Starting phenix.real_space_refine on Thu Feb 5 02:34:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v86_64831/02_2026/9v86_64831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v86_64831/02_2026/9v86_64831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v86_64831/02_2026/9v86_64831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v86_64831/02_2026/9v86_64831.map" model { file = "/net/cci-nas-00/data/ceres_data/9v86_64831/02_2026/9v86_64831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v86_64831/02_2026/9v86_64831.cif" } resolution = 3.04 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= 0.022 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 65 5.16 5 C 9060 2.51 5 N 2476 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 14073 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 5752 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'PTRANS': 46, 'TRANS': 768} Chain breaks: 17 Unresolved non-hydrogen bonds: 835 Unresolved non-hydrogen angles: 1061 Unresolved non-hydrogen dihedrals: 669 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'HIS:plan': 7, 'ARG:plan': 26, 'TRP:plan': 3, 'TYR:plan': 3, 'GLN:plan1': 17, 'ASN:plan1': 6, 'PHE:plan': 8, 'ASP:plan': 15, 'GLU:plan': 31} Unresolved non-hydrogen planarities: 516 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2818 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 4 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 4, 'GLN:plan1': 4, 'ASP:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2910 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 12, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 154 Chain: "D" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2593 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 17, 'TRANS': 381} Chain breaks: 3 Unresolved non-hydrogen bonds: 651 Unresolved non-hydrogen angles: 820 Unresolved non-hydrogen dihedrals: 544 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 12, 'GLU:plan': 18, 'PHE:plan': 6, 'HIS:plan': 6, 'TYR:plan': 8, 'ASP:plan': 10, 'ASN:plan1': 7, 'ARG:plan': 11, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 366 Time building chain proxies: 2.55, per 1000 atoms: 0.18 Number of scatterers: 14073 At special positions: 0 Unit cell: (102.85, 127.5, 254.15, 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 65 16.00 O 2472 8.00 N 2476 7.00 C 9060 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: 0.96 Conformation dependent library (CDL) restraints added in 718.0 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 22 sheets defined 34.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 2227 through 2231 removed outlier: 3.920A pdb=" N CYS A2230 " --> pdb=" O PRO A2227 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2249 removed outlier: 3.530A pdb=" N GLN A2243 " --> pdb=" O TRP A2239 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A2247 " --> pdb=" O GLN A2243 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A2248 " --> pdb=" O ASN A2244 " (cutoff:3.500A) Processing helix chain 'A' and resid 2330 through 2334 Processing helix chain 'A' and resid 2366 through 2391 Processing helix chain 'A' and resid 2500 through 2512 Processing helix chain 'A' and resid 2524 through 2533 Processing helix chain 'A' and resid 2554 through 2569 removed outlier: 3.903A pdb=" N SER A2559 " --> pdb=" O PRO A2555 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU A2560 " --> pdb=" O SER A2556 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A2562 " --> pdb=" O LEU A2558 " (cutoff:3.500A) Processing helix chain 'A' and resid 2667 through 2688 Processing helix chain 'A' and resid 2690 through 2695 Processing helix chain 'A' and resid 2697 through 2701 Processing helix chain 'A' and resid 2728 through 2732 Processing helix chain 'A' and resid 2763 through 2767 removed outlier: 3.519A pdb=" N GLU A2766 " --> pdb=" O PRO A2763 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A2767 " --> pdb=" O PHE A2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2763 through 2767' Processing helix chain 'A' and resid 2789 through 2794 removed outlier: 3.708A pdb=" N GLY A2794 " --> pdb=" O VAL A2790 " (cutoff:3.500A) Processing helix chain 'A' and resid 2794 through 2814 removed outlier: 3.567A pdb=" N ARG A2805 " --> pdb=" O LYS A2801 " (cutoff:3.500A) Processing helix chain 'A' and resid 2815 through 2823 removed outlier: 3.679A pdb=" N VAL A2819 " --> pdb=" O GLU A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2833 through 2843 Processing helix chain 'A' and resid 2857 through 2861 Processing helix chain 'A' and resid 2908 through 2926 Processing helix chain 'A' and resid 3027 through 3039 Processing helix chain 'A' and resid 3041 through 3060 Processing helix chain 'A' and resid 3070 through 3082 Processing helix chain 'A' and resid 3106 through 3117 Processing helix chain 'A' and resid 3118 through 3122 removed outlier: 3.652A pdb=" N HIS A3122 " --> pdb=" O SER A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3181 through 3185 Processing helix chain 'A' and resid 3248 through 3283 removed outlier: 3.738A pdb=" N MET A3257 " --> pdb=" O ALA A3253 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY A3271 " --> pdb=" O ARG A3267 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A3272 " --> pdb=" O LEU A3268 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A3276 " --> pdb=" O HIS A3272 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A3278 " --> pdb=" O ARG A3274 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A3279 " --> pdb=" O ARG A3275 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS A3280 " --> pdb=" O ASP A3276 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A3281 " --> pdb=" O THR A3277 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A3283 " --> pdb=" O TRP A3279 " (cutoff:3.500A) Processing helix chain 'A' and resid 3301 through 3309 removed outlier: 3.586A pdb=" N LEU A3307 " --> pdb=" O GLU A3303 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A3308 " --> pdb=" O LEU A3304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A3309 " --> pdb=" O GLU A3305 " (cutoff:3.500A) Processing helix chain 'A' and resid 3317 through 3319 No H-bonds generated for 'chain 'A' and resid 3317 through 3319' Processing helix chain 'A' and resid 3320 through 3329 removed outlier: 4.080A pdb=" N CYS A3325 " --> pdb=" O GLN A3322 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET A3329 " --> pdb=" O PHE A3326 " (cutoff:3.500A) Processing helix chain 'A' and resid 3330 through 3345 removed outlier: 3.669A pdb=" N TYR A3334 " --> pdb=" O THR A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3410 through 3430 removed outlier: 4.279A pdb=" N HIS A3414 " --> pdb=" O VAL A3410 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N HIS A3415 " --> pdb=" O SER A3411 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A3416 " --> pdb=" O THR A3412 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A3420 " --> pdb=" O LEU A3416 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A3425 " --> pdb=" O ASN A3421 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 412 removed outlier: 4.191A pdb=" N HIS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 431 Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 396 through 419 Processing helix chain 'D' and resid 13 through 24 removed outlier: 4.089A pdb=" N VAL D 17 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 removed outlier: 3.698A pdb=" N ASN D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 71 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 121 through 150 removed outlier: 4.012A pdb=" N LEU D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 172 removed outlier: 3.803A pdb=" N LEU D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ALA D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 206 removed outlier: 4.067A pdb=" N LEU D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 227 removed outlier: 4.153A pdb=" N THR D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TRP D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 273 removed outlier: 3.521A pdb=" N TYR D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 277 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.711A pdb=" N ILE D 301 " --> pdb=" O PHE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 363 through 371 removed outlier: 4.275A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 378 Processing helix chain 'D' and resid 416 through 431 removed outlier: 4.322A pdb=" N ILE D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 422 " --> pdb=" O HIS D 418 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 438 Processing sheet with id=AA1, first strand: chain 'A' and resid 2278 through 2281 Processing sheet with id=AA2, first strand: chain 'A' and resid 2588 through 2589 removed outlier: 4.155A pdb=" N PHE A2577 " --> pdb=" O LEU A2609 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2653 through 2654 removed outlier: 3.513A pdb=" N GLU A2653 " --> pdb=" O GLN A2660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2845 through 2853 removed outlier: 5.657A pdb=" N LEU A2846 " --> pdb=" O ALA A3009 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A3009 " --> pdb=" O LEU A2846 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS A2848 " --> pdb=" O GLN A3007 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3092 through 3100 Processing sheet with id=AA6, first strand: chain 'A' and resid 3127 through 3128 removed outlier: 3.592A pdb=" N GLU A3138 " --> pdb=" O MET A3128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3312 through 3315 removed outlier: 3.566A pdb=" N PHE A3377 " --> pdb=" O SER A3386 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A3388 " --> pdb=" O LEU A3375 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A3362 " --> pdb=" O VAL A3376 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A3378 " --> pdb=" O GLN A3360 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A3363 " --> pdb=" O ARG A3350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.634A pdb=" N ARG B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLN B 345 " --> pdb=" O ARG B 2 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.860A pdb=" N LYS B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER B 366 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 357 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS B 368 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA B 355 " --> pdb=" O CYS B 368 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 370 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE B 353 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 372 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AB2, first strand: chain 'B' and resid 65 through 71 removed outlier: 4.460A pdb=" N TRP B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 92 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 119 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 127 through 133 removed outlier: 3.703A pdb=" N VAL B 129 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 152 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 176 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 154 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AB5, first strand: chain 'B' and resid 256 through 259 removed outlier: 3.897A pdb=" N THR B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU B 289 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU B 297 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 14 through 21 removed outlier: 6.901A pdb=" N ILE C 392 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE C 19 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C 390 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU C 381 " --> pdb=" O HIS C 371 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS C 371 " --> pdb=" O GLU C 381 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA C 383 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET C 369 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 385 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.794A pdb=" N LEU C 42 " --> pdb=" O ALA C 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 79 through 87 removed outlier: 5.695A pdb=" N ILE C 80 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE C 102 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 145 through 153 removed outlier: 3.822A pdb=" N GLN C 145 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N THR C 159 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLU C 175 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 172 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.711A pdb=" N TRP C 203 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP C 232 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL C 238 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 250 through 257 removed outlier: 3.602A pdb=" N ARG C 252 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 310 through 316 removed outlier: 6.177A pdb=" N LYS C 339 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU C 356 " --> pdb=" O LYS C 339 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 348 through 351 removed outlier: 6.728A pdb=" N ALA D 348 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N PHE D 317 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL D 350 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN D 312 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 396 " --> pdb=" O ILE D 404 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1908 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: 2.24 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4659 1.34 - 1.46: 3198 1.46 - 1.58: 6434 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 14391 Sorted by residual: bond pdb=" C ARG A2620 " pdb=" N PRO A2621 " ideal model delta sigma weight residual 1.335 1.370 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" C PRO A3249 " pdb=" N PRO A3250 " ideal model delta sigma weight residual 1.335 1.368 -0.032 1.36e-02 5.41e+03 5.68e+00 bond pdb=" C ALA D 276 " pdb=" N LEU D 277 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.52e-02 4.33e+03 3.63e+00 bond pdb=" CA LEU D 375 " pdb=" C LEU D 375 " ideal model delta sigma weight residual 1.522 1.499 0.024 1.40e-02 5.10e+03 2.83e+00 bond pdb=" CB PRO D 178 " pdb=" CG PRO D 178 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.75e+00 ... (remaining 14386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 19306 2.28 - 4.55: 325 4.55 - 6.83: 43 6.83 - 9.10: 9 9.10 - 11.38: 3 Bond angle restraints: 19686 Sorted by residual: angle pdb=" N ILE D 365 " pdb=" CA ILE D 365 " pdb=" C ILE D 365 " ideal model delta sigma weight residual 112.90 106.46 6.44 9.60e-01 1.09e+00 4.50e+01 angle pdb=" N ILE A2733 " pdb=" CA ILE A2733 " pdb=" C ILE A2733 " ideal model delta sigma weight residual 112.90 107.42 5.48 9.60e-01 1.09e+00 3.26e+01 angle pdb=" N ASP A3356 " pdb=" CA ASP A3356 " pdb=" C ASP A3356 " ideal model delta sigma weight residual 114.64 106.67 7.97 1.52e+00 4.33e-01 2.75e+01 angle pdb=" N VAL D 389 " pdb=" CA VAL D 389 " pdb=" C VAL D 389 " ideal model delta sigma weight residual 113.71 109.12 4.59 9.50e-01 1.11e+00 2.33e+01 angle pdb=" N VAL D 364 " pdb=" CA VAL D 364 " pdb=" C VAL D 364 " ideal model delta sigma weight residual 113.39 107.38 6.01 1.47e+00 4.63e-01 1.67e+01 ... (remaining 19681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7376 17.83 - 35.67: 788 35.67 - 53.50: 195 53.50 - 71.34: 40 71.34 - 89.17: 17 Dihedral angle restraints: 8416 sinusoidal: 2646 harmonic: 5770 Sorted by residual: dihedral pdb=" CA SER D 150 " pdb=" C SER D 150 " pdb=" N THR D 151 " pdb=" CA THR D 151 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU A2581 " pdb=" C LEU A2581 " pdb=" N GLY A2582 " pdb=" CA GLY A2582 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA HIS A2690 " pdb=" C HIS A2690 " pdb=" N LEU A2691 " pdb=" CA LEU A2691 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1652 0.039 - 0.078: 492 0.078 - 0.117: 161 0.117 - 0.156: 23 0.156 - 0.195: 5 Chirality restraints: 2333 Sorted by residual: chirality pdb=" CA PRO D 178 " pdb=" N PRO D 178 " pdb=" C PRO D 178 " pdb=" CB PRO D 178 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA PRO A3399 " pdb=" N PRO A3399 " pdb=" C PRO A3399 " pdb=" CB PRO A3399 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CA PRO A2719 " pdb=" N PRO A2719 " pdb=" C PRO A2719 " pdb=" CB PRO A2719 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.65e-01 ... (remaining 2330 not shown) Planarity restraints: 2546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A3398 " -0.073 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A3399 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A3399 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A3399 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 177 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 178 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 178 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 178 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A2718 " -0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO A2719 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A2719 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A2719 " -0.052 5.00e-02 4.00e+02 ... (remaining 2543 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 344 2.69 - 3.24: 13186 3.24 - 3.80: 21693 3.80 - 4.35: 26375 4.35 - 4.90: 45085 Nonbonded interactions: 106683 Sorted by model distance: nonbonded pdb=" OG1 THR B 280 " pdb=" OD1 ASP B 282 " model vdw 2.140 3.040 nonbonded pdb=" OE1 GLN C 246 " pdb=" OH TYR C 287 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR B 207 " pdb=" OD2 ASP B 295 " model vdw 2.190 3.040 nonbonded pdb=" NE ARG A2631 " pdb=" O TRP A2666 " model vdw 2.213 3.120 nonbonded pdb=" O MET A2812 " pdb=" ND2 ASN A2816 " model vdw 2.244 3.120 ... (remaining 106678 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: 11.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 14391 Z= 0.174 Angle : 0.741 11.379 19686 Z= 0.424 Chirality : 0.042 0.195 2333 Planarity : 0.006 0.110 2546 Dihedral : 16.728 89.171 4656 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.25 % Favored : 92.29 % Rotamer: Outliers : 3.72 % Allowed : 27.91 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.20), residues: 1932 helix: 0.79 (0.22), residues: 605 sheet: -0.37 (0.24), residues: 522 loop : -2.15 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 227 TYR 0.020 0.001 TYR A2664 PHE 0.015 0.001 PHE A3425 TRP 0.024 0.002 TRP D 361 HIS 0.004 0.001 HIS D 217 Details of bonding type rmsd covalent geometry : bond 0.00346 (14391) covalent geometry : angle 0.74084 (19686) hydrogen bonds : bond 0.18415 ( 693) hydrogen bonds : angle 6.97541 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2697 SER cc_start: 0.7078 (m) cc_final: 0.6498 (p) REVERT: B 8 GLN cc_start: 0.2621 (mp10) cc_final: 0.2391 (pp30) REVERT: B 45 VAL cc_start: 0.5891 (OUTLIER) cc_final: 0.5601 (t) REVERT: B 285 LEU cc_start: 0.5255 (mt) cc_final: 0.3825 (mt) REVERT: B 332 THR cc_start: 0.2593 (m) cc_final: 0.2144 (p) REVERT: B 335 ILE cc_start: 0.5451 (mt) cc_final: 0.4797 (mt) REVERT: B 354 CYS cc_start: 0.3607 (t) cc_final: 0.2932 (p) REVERT: B 429 LEU cc_start: 0.6616 (mt) cc_final: 0.6139 (tp) REVERT: B 430 TYR cc_start: 0.1639 (m-80) cc_final: 0.1232 (m-80) REVERT: C 95 LEU cc_start: 0.6291 (tp) cc_final: 0.5888 (tt) REVERT: C 125 TYR cc_start: 0.7292 (m-80) cc_final: 0.6545 (t80) REVERT: C 151 VAL cc_start: 0.6253 (m) cc_final: 0.5733 (p) REVERT: C 161 PHE cc_start: 0.0861 (OUTLIER) cc_final: 0.0657 (m-80) REVERT: C 172 LEU cc_start: 0.7780 (tt) cc_final: 0.7478 (tt) REVERT: C 209 PHE cc_start: 0.0202 (m-10) cc_final: -0.0289 (m-10) REVERT: C 231 VAL cc_start: 0.7880 (t) cc_final: 0.7401 (p) REVERT: C 232 ASP cc_start: 0.6898 (t70) cc_final: 0.6481 (m-30) REVERT: C 311 LEU cc_start: 0.7483 (mp) cc_final: 0.7223 (mt) REVERT: C 319 ASP cc_start: 0.3990 (m-30) cc_final: 0.3538 (m-30) REVERT: C 328 VAL cc_start: 0.6164 (t) cc_final: 0.5491 (m) REVERT: C 373 ASP cc_start: 0.1822 (t0) cc_final: 0.1398 (t70) REVERT: C 382 LEU cc_start: 0.6082 (tp) cc_final: 0.5572 (tp) REVERT: C 384 VAL cc_start: 0.5424 (t) cc_final: 0.4709 (m) outliers start: 45 outliers final: 8 residues processed: 295 average time/residue: 0.1084 time to fit residues: 47.6981 Evaluate side-chains 160 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2700 LEU Chi-restraints excluded: chain A residue 2979 THR Chi-restraints excluded: chain A residue 3058 VAL Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3365 LEU Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3427 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain D residue 386 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2816 ASN ** A2982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3091 ASN B 75 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS B 405 HIS B 426 HIS C 207 HIS C 222 GLN C 399 GLN D 220 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.095907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.075194 restraints weight = 78216.381| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 5.05 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 14391 Z= 0.229 Angle : 0.826 10.333 19686 Z= 0.420 Chirality : 0.048 0.235 2333 Planarity : 0.007 0.109 2546 Dihedral : 5.714 54.375 2088 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.76 % Favored : 91.77 % Rotamer: Outliers : 6.85 % Allowed : 24.94 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1932 helix: 0.95 (0.21), residues: 596 sheet: -0.37 (0.23), residues: 519 loop : -2.30 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 214 TYR 0.025 0.003 TYR A3334 PHE 0.046 0.003 PHE A3326 TRP 0.022 0.002 TRP B 328 HIS 0.016 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00497 (14391) covalent geometry : angle 0.82640 (19686) hydrogen bonds : bond 0.04411 ( 693) hydrogen bonds : angle 5.32944 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 149 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2709 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8866 (pp) REVERT: A 2710 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7265 (t0) REVERT: A 2996 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8451 (mt) REVERT: A 3308 LEU cc_start: 0.8501 (pp) cc_final: 0.8240 (mp) REVERT: A 3414 HIS cc_start: 0.9128 (m-70) cc_final: 0.8916 (m90) REVERT: B 92 LEU cc_start: 0.6982 (mt) cc_final: 0.6749 (tt) REVERT: C 161 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: C 258 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6516 (mt) REVERT: C 377 ASP cc_start: 0.6496 (p0) cc_final: 0.6070 (m-30) REVERT: D 206 GLU cc_start: 0.8842 (pp20) cc_final: 0.8607 (mm-30) REVERT: D 285 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7201 (tm-30) REVERT: D 286 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8268 (ptp) REVERT: D 363 ASN cc_start: 0.8264 (t0) cc_final: 0.7881 (t0) REVERT: D 368 MET cc_start: 0.1355 (tpt) cc_final: 0.0700 (tpt) outliers start: 83 outliers final: 30 residues processed: 217 average time/residue: 0.0992 time to fit residues: 32.8468 Evaluate side-chains 145 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2700 LEU Chi-restraints excluded: chain A residue 2709 LEU Chi-restraints excluded: chain A residue 2710 ASP Chi-restraints excluded: chain A residue 2846 LEU Chi-restraints excluded: chain A residue 2849 TYR Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3389 VAL Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 386 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 118 optimal weight: 0.5980 chunk 110 optimal weight: 0.0870 chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 0.2980 chunk 108 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2982 HIS A3091 ASN ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3414 HIS C 233 GLN C 395 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.094620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.073738 restraints weight = 77004.247| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 4.79 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14391 Z= 0.129 Angle : 0.645 9.964 19686 Z= 0.320 Chirality : 0.042 0.193 2333 Planarity : 0.006 0.107 2546 Dihedral : 4.820 52.983 2081 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.80 % Favored : 93.74 % Rotamer: Outliers : 4.21 % Allowed : 25.27 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.20), residues: 1932 helix: 1.52 (0.22), residues: 611 sheet: -0.29 (0.23), residues: 539 loop : -2.12 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2528 TYR 0.015 0.001 TYR A3334 PHE 0.020 0.001 PHE D 22 TRP 0.014 0.001 TRP C 358 HIS 0.005 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00303 (14391) covalent geometry : angle 0.64502 (19686) hydrogen bonds : bond 0.03522 ( 693) hydrogen bonds : angle 4.72017 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 117 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2709 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8904 (pp) REVERT: A 2710 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7198 (t0) REVERT: A 3308 LEU cc_start: 0.8456 (pp) cc_final: 0.8159 (mp) REVERT: A 3334 TYR cc_start: 0.8854 (m-80) cc_final: 0.8576 (m-80) REVERT: A 3414 HIS cc_start: 0.9125 (m90) cc_final: 0.8896 (m90) REVERT: B 64 MET cc_start: 0.5201 (tmm) cc_final: 0.4999 (tmm) REVERT: C 232 ASP cc_start: 0.6713 (t0) cc_final: 0.6472 (t0) REVERT: C 258 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6812 (mt) REVERT: C 319 ASP cc_start: 0.4639 (m-30) cc_final: 0.4365 (m-30) REVERT: D 259 MET cc_start: 0.9277 (mmm) cc_final: 0.8675 (mmm) REVERT: D 285 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 286 MET cc_start: 0.8879 (ttt) cc_final: 0.7858 (ptm) REVERT: D 287 LYS cc_start: 0.9559 (mmtt) cc_final: 0.9184 (mmmt) REVERT: D 411 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8278 (tppt) outliers start: 51 outliers final: 28 residues processed: 157 average time/residue: 0.0879 time to fit residues: 22.1979 Evaluate side-chains 137 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2700 LEU Chi-restraints excluded: chain A residue 2709 LEU Chi-restraints excluded: chain A residue 2710 ASP Chi-restraints excluded: chain A residue 2830 MET Chi-restraints excluded: chain A residue 3004 CYS Chi-restraints excluded: chain A residue 3059 LEU Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3356 ASP Chi-restraints excluded: chain A residue 3364 VAL Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 313 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.0030 chunk 131 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 190 optimal weight: 40.0000 chunk 55 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2704 HIS A2999 GLN A3091 ASN A3146 HIS ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 233 GLN D 60 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.084163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.060849 restraints weight = 73174.654| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.12 r_work: 0.3350 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.8417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 14391 Z= 0.320 Angle : 0.888 12.086 19686 Z= 0.460 Chirality : 0.051 0.391 2333 Planarity : 0.007 0.104 2546 Dihedral : 5.950 48.832 2079 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.95 % Favored : 90.58 % Rotamer: Outliers : 6.11 % Allowed : 25.35 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1932 helix: 1.06 (0.22), residues: 603 sheet: -0.62 (0.22), residues: 540 loop : -2.28 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 215 TYR 0.055 0.003 TYR B 358 PHE 0.029 0.003 PHE B 374 TRP 0.043 0.002 TRP B 382 HIS 0.012 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00734 (14391) covalent geometry : angle 0.88788 (19686) hydrogen bonds : bond 0.05194 ( 693) hydrogen bonds : angle 5.59259 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 109 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3414 HIS cc_start: 0.9130 (m90) cc_final: 0.8899 (m90) REVERT: B 67 CYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7253 (m) REVERT: B 382 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.8055 (p90) REVERT: D 259 MET cc_start: 0.9455 (mmm) cc_final: 0.8864 (mmm) REVERT: D 363 ASN cc_start: 0.7570 (t0) cc_final: 0.7029 (p0) REVERT: D 411 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7321 (mmmt) outliers start: 74 outliers final: 40 residues processed: 171 average time/residue: 0.1064 time to fit residues: 27.9688 Evaluate side-chains 130 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2799 GLU Chi-restraints excluded: chain A residue 2846 LEU Chi-restraints excluded: chain A residue 2849 TYR Chi-restraints excluded: chain A residue 2850 CYS Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3364 VAL Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3389 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3421 ASN Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 TRP 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 350 ILE Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 182 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2999 GLN A3091 ASN ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 349 ASN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.084084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.060339 restraints weight = 72862.678| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.09 r_work: 0.3318 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.8538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 14391 Z= 0.151 Angle : 0.677 13.312 19686 Z= 0.336 Chirality : 0.043 0.225 2333 Planarity : 0.006 0.101 2546 Dihedral : 4.870 35.420 2075 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.16 % Favored : 93.37 % Rotamer: Outliers : 3.06 % Allowed : 27.58 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.20), residues: 1932 helix: 1.68 (0.22), residues: 601 sheet: -0.41 (0.23), residues: 533 loop : -2.06 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2606 TYR 0.014 0.001 TYR B 48 PHE 0.033 0.002 PHE B 90 TRP 0.022 0.002 TRP B 382 HIS 0.019 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00357 (14391) covalent geometry : angle 0.67713 (19686) hydrogen bonds : bond 0.03519 ( 693) hydrogen bonds : angle 4.82166 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2506 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8412 (tpp80) REVERT: A 3308 LEU cc_start: 0.8406 (pp) cc_final: 0.8092 (mm) REVERT: A 3334 TYR cc_start: 0.8994 (m-80) cc_final: 0.8672 (m-80) REVERT: A 3414 HIS cc_start: 0.9152 (m90) cc_final: 0.8873 (m90) REVERT: B 2 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.6340 (mtm-85) REVERT: B 9 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7064 (mtt180) REVERT: B 343 ARG cc_start: 0.8994 (mpt-90) cc_final: 0.8664 (mtt90) REVERT: C 319 ASP cc_start: 0.7617 (m-30) cc_final: 0.7388 (t0) REVERT: D 206 GLU cc_start: 0.9341 (tp30) cc_final: 0.8802 (pp20) REVERT: D 259 MET cc_start: 0.9413 (mmm) cc_final: 0.8801 (mmm) REVERT: D 345 GLN cc_start: 0.8961 (tm130) cc_final: 0.8674 (tp40) REVERT: D 411 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7381 (mmmt) outliers start: 37 outliers final: 27 residues processed: 131 average time/residue: 0.1090 time to fit residues: 21.5675 Evaluate side-chains 124 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2799 GLU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3059 LEU Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3356 ASP Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3421 ASN Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 231 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 62 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 40.0000 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.082985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.058987 restraints weight = 71625.122| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 4.00 r_work: 0.3274 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 14391 Z= 0.165 Angle : 0.650 11.050 19686 Z= 0.325 Chirality : 0.043 0.198 2333 Planarity : 0.006 0.099 2546 Dihedral : 4.647 30.792 2075 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.45 % Favored : 92.08 % Rotamer: Outliers : 3.88 % Allowed : 26.09 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.20), residues: 1932 helix: 1.78 (0.22), residues: 609 sheet: -0.20 (0.23), residues: 527 loop : -2.03 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2631 TYR 0.013 0.001 TYR A2849 PHE 0.028 0.002 PHE B 90 TRP 0.017 0.001 TRP B 382 HIS 0.009 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00380 (14391) covalent geometry : angle 0.64952 (19686) hydrogen bonds : bond 0.03430 ( 693) hydrogen bonds : angle 4.65335 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 103 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2506 ARG cc_start: 0.8712 (tpp-160) cc_final: 0.8493 (tpp80) REVERT: A 2632 PHE cc_start: 0.8070 (t80) cc_final: 0.7835 (m-80) REVERT: A 3308 LEU cc_start: 0.8360 (pp) cc_final: 0.7979 (mp) REVERT: A 3334 TYR cc_start: 0.9000 (m-80) cc_final: 0.8718 (m-80) REVERT: A 3414 HIS cc_start: 0.9144 (m90) cc_final: 0.8858 (m90) REVERT: B 2 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.6419 (mtm-85) REVERT: B 343 ARG cc_start: 0.9007 (mpt-90) cc_final: 0.8633 (mtt90) REVERT: C 258 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7765 (mt) REVERT: D 206 GLU cc_start: 0.9309 (tp30) cc_final: 0.8891 (pp20) REVERT: D 259 MET cc_start: 0.9430 (mmm) cc_final: 0.8838 (mmm) REVERT: D 411 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7254 (mmmt) outliers start: 47 outliers final: 27 residues processed: 140 average time/residue: 0.1019 time to fit residues: 21.5658 Evaluate side-chains 120 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2849 TYR Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3389 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 10 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 61 optimal weight: 0.5980 chunk 166 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3322 GLN ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.081784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.057819 restraints weight = 72442.050| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.95 r_work: 0.3235 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.9411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 14391 Z= 0.166 Angle : 0.663 11.045 19686 Z= 0.332 Chirality : 0.043 0.207 2333 Planarity : 0.006 0.096 2546 Dihedral : 4.618 33.102 2075 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.90 % Favored : 93.63 % Rotamer: Outliers : 3.80 % Allowed : 26.59 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.20), residues: 1932 helix: 1.94 (0.22), residues: 609 sheet: -0.24 (0.23), residues: 552 loop : -1.91 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 351 TYR 0.018 0.001 TYR B 48 PHE 0.026 0.001 PHE B 90 TRP 0.013 0.001 TRP C 358 HIS 0.008 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00393 (14391) covalent geometry : angle 0.66341 (19686) hydrogen bonds : bond 0.03344 ( 693) hydrogen bonds : angle 4.60060 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2506 ARG cc_start: 0.8747 (tpp-160) cc_final: 0.8545 (tpp80) REVERT: A 2996 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8765 (mt) REVERT: A 3308 LEU cc_start: 0.8516 (pp) cc_final: 0.8298 (mm) REVERT: A 3334 TYR cc_start: 0.8971 (m-80) cc_final: 0.8690 (m-80) REVERT: A 3414 HIS cc_start: 0.9159 (m90) cc_final: 0.8875 (m90) REVERT: B 2 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.6446 (mtm-85) REVERT: B 25 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7764 (pp) REVERT: B 291 MET cc_start: 0.8523 (ppp) cc_final: 0.8043 (ppp) REVERT: B 343 ARG cc_start: 0.8997 (mpt-90) cc_final: 0.8627 (mtt90) REVERT: D 259 MET cc_start: 0.9451 (mmm) cc_final: 0.8851 (mmm) REVERT: D 285 GLU cc_start: 0.8566 (tp30) cc_final: 0.8154 (tm-30) REVERT: D 286 MET cc_start: 0.8808 (tpp) cc_final: 0.8182 (ptp) REVERT: D 411 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7399 (mmmt) outliers start: 46 outliers final: 32 residues processed: 136 average time/residue: 0.1049 time to fit residues: 21.8002 Evaluate side-chains 127 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2799 GLU Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3059 LEU Chi-restraints excluded: chain A residue 3257 MET Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3356 ASP Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3421 ASN Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 231 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 109 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 154 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3185 HIS ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.080895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056728 restraints weight = 71589.277| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.87 r_work: 0.3198 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.9807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14391 Z= 0.165 Angle : 0.665 12.182 19686 Z= 0.329 Chirality : 0.043 0.241 2333 Planarity : 0.006 0.094 2546 Dihedral : 4.549 29.620 2075 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.68 % Favored : 92.86 % Rotamer: Outliers : 3.22 % Allowed : 27.00 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1932 helix: 1.95 (0.22), residues: 611 sheet: -0.15 (0.23), residues: 551 loop : -1.81 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2631 TYR 0.014 0.001 TYR D 272 PHE 0.016 0.001 PHE B 90 TRP 0.018 0.001 TRP B 382 HIS 0.009 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00391 (14391) covalent geometry : angle 0.66537 (19686) hydrogen bonds : bond 0.03259 ( 693) hydrogen bonds : angle 4.52652 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2506 ARG cc_start: 0.8827 (tpp-160) cc_final: 0.8612 (tpp80) REVERT: A 2996 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8773 (mt) REVERT: A 3308 LEU cc_start: 0.8466 (pp) cc_final: 0.8266 (mm) REVERT: A 3334 TYR cc_start: 0.8985 (m-80) cc_final: 0.8682 (m-80) REVERT: A 3414 HIS cc_start: 0.9151 (m90) cc_final: 0.8901 (m90) REVERT: B 2 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.6513 (mtm-85) REVERT: B 25 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7970 (pp) REVERT: B 291 MET cc_start: 0.8546 (ppp) cc_final: 0.8063 (ppp) REVERT: B 343 ARG cc_start: 0.9011 (mpt-90) cc_final: 0.8697 (mtt90) REVERT: C 258 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7561 (mt) REVERT: D 206 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8910 (pp20) REVERT: D 259 MET cc_start: 0.9437 (mmm) cc_final: 0.8873 (mmm) REVERT: D 411 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7473 (mmmt) outliers start: 39 outliers final: 31 residues processed: 126 average time/residue: 0.1089 time to fit residues: 21.0144 Evaluate side-chains 125 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2799 GLU Chi-restraints excluded: chain A residue 2849 TYR Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3421 ASN Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 107 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3185 HIS ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.081095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.057136 restraints weight = 71606.425| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.80 r_work: 0.3198 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.9929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14391 Z= 0.135 Angle : 0.653 11.214 19686 Z= 0.322 Chirality : 0.042 0.257 2333 Planarity : 0.005 0.092 2546 Dihedral : 4.416 32.175 2075 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.00 % Favored : 93.48 % Rotamer: Outliers : 3.06 % Allowed : 27.17 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.20), residues: 1932 helix: 2.00 (0.22), residues: 609 sheet: -0.16 (0.23), residues: 557 loop : -1.74 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 351 TYR 0.013 0.001 TYR D 272 PHE 0.020 0.001 PHE B 90 TRP 0.015 0.001 TRP B 382 HIS 0.008 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00326 (14391) covalent geometry : angle 0.65286 (19686) hydrogen bonds : bond 0.03098 ( 693) hydrogen bonds : angle 4.50969 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2506 ARG cc_start: 0.8920 (tpp-160) cc_final: 0.8690 (tpp80) REVERT: A 2996 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8794 (mt) REVERT: A 3334 TYR cc_start: 0.8908 (m-80) cc_final: 0.8560 (m-80) REVERT: A 3414 HIS cc_start: 0.9088 (m90) cc_final: 0.8751 (m90) REVERT: B 2 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.6520 (mtm-85) REVERT: B 25 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8040 (pp) REVERT: B 291 MET cc_start: 0.8552 (ppp) cc_final: 0.8089 (ppp) REVERT: B 343 ARG cc_start: 0.8974 (mpt-90) cc_final: 0.8704 (mtt90) REVERT: C 258 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7559 (mt) REVERT: D 259 MET cc_start: 0.9474 (mmm) cc_final: 0.8886 (mmm) REVERT: D 286 MET cc_start: 0.8791 (tpp) cc_final: 0.8330 (ptm) outliers start: 37 outliers final: 28 residues processed: 116 average time/residue: 0.1045 time to fit residues: 18.4184 Evaluate side-chains 120 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2799 GLU Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3421 ASN Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 0 optimal weight: 50.0000 chunk 49 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3185 HIS ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.080815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.056696 restraints weight = 71527.828| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.84 r_work: 0.3188 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 1.0074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14391 Z= 0.141 Angle : 0.654 11.945 19686 Z= 0.320 Chirality : 0.042 0.288 2333 Planarity : 0.005 0.092 2546 Dihedral : 4.318 23.841 2071 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.00 % Favored : 93.48 % Rotamer: Outliers : 3.22 % Allowed : 27.09 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.20), residues: 1932 helix: 2.07 (0.22), residues: 609 sheet: -0.11 (0.23), residues: 554 loop : -1.74 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 351 TYR 0.012 0.001 TYR D 308 PHE 0.020 0.001 PHE B 90 TRP 0.015 0.001 TRP B 382 HIS 0.007 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00342 (14391) covalent geometry : angle 0.65422 (19686) hydrogen bonds : bond 0.03072 ( 693) hydrogen bonds : angle 4.45246 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2506 ARG cc_start: 0.8907 (tpp-160) cc_final: 0.8694 (tpp80) REVERT: A 2996 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8734 (mt) REVERT: A 3040 MET cc_start: 0.8958 (mtp) cc_final: 0.8745 (mtt) REVERT: A 3334 TYR cc_start: 0.8912 (m-80) cc_final: 0.8572 (m-80) REVERT: A 3414 HIS cc_start: 0.9109 (m90) cc_final: 0.8782 (m90) REVERT: B 2 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.6533 (mtm-85) REVERT: B 25 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8055 (pp) REVERT: B 291 MET cc_start: 0.8568 (ppp) cc_final: 0.8118 (ppp) REVERT: B 343 ARG cc_start: 0.8970 (mpt-90) cc_final: 0.8713 (mtt90) REVERT: C 258 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7535 (mt) REVERT: D 259 MET cc_start: 0.9450 (mmm) cc_final: 0.8855 (mmm) REVERT: D 286 MET cc_start: 0.8795 (tpp) cc_final: 0.8371 (ptm) outliers start: 39 outliers final: 32 residues processed: 117 average time/residue: 0.1063 time to fit residues: 18.6639 Evaluate side-chains 123 residues out of total 1747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2525 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2609 LEU Chi-restraints excluded: chain A residue 2654 VAL Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2799 GLU Chi-restraints excluded: chain A residue 2996 LEU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3339 LYS Chi-restraints excluded: chain A residue 3374 VAL Chi-restraints excluded: chain A residue 3375 LEU Chi-restraints excluded: chain A residue 3376 VAL Chi-restraints excluded: chain A residue 3389 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3421 ASN Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 410 HIS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 89 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 164 optimal weight: 50.0000 chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** 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 = 0.4032 r_free = 0.4032 target = 0.080749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.056641 restraints weight = 71378.150| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.83 r_work: 0.3197 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 1.0190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 14391 Z= 0.133 Angle : 0.651 12.470 19686 Z= 0.320 Chirality : 0.042 0.287 2333 Planarity : 0.005 0.091 2546 Dihedral : 4.279 23.693 2071 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.95 % Favored : 93.53 % Rotamer: Outliers : 3.06 % Allowed : 27.09 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1932 helix: 2.04 (0.22), residues: 608 sheet: -0.08 (0.22), residues: 551 loop : -1.72 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 351 TYR 0.012 0.001 TYR D 308 PHE 0.023 0.001 PHE A2632 TRP 0.016 0.001 TRP B 382 HIS 0.007 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00324 (14391) covalent geometry : angle 0.65113 (19686) hydrogen bonds : bond 0.03032 ( 693) hydrogen bonds : angle 4.47619 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5722.26 seconds wall clock time: 97 minutes 48.74 seconds (5868.74 seconds total)