-chains REVERT: A 2530 MET cc_start: 0.9238 (tmm) cc_final: 0.8790 (tmm) REVERT: A 2711 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6574 (m-80) REVERT: A 3341 LEU cc_start: 0.9764 (tt) cc_final: 0.9532 (pp) REVERT: A 3391 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8567 (p90) REVERT: A 3393 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: C 22 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: D 174 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8291 (mtm110) REVERT: D 259 MET cc_start: 0.9200 (mmp) cc_final: 0.8955 (mmp) outliers start: 68 outliers final: 38 residues processed: 115 average time/residue: 0.1044 time to fit residues: 19.8818 Evaluate side-chains 92 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 49 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3004 CYS Chi-restraints excluded: chain A residue 3122 HIS Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3319 ILE Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3393 GLU Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain A residue 3429 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 298 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 70.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.067795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048551 restraints weight = 130426.680| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 6.01 r_work: 0.3170 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15950 Z= 0.179 Angle : 0.614 10.353 21873 Z= 0.307 Chirality : 0.042 0.208 2627 Planarity : 0.005 0.087 2871 Dihedral : 4.214 21.551 2366 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.51 % Favored : 93.26 % Rotamer: Outliers : 3.36 % Allowed : 26.40 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 2226 helix: 1.98 (0.20), residues: 746 sheet: -0.66 (0.21), residues: 616 loop : -1.85 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 288 TYR 0.012 0.001 TYR A3047 PHE 0.023 0.001 PHE A2632 TRP 0.021 0.001 TRP D 207 HIS 0.009 0.001 HIS A2848 Details of bonding type rmsd covalent geometry : bond 0.00409 (15950) covalent geometry : angle 0.61400 (21873) hydrogen bonds : bond 0.03221 ( 820) hydrogen bonds : angle 4.51535 ( 2283) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 50 time to evaluate : 0.742 Fit side-chains REVERT: A 2530 MET cc_start: 0.9241 (tmm) cc_final: 0.8710 (tmm) REVERT: A 2711 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: A 3123 MET cc_start: 0.8649 (mmp) cc_final: 0.7641 (mmp) REVERT: A 3341 LEU cc_start: 0.9774 (tt) cc_final: 0.9547 (pp) REVERT: C 22 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: D 259 MET cc_start: 0.9210 (mmp) cc_final: 0.8952 (mmp) outliers start: 42 outliers final: 34 residues processed: 91 average time/residue: 0.1008 time to fit residues: 16.0173 Evaluate side-chains 85 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 49 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2592 SER Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3104 LEU Chi-restraints excluded: chain A residue 3122 HIS Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3319 ILE Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain A residue 3429 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 188 optimal weight: 0.1980 chunk 173 optimal weight: 0.9990 chunk 193 optimal weight: 50.0000 chunk 169 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 83 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3007 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.068468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.049425 restraints weight = 130482.497| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 6.43 r_work: 0.3189 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15950 Z= 0.116 Angle : 0.571 10.195 21873 Z= 0.284 Chirality : 0.041 0.206 2627 Planarity : 0.005 0.085 2871 Dihedral : 3.962 18.921 2366 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.15 % Favored : 93.62 % Rotamer: Outliers : 2.88 % Allowed : 26.08 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 2226 helix: 2.03 (0.20), residues: 755 sheet: -0.43 (0.21), residues: 608 loop : -1.77 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3037 TYR 0.011 0.001 TYR D 143 PHE 0.018 0.001 PHE A2632 TRP 0.017 0.001 TRP A2684 HIS 0.007 0.001 HIS A2848 Details of bonding type rmsd covalent geometry : bond 0.00276 (15950) covalent geometry : angle 0.57135 (21873) hydrogen bonds : bond 0.02834 ( 820) hydrogen bonds : angle 4.31194 ( 2283) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 50 time to evaluate : 0.672 Fit side-chains REVERT: A 2530 MET cc_start: 0.9233 (tmm) cc_final: 0.8716 (tmm) REVERT: A 2711 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: A 3341 LEU cc_start: 0.9775 (tt) cc_final: 0.9556 (pp) REVERT: A 3391 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8842 (p90) REVERT: B 199 MET cc_start: 0.8621 (ptp) cc_final: 0.8143 (pmm) REVERT: B 323 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8775 (m) REVERT: C 22 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7283 (m-10) REVERT: D 259 MET cc_start: 0.9219 (mmp) cc_final: 0.8926 (mmp) outliers start: 36 outliers final: 27 residues processed: 85 average time/residue: 0.1036 time to fit residues: 15.2450 Evaluate side-chains 80 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2592 SER Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3104 LEU Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3319 ILE Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain A residue 3429 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 97 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.067953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.048912 restraints weight = 131053.621| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 6.51 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15950 Z= 0.179 Angle : 0.602 10.112 21873 Z= 0.300 Chirality : 0.041 0.205 2627 Planarity : 0.005 0.084 2871 Dihedral : 4.067 21.256 2366 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.05 % Favored : 92.77 % Rotamer: Outliers : 2.96 % Allowed : 25.92 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 2226 helix: 2.13 (0.20), residues: 746 sheet: -0.49 (0.21), residues: 621 loop : -1.73 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 174 TYR 0.010 0.001 TYR B 48 PHE 0.023 0.001 PHE A2632 TRP 0.015 0.001 TRP D 207 HIS 0.007 0.001 HIS A2848 Details of bonding type rmsd covalent geometry : bond 0.00411 (15950) covalent geometry : angle 0.60195 (21873) hydrogen bonds : bond 0.03090 ( 820) hydrogen bonds : angle 4.36550 ( 2283) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 0.644 Fit side-chains REVERT: A 2530 MET cc_start: 0.9157 (tmm) cc_final: 0.8630 (tmm) REVERT: A 2711 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: A 3123 MET cc_start: 0.8674 (mmp) cc_final: 0.7694 (mmp) REVERT: A 3341 LEU cc_start: 0.9776 (tt) cc_final: 0.9543 (pp) REVERT: A 3391 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8531 (p90) REVERT: C 22 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6883 (m-10) REVERT: D 259 MET cc_start: 0.9257 (mmp) cc_final: 0.8988 (mmp) REVERT: D 286 MET cc_start: 0.5073 (tpt) cc_final: 0.4542 (tpt) outliers start: 37 outliers final: 32 residues processed: 86 average time/residue: 0.1007 time to fit residues: 15.0054 Evaluate side-chains 84 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 49 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2592 SER Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3104 LEU Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3319 ILE Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain A residue 3429 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 21 optimal weight: 30.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.068316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.048779 restraints weight = 129264.406| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 6.43 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15950 Z= 0.130 Angle : 0.575 10.088 21873 Z= 0.286 Chirality : 0.041 0.206 2627 Planarity : 0.005 0.082 2871 Dihedral : 3.955 19.760 2366 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.11 % Favored : 93.71 % Rotamer: Outliers : 2.72 % Allowed : 26.32 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 2226 helix: 2.10 (0.20), residues: 752 sheet: -0.36 (0.21), residues: 613 loop : -1.69 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3392 TYR 0.009 0.001 TYR D 143 PHE 0.019 0.001 PHE A2632 TRP 0.016 0.001 TRP A2684 HIS 0.006 0.001 HIS A2848 Details of bonding type rmsd covalent geometry : bond 0.00307 (15950) covalent geometry : angle 0.57450 (21873) hydrogen bonds : bond 0.02874 ( 820) hydrogen bonds : angle 4.27757 ( 2283) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 49 time to evaluate : 0.724 Fit side-chains REVERT: A 2530 MET cc_start: 0.9115 (tmm) cc_final: 0.8566 (tmm) REVERT: A 2711 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: A 3123 MET cc_start: 0.8647 (mmp) cc_final: 0.7671 (mmp) REVERT: A 3341 LEU cc_start: 0.9778 (tt) cc_final: 0.9546 (pp) REVERT: A 3391 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8653 (p90) REVERT: B 323 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8562 (m) REVERT: C 22 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6767 (m-10) REVERT: D 259 MET cc_start: 0.9221 (mmp) cc_final: 0.8969 (mmp) REVERT: D 286 MET cc_start: 0.5216 (tpt) cc_final: 0.4588 (tpt) outliers start: 34 outliers final: 29 residues processed: 82 average time/residue: 0.1001 time to fit residues: 14.3614 Evaluate side-chains 82 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 49 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2384 ASP Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2548 MET Chi-restraints excluded: chain A residue 2711 PHE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3194 VAL Chi-restraints excluded: chain A residue 3319 ILE Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3414 HIS Chi-restraints excluded: chain A residue 3429 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 32 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 162 optimal weight: 0.0970 chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 207 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.068558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.049022 restraints weight = 128850.396| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 6.46 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15950 Z= 0.114 Angle : 0.568 10.841 21873 Z= 0.281 Chirality : 0.041 0.204 2627 Planarity : 0.005 0.081 2871 Dihedral : 3.813 18.626 2366 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 2.72 % Allowed : 26.56 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 2226 helix: 2.18 (0.20), residues: 758 sheet: -0.35 (0.21), residues: 622 loop : -1.57 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3037 TYR 0.013 0.001 TYR D 147 PHE 0.019 0.001 PHE A2632 TRP 0.016 0.001 TRP A2684 HIS 0.006 0.001 HIS A2848 Details of bonding type rmsd covalent geometry : bond 0.00273 (15950) covalent geometry : angle 0.56830 (21873) hydrogen bonds : bond 0.02702 ( 820) hydrogen bonds : angle 4.14115 ( 2283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9934.20 seconds wall clock time: 169 minutes 0.22 seconds (10140.22 seconds total)