Starting phenix.real_space_refine on Wed Feb 4 23:47:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9n_64877/02_2026/9v9n_64877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9n_64877/02_2026/9v9n_64877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v9n_64877/02_2026/9v9n_64877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9n_64877/02_2026/9v9n_64877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v9n_64877/02_2026/9v9n_64877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9n_64877/02_2026/9v9n_64877.map" } resolution = 3.08 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= -0.000 sd= 0.021 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 58 5.16 5 C 8603 2.51 5 N 2358 2.21 5 O 2371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13390 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5076 Classifications: {'peptide': 750} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 39, 'TRANS': 710} Chain breaks: 22 Unresolved non-hydrogen bonds: 1050 Unresolved non-hydrogen angles: 1339 Unresolved non-hydrogen dihedrals: 853 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'HIS:plan': 10, 'ARG:plan': 36, 'TRP:plan': 4, 'TYR:plan': 6, 'GLN:plan1': 15, 'ASN:plan1': 5, 'PHE:plan': 13, 'ASP:plan': 20, 'GLU:plan': 31} Unresolved non-hydrogen planarities: 645 Chain: "B" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2726 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 12, 'TRANS': 364} Chain breaks: 5 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 6, 'ARG:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "C" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2972 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain breaks: 2 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 13, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2616 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 17, 'TRANS': 370} Chain breaks: 4 Unresolved non-hydrogen bonds: 542 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 19, 'ASP:plan': 11, 'ASN:plan1': 4, 'ARG:plan': 7, 'TRP:plan': 1, 'TYR:plan': 4, 'HIS:plan': 5, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 282 Time building chain proxies: 3.50, per 1000 atoms: 0.26 Number of scatterers: 13390 At special positions: 0 Unit cell: (100.3, 131.75, 252.45, 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 58 16.00 O 2371 8.00 N 2358 7.00 C 8603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 655.4 milliseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3622 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 22 sheets defined 34.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 2227 through 2231 removed outlier: 4.045A pdb=" N CYS A2230 " --> pdb=" O PRO A2227 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2249 removed outlier: 4.195A pdb=" N ILE A2247 " --> pdb=" O GLN A2243 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A2248 " --> pdb=" O ASN A2244 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2391 removed outlier: 3.552A pdb=" N ILE A2387 " --> pdb=" O ALA A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2503 through 2513 removed outlier: 3.817A pdb=" N THR A2507 " --> pdb=" O GLN A2503 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN A2509 " --> pdb=" O ARG A2505 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A2512 " --> pdb=" O THR A2508 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2533 removed outlier: 3.540A pdb=" N ARG A2524 " --> pdb=" O PRO A2520 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA A2526 " --> pdb=" O PHE A2522 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN A2527 " --> pdb=" O ALA A2523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG A2528 " --> pdb=" O ARG A2524 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A2533 " --> pdb=" O TRP A2529 " (cutoff:3.500A) Processing helix chain 'A' and resid 2552 through 2569 removed outlier: 4.371A pdb=" N SER A2556 " --> pdb=" O PHE A2552 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU A2560 " --> pdb=" O SER A2556 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2618 No H-bonds generated for 'chain 'A' and resid 2616 through 2618' Processing helix chain 'A' and resid 2667 through 2690 Processing helix chain 'A' and resid 2692 through 2700 removed outlier: 3.526A pdb=" N LEU A2700 " --> pdb=" O LEU A2696 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2767 Processing helix chain 'A' and resid 2789 through 2794 removed outlier: 3.549A pdb=" N GLY A2794 " --> pdb=" O VAL A2790 " (cutoff:3.500A) Processing helix chain 'A' and resid 2796 through 2801 Processing helix chain 'A' and resid 2807 through 2823 removed outlier: 4.039A pdb=" N LYS A2813 " --> pdb=" O GLU A2809 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A2814 " --> pdb=" O ARG A2810 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A2817 " --> pdb=" O LYS A2813 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A2823 " --> pdb=" O VAL A2819 " (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 2907 through 2926 removed outlier: 4.008A pdb=" N LEU A2912 " --> pdb=" O TRP A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 3026 through 3031 removed outlier: 4.260A pdb=" N THR A3030 " --> pdb=" O SER A3026 " (cutoff:3.500A) Processing helix chain 'A' and resid 3032 through 3039 removed outlier: 4.153A pdb=" N VAL A3036 " --> pdb=" O GLU A3032 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A3037 " --> pdb=" O CYS A3033 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3060 removed outlier: 3.720A pdb=" N PHE A3045 " --> pdb=" O HIS A3041 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A3046 " --> pdb=" O VAL A3042 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A3054 " --> pdb=" O HIS A3050 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS A3055 " --> pdb=" O LEU A3051 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A3056 " --> pdb=" O ARG A3052 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS A3057 " --> pdb=" O LEU A3053 " (cutoff:3.500A) Processing helix chain 'A' and resid 3070 through 3082 Processing helix chain 'A' and resid 3106 through 3117 removed outlier: 3.585A pdb=" N ASN A3112 " --> pdb=" O HIS A3108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A3117 " --> pdb=" O TYR A3113 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3186 Processing helix chain 'A' and resid 3249 through 3268 removed outlier: 4.025A pdb=" N VAL A3266 " --> pdb=" O LEU A3262 " (cutoff:3.500A) Processing helix chain 'A' and resid 3270 through 3282 removed outlier: 3.660A pdb=" N ARG A3274 " --> pdb=" O GLY A3270 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A3276 " --> pdb=" O HIS A3272 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A3277 " --> pdb=" O CYS A3273 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A3282 " --> pdb=" O LEU A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3310 removed outlier: 3.717A pdb=" N GLU A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A3310 " --> pdb=" O GLU A3306 " (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 3321 through 3329 removed outlier: 3.551A pdb=" N ASP A3324 " --> pdb=" O PRO A3321 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A3326 " --> pdb=" O LEU A3323 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A3329 " --> pdb=" O PHE A3326 " (cutoff:3.500A) Processing helix chain 'A' and resid 3330 through 3345 removed outlier: 4.039A pdb=" N TYR A3334 " --> pdb=" O THR A3330 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A3335 " --> pdb=" O VAL A3331 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A3339 " --> pdb=" O GLN A3335 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A3340 " --> pdb=" O SER A3336 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A3341 " --> pdb=" O LEU A3337 " (cutoff:3.500A) Processing helix chain 'A' and resid 3410 through 3432 removed outlier: 3.924A pdb=" N HIS A3414 " --> pdb=" O VAL A3410 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A3418 " --> pdb=" O HIS A3414 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A3419 " --> pdb=" O HIS A3415 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A3420 " --> pdb=" O LEU A3416 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR A3422 " --> pdb=" O SER A3418 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A3427 " --> pdb=" O ALA A3423 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A3432 " --> pdb=" O TRP A3428 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 399 Processing helix chain 'B' and resid 401 through 411 removed outlier: 4.121A pdb=" N HIS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 431 Processing helix chain 'C' and resid 126 through 132 removed outlier: 4.144A pdb=" N GLN C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 396 through 413 removed outlier: 3.698A pdb=" N LEU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 3.621A pdb=" N LEU D 25 " --> pdb=" O PHE D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.908A pdb=" N GLU D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 71 removed outlier: 4.030A pdb=" N LEU D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 116 through 150 removed outlier: 4.488A pdb=" N LEU D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.474A pdb=" N ALA D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 204 removed outlier: 3.627A pdb=" N GLN D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 208 through 227 removed outlier: 3.893A pdb=" N LEU D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 273 Processing helix chain 'D' and resid 274 through 280 removed outlier: 3.707A pdb=" N GLN D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 removed outlier: 4.211A pdb=" N LEU D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 removed outlier: 3.551A pdb=" N SER D 303 " --> pdb=" O GLY D 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.880A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 433 through 438 Processing sheet with id=AA1, first strand: chain 'A' and resid 2278 through 2279 Processing sheet with id=AA2, first strand: chain 'A' and resid 2572 through 2575 removed outlier: 3.783A pdb=" N LEU A2608 " --> pdb=" O VAL A2654 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A2654 " --> pdb=" O LEU A2608 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A2652 " --> pdb=" O LEU A2610 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2845 through 2853 removed outlier: 5.715A pdb=" N LEU A2846 " --> pdb=" O ALA A3009 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A3009 " --> pdb=" O LEU A2846 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A2848 " --> pdb=" O GLN A3007 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A2997 " --> pdb=" O CYS A3004 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A2993 " --> pdb=" O PHE A3008 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3092 through 3100 removed outlier: 3.534A pdb=" N HIS A3092 " --> pdb=" O LEU A3195 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A3168 " --> pdb=" O PHE A3192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A3167 " --> pdb=" O SER A3143 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A3143 " --> pdb=" O LEU A3167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 3127 through 3128 removed outlier: 4.095A pdb=" N GLU A3138 " --> pdb=" O MET A3128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 3312 through 3315 removed outlier: 3.930A pdb=" N THR A3388 " --> pdb=" O LEU A3375 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A3374 " --> pdb=" O VAL A3364 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A3363 " --> pdb=" O ARG A3350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3312 through 3315 removed outlier: 3.930A pdb=" N THR A3388 " --> pdb=" O LEU A3375 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A3386 " --> pdb=" O PHE A3377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 3 removed outlier: 6.913A pdb=" N ARG B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLN B 345 " --> pdb=" O ARG B 2 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 13 removed outlier: 4.038A pdb=" N LYS B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 352 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 26 removed outlier: 3.645A pdb=" N LEU B 57 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 65 through 71 removed outlier: 3.522A pdb=" N CYS B 67 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 92 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.730A 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: 4.134A pdb=" N LEU B 143 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B 175 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG B 156 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER B 173 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU B 158 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU B 171 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 186 through 190 removed outlier: 4.663A pdb=" N LEU B 198 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 256 through 259 removed outlier: 3.700A pdb=" N THR B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 285 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 300 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 287 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 14 through 21 removed outlier: 6.795A pdb=" N ILE C 392 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C 19 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL C 390 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA C 383 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET C 369 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.632A 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: 4.222A pdb=" N VAL C 50 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 79 through 87 removed outlier: 5.645A pdb=" N ILE C 80 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE C 102 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE C 101 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 146 through 153 removed outlier: 8.781A pdb=" N THR C 159 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU C 175 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 173 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 4.095A 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: 3.778A pdb=" N TRP C 203 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 226 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 243 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 228 " --> pdb=" O MET C 241 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N MET C 241 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS C 230 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 250 through 257 removed outlier: 3.589A pdb=" N ARG C 252 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP C 297 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 310 through 316 removed outlier: 3.553A pdb=" N ALA C 329 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS C 337 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 314 through 317 632 hydrogen bonds defined for protein. 1764 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: 2.69 Time building geometry restraints manager: 1.79 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: 4445 1.34 - 1.46: 3214 1.46 - 1.58: 5934 1.58 - 1.70: 2 1.70 - 1.82: 87 Bond restraints: 13682 Sorted by residual: bond pdb=" CB PRO D 357 " pdb=" CG PRO D 357 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.08e+00 bond pdb=" CB PRO D 116 " pdb=" CG PRO D 116 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.43e+00 bond pdb=" C ALA D 115 " pdb=" N PRO D 116 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.67e+00 bond pdb=" CA GLN D 280 " pdb=" CB GLN D 280 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.30e-02 5.92e+03 2.48e+00 bond pdb=" CB PRO D 295 " pdb=" CG PRO D 295 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.85e+00 ... (remaining 13677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 18310 2.29 - 4.59: 343 4.59 - 6.88: 54 6.88 - 9.18: 8 9.18 - 11.47: 3 Bond angle restraints: 18718 Sorted by residual: angle pdb=" C HIS D 117 " pdb=" CA HIS D 117 " pdb=" CB HIS D 117 " ideal model delta sigma weight residual 116.54 109.57 6.97 1.15e+00 7.56e-01 3.68e+01 angle pdb=" N LEU D 180 " pdb=" CA LEU D 180 " pdb=" C LEU D 180 " ideal model delta sigma weight residual 114.16 105.76 8.40 1.48e+00 4.57e-01 3.22e+01 angle pdb=" N ILE D 365 " pdb=" CA ILE D 365 " pdb=" C ILE D 365 " ideal model delta sigma weight residual 113.71 108.46 5.25 9.50e-01 1.11e+00 3.06e+01 angle pdb=" N THR D 288 " pdb=" CA THR D 288 " pdb=" C THR D 288 " ideal model delta sigma weight residual 113.18 106.18 7.00 1.33e+00 5.65e-01 2.77e+01 angle pdb=" N LYS A3280 " pdb=" CA LYS A3280 " pdb=" C LYS A3280 " ideal model delta sigma weight residual 114.04 108.46 5.58 1.24e+00 6.50e-01 2.02e+01 ... (remaining 18713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7027 17.95 - 35.89: 741 35.89 - 53.84: 161 53.84 - 71.78: 36 71.78 - 89.73: 12 Dihedral angle restraints: 7977 sinusoidal: 2430 harmonic: 5547 Sorted by residual: dihedral pdb=" CA TRP D 361 " pdb=" C TRP D 361 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " ideal model delta harmonic sigma weight residual 180.00 145.01 34.99 0 5.00e+00 4.00e-02 4.90e+01 dihedral pdb=" CA ASN D 294 " pdb=" C ASN D 294 " pdb=" N PRO D 295 " pdb=" CA PRO D 295 " ideal model delta harmonic sigma weight residual -180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE D 179 " pdb=" C ILE D 179 " pdb=" N LEU D 180 " pdb=" CA LEU D 180 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 7974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1784 0.050 - 0.100: 358 0.100 - 0.150: 79 0.150 - 0.200: 2 0.200 - 0.250: 2 Chirality restraints: 2225 Sorted by residual: chirality pdb=" CA PRO D 357 " pdb=" N PRO D 357 " pdb=" C PRO D 357 " pdb=" CB PRO D 357 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO D 116 " pdb=" N PRO D 116 " pdb=" C PRO D 116 " pdb=" CB PRO D 116 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO D 295 " pdb=" N PRO D 295 " pdb=" C PRO D 295 " pdb=" CB PRO D 295 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 2222 not shown) Planarity restraints: 2421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 356 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO D 357 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO D 357 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO D 357 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 115 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO D 116 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 294 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO D 295 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO D 295 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 295 " 0.055 5.00e-02 4.00e+02 ... (remaining 2418 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 426 2.69 - 3.24: 12750 3.24 - 3.80: 20151 3.80 - 4.35: 25182 4.35 - 4.90: 42459 Nonbonded interactions: 100968 Sorted by model distance: nonbonded pdb=" O LEU D 378 " pdb=" NZ LYS D 431 " model vdw 2.139 3.120 nonbonded pdb=" O TYR A2923 " pdb=" OG SER A2926 " model vdw 2.144 3.040 nonbonded pdb=" NH2 ARG A2551 " pdb=" O LEU C 245 " model vdw 2.159 3.120 nonbonded pdb=" OG1 THR B 280 " pdb=" OD1 ASP B 282 " model vdw 2.160 3.040 nonbonded pdb=" ND1 HIS A2580 " pdb=" OG SER A2583 " model vdw 2.200 3.120 ... (remaining 100963 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: 15.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 13682 Z= 0.179 Angle : 0.786 11.471 18718 Z= 0.456 Chirality : 0.043 0.250 2225 Planarity : 0.007 0.129 2421 Dihedral : 16.480 89.729 4355 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.17 % Favored : 92.23 % Rotamer: Outliers : 4.53 % Allowed : 29.22 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.88 (0.20), residues: 1840 helix: -0.18 (0.24), residues: 542 sheet: -1.00 (0.23), residues: 522 loop : -2.14 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2806 TYR 0.011 0.001 TYR D 143 PHE 0.010 0.001 PHE A2764 TRP 0.011 0.001 TRP A3145 HIS 0.006 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00386 (13682) covalent geometry : angle 0.78579 (18718) hydrogen bonds : bond 0.21670 ( 625) hydrogen bonds : angle 8.05565 ( 1764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 77 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2578 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: A 2768 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8370 (pp) REVERT: A 2861 TRP cc_start: 0.7896 (OUTLIER) cc_final: 0.6931 (m100) REVERT: A 3382 LEU cc_start: 0.8363 (pt) cc_final: 0.8146 (pt) REVERT: D 99 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.6999 (p0) REVERT: D 230 PHE cc_start: 0.6777 (OUTLIER) cc_final: 0.6335 (m-80) outliers start: 51 outliers final: 40 residues processed: 120 average time/residue: 0.0966 time to fit residues: 18.5949 Evaluate side-chains 122 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2567 SER Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 3001 CYS Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3091 ASN Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3164 ASP Chi-restraints excluded: chain A residue 3266 VAL Chi-restraints excluded: chain A residue 3341 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3388 THR Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0050 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2509 GLN A2999 GLN A3007 GLN ** A3091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3322 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.079150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.058783 restraints weight = 82254.271| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 5.26 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13682 Z= 0.184 Angle : 0.660 11.754 18718 Z= 0.342 Chirality : 0.043 0.244 2225 Planarity : 0.007 0.127 2421 Dihedral : 7.387 65.390 2050 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.55 % Favored : 91.90 % Rotamer: Outliers : 5.95 % Allowed : 26.38 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.06 % 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: -1.75 (0.20), residues: 1840 helix: -0.05 (0.23), residues: 577 sheet: -1.09 (0.22), residues: 550 loop : -2.05 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2613 TYR 0.014 0.001 TYR A2923 PHE 0.012 0.001 PHE A2916 TRP 0.010 0.001 TRP B 299 HIS 0.005 0.001 HIS A3092 Details of bonding type rmsd covalent geometry : bond 0.00426 (13682) covalent geometry : angle 0.66009 (18718) hydrogen bonds : bond 0.04485 ( 625) hydrogen bonds : angle 5.86664 ( 1764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 78 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2578 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: A 2580 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.5388 (p90) REVERT: A 2768 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8362 (pp) REVERT: A 2814 MET cc_start: 0.7130 (tmm) cc_final: 0.6892 (tmm) REVERT: A 2861 TRP cc_start: 0.7862 (OUTLIER) cc_final: 0.6918 (m100) REVERT: A 3307 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6163 (tt) REVERT: B 375 ASN cc_start: 0.8822 (t0) cc_final: 0.8604 (t0) REVERT: C 137 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8792 (tp) REVERT: C 391 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7323 (m170) REVERT: D 230 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6145 (m-80) outliers start: 67 outliers final: 40 residues processed: 140 average time/residue: 0.0928 time to fit residues: 21.1342 Evaluate side-chains 122 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 74 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2580 HIS Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2839 THR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3164 ASP Chi-restraints excluded: chain A residue 3266 VAL Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 189 THR 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 346 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 403 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 141 optimal weight: 0.0870 chunk 148 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2698 GLN A2796 GLN A2999 GLN ** A3091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.079903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.060089 restraints weight = 82330.396| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 4.66 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13682 Z= 0.125 Angle : 0.610 12.399 18718 Z= 0.310 Chirality : 0.042 0.241 2225 Planarity : 0.006 0.123 2421 Dihedral : 6.625 66.277 2022 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.03 % Favored : 93.42 % Rotamer: Outliers : 5.15 % Allowed : 26.20 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.50 (0.20), residues: 1840 helix: 0.29 (0.23), residues: 567 sheet: -0.96 (0.22), residues: 546 loop : -1.99 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 174 TYR 0.009 0.001 TYR A2923 PHE 0.021 0.001 PHE D 22 TRP 0.010 0.001 TRP A3428 HIS 0.004 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00303 (13682) covalent geometry : angle 0.61025 (18718) hydrogen bonds : bond 0.03677 ( 625) hydrogen bonds : angle 5.43937 ( 1764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 77 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2578 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: A 2580 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.5593 (p90) REVERT: A 2768 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8277 (pp) REVERT: A 2814 MET cc_start: 0.6869 (tmm) cc_final: 0.6596 (tmm) REVERT: B 114 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8850 (pt0) REVERT: B 375 ASN cc_start: 0.8896 (t0) cc_final: 0.8597 (t0) REVERT: C 137 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8835 (tp) REVERT: C 391 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7257 (m170) REVERT: C 397 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6856 (mp) REVERT: D 230 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6459 (m-80) outliers start: 58 outliers final: 38 residues processed: 130 average time/residue: 0.0972 time to fit residues: 20.0330 Evaluate side-chains 120 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 74 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2580 HIS Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2796 GLN Chi-restraints excluded: chain A residue 2999 GLN Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3164 ASP Chi-restraints excluded: chain A residue 3248 PHE Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 TRP Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 90 optimal weight: 0.0570 chunk 5 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 0.0010 chunk 45 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2535 GLN A3082 HIS B 30 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 294 ASN 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 = 0.078226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.057782 restraints weight = 82464.095| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 5.09 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 13682 Z= 0.238 Angle : 0.675 12.104 18718 Z= 0.345 Chirality : 0.044 0.235 2225 Planarity : 0.006 0.120 2421 Dihedral : 6.404 53.068 2013 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.93 % Favored : 91.63 % Rotamer: Outliers : 7.19 % Allowed : 24.87 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.53 (0.20), residues: 1840 helix: 0.37 (0.23), residues: 572 sheet: -1.05 (0.22), residues: 549 loop : -2.06 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 174 TYR 0.013 0.001 TYR A2923 PHE 0.011 0.002 PHE A2552 TRP 0.010 0.002 TRP B 299 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00549 (13682) covalent geometry : angle 0.67495 (18718) hydrogen bonds : bond 0.03928 ( 625) hydrogen bonds : angle 5.43751 ( 1764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 75 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2768 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8402 (pp) REVERT: A 2814 MET cc_start: 0.7055 (tmm) cc_final: 0.6729 (tmm) REVERT: A 2861 TRP cc_start: 0.7987 (OUTLIER) cc_final: 0.7069 (m100) REVERT: B 114 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8852 (pt0) REVERT: B 122 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8492 (m90) REVERT: B 135 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9132 (tp) REVERT: B 350 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8330 (mm) REVERT: B 375 ASN cc_start: 0.8986 (t0) cc_final: 0.8707 (t0) REVERT: C 137 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8792 (tt) REVERT: C 391 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7358 (m170) REVERT: C 397 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7271 (mp) REVERT: D 230 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6304 (m-80) outliers start: 81 outliers final: 52 residues processed: 149 average time/residue: 0.0869 time to fit residues: 21.1987 Evaluate side-chains 134 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 72 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2839 THR Chi-restraints excluded: chain A residue 2849 TYR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 2999 GLN Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3164 ASP Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU 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 301 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 12 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 4 optimal weight: 50.0000 chunk 152 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2922 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.076824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.056535 restraints weight = 83443.384| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.87 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 13682 Z= 0.293 Angle : 0.721 9.346 18718 Z= 0.373 Chirality : 0.046 0.228 2225 Planarity : 0.007 0.119 2421 Dihedral : 6.687 55.542 2011 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.80 % Favored : 90.76 % Rotamer: Outliers : 7.10 % Allowed : 24.96 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -1.62 (0.20), residues: 1840 helix: 0.45 (0.23), residues: 571 sheet: -1.14 (0.22), residues: 549 loop : -2.23 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 279 TYR 0.013 0.002 TYR C 225 PHE 0.014 0.002 PHE A3248 TRP 0.014 0.002 TRP B 299 HIS 0.008 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00669 (13682) covalent geometry : angle 0.72103 (18718) hydrogen bonds : bond 0.04166 ( 625) hydrogen bonds : angle 5.65046 ( 1764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 67 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 2768 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8412 (pp) REVERT: A 2814 MET cc_start: 0.7031 (tmm) cc_final: 0.6677 (tmm) REVERT: A 2861 TRP cc_start: 0.8023 (OUTLIER) cc_final: 0.7258 (m100) REVERT: A 2999 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (pp30) REVERT: A 3307 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5305 (tt) REVERT: B 114 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8736 (pt0) REVERT: B 122 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.8472 (m90) REVERT: B 350 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 375 ASN cc_start: 0.9062 (t0) cc_final: 0.8782 (t0) REVERT: C 137 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8795 (tp) REVERT: C 397 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7350 (mp) REVERT: D 230 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6239 (m-80) outliers start: 80 outliers final: 53 residues processed: 141 average time/residue: 0.1004 time to fit residues: 22.5846 Evaluate side-chains 128 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 65 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2691 LEU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2839 THR Chi-restraints excluded: chain A residue 2849 TYR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 2999 GLN Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3054 VAL Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU 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 301 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 393 TYR Chi-restraints excluded: chain D residue 403 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 89 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 4 optimal weight: 0.0770 chunk 142 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 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 = 0.4120 r_free = 0.4120 target = 0.078599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.058324 restraints weight = 81964.821| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 5.00 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13682 Z= 0.142 Angle : 0.617 10.176 18718 Z= 0.312 Chirality : 0.042 0.222 2225 Planarity : 0.006 0.115 2421 Dihedral : 6.131 55.558 2006 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.74 % Favored : 92.83 % Rotamer: Outliers : 5.06 % Allowed : 26.73 % 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: -1.28 (0.20), residues: 1840 helix: 0.75 (0.23), residues: 578 sheet: -0.89 (0.23), residues: 535 loop : -2.10 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 364 TYR 0.011 0.001 TYR D 330 PHE 0.012 0.001 PHE D 22 TRP 0.014 0.001 TRP A3333 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00344 (13682) covalent geometry : angle 0.61691 (18718) hydrogen bonds : bond 0.03302 ( 625) hydrogen bonds : angle 5.23183 ( 1764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 69 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 2768 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8321 (pp) REVERT: A 2814 MET cc_start: 0.6968 (tmm) cc_final: 0.6661 (tmm) REVERT: A 2861 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7238 (m100) REVERT: A 3307 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5387 (tt) REVERT: B 114 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8802 (pt0) REVERT: B 375 ASN cc_start: 0.9037 (t0) cc_final: 0.8724 (t0) REVERT: C 137 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8857 (tp) REVERT: C 397 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7108 (mp) REVERT: D 230 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: D 330 TYR cc_start: 0.6189 (t80) cc_final: 0.5886 (t80) outliers start: 57 outliers final: 41 residues processed: 120 average time/residue: 0.0875 time to fit residues: 17.6064 Evaluate side-chains 116 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 68 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2580 HIS Chi-restraints excluded: chain A residue 2691 LEU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3248 PHE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU 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 346 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 52 optimal weight: 0.0970 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 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 = 0.4140 r_free = 0.4140 target = 0.079404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.059177 restraints weight = 81887.966| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 5.23 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13682 Z= 0.115 Angle : 0.589 9.942 18718 Z= 0.295 Chirality : 0.042 0.218 2225 Planarity : 0.006 0.112 2421 Dihedral : 5.767 55.098 2006 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.14 % Favored : 93.42 % Rotamer: Outliers : 4.80 % Allowed : 27.26 % Favored : 67.94 % 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: -1.05 (0.20), residues: 1840 helix: 0.85 (0.23), residues: 592 sheet: -0.69 (0.23), residues: 534 loop : -1.99 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 364 TYR 0.013 0.001 TYR D 330 PHE 0.011 0.001 PHE A3003 TRP 0.013 0.001 TRP A3428 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00288 (13682) covalent geometry : angle 0.58897 (18718) hydrogen bonds : bond 0.02961 ( 625) hydrogen bonds : angle 4.93542 ( 1764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 75 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 2578 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: A 2768 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8301 (pp) REVERT: A 2814 MET cc_start: 0.6839 (tmm) cc_final: 0.6520 (tmm) REVERT: A 2861 TRP cc_start: 0.7942 (OUTLIER) cc_final: 0.7215 (m100) REVERT: A 3307 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5405 (tt) REVERT: A 3365 LEU cc_start: 0.9303 (tt) cc_final: 0.9003 (pp) REVERT: B 114 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8792 (pt0) REVERT: B 375 ASN cc_start: 0.9029 (t0) cc_final: 0.8667 (t0) REVERT: C 137 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8856 (tp) REVERT: C 397 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6878 (mp) REVERT: D 230 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.6138 (m-80) outliers start: 54 outliers final: 38 residues processed: 124 average time/residue: 0.0871 time to fit residues: 18.0454 Evaluate side-chains 115 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 69 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2580 HIS Chi-restraints excluded: chain A residue 2691 LEU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3248 PHE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU 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 346 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 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 = 0.4105 r_free = 0.4105 target = 0.077655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.057923 restraints weight = 81040.518| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.65 r_work: 0.3322 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13682 Z= 0.193 Angle : 0.639 10.012 18718 Z= 0.324 Chirality : 0.043 0.214 2225 Planarity : 0.006 0.110 2421 Dihedral : 5.934 54.969 2003 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.34 % Favored : 92.28 % Rotamer: Outliers : 5.24 % Allowed : 27.26 % Favored : 67.50 % 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: -1.04 (0.20), residues: 1840 helix: 0.97 (0.23), residues: 589 sheet: -0.75 (0.23), residues: 536 loop : -2.03 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.015 0.001 TYR D 330 PHE 0.012 0.001 PHE D 131 TRP 0.009 0.001 TRP A3428 HIS 0.006 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00456 (13682) covalent geometry : angle 0.63881 (18718) hydrogen bonds : bond 0.03338 ( 625) hydrogen bonds : angle 5.07706 ( 1764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 70 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 2768 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8476 (pp) REVERT: A 2814 MET cc_start: 0.6748 (tmm) cc_final: 0.6416 (tmm) REVERT: A 2861 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.7232 (m100) REVERT: A 3307 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5228 (tt) REVERT: B 114 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8809 (pt0) REVERT: B 350 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 375 ASN cc_start: 0.9320 (t0) cc_final: 0.9042 (t0) REVERT: C 137 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8961 (tt) REVERT: C 397 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7319 (mp) REVERT: D 168 MET cc_start: 0.9296 (pmm) cc_final: 0.9065 (pmm) REVERT: D 230 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6471 (m-80) outliers start: 59 outliers final: 45 residues processed: 124 average time/residue: 0.0912 time to fit residues: 18.9014 Evaluate side-chains 121 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 68 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2580 HIS Chi-restraints excluded: chain A residue 2691 LEU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2816 ASN Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3248 PHE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3391 PHE Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR 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 346 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 403 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 188 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 294 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 = 0.4129 r_free = 0.4129 target = 0.078524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058447 restraints weight = 81469.662| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 5.01 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13682 Z= 0.126 Angle : 0.614 10.797 18718 Z= 0.307 Chirality : 0.042 0.211 2225 Planarity : 0.006 0.108 2421 Dihedral : 5.748 56.158 2003 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.30 % Favored : 93.26 % Rotamer: Outliers : 4.80 % Allowed : 27.53 % Favored : 67.67 % 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: -0.90 (0.20), residues: 1840 helix: 1.06 (0.23), residues: 588 sheet: -0.66 (0.23), residues: 533 loop : -1.93 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.009 0.001 TYR A3361 PHE 0.011 0.001 PHE D 22 TRP 0.012 0.001 TRP B 299 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00314 (13682) covalent geometry : angle 0.61441 (18718) hydrogen bonds : bond 0.02974 ( 625) hydrogen bonds : angle 4.93060 ( 1764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 71 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 2578 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: A 2768 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8354 (pp) REVERT: A 2814 MET cc_start: 0.6812 (tmm) cc_final: 0.6495 (tmm) REVERT: A 2861 TRP cc_start: 0.7936 (OUTLIER) cc_final: 0.7244 (m100) REVERT: A 2999 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8089 (pp30) REVERT: A 3307 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5436 (tt) REVERT: B 114 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8797 (pt0) REVERT: B 375 ASN cc_start: 0.9072 (t0) cc_final: 0.8718 (t0) REVERT: C 137 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8860 (tt) REVERT: C 397 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6911 (mp) REVERT: D 168 MET cc_start: 0.9125 (pmm) cc_final: 0.8882 (pmm) REVERT: D 230 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: D 356 ARG cc_start: 0.5978 (mtt90) cc_final: 0.5061 (ttp-170) outliers start: 54 outliers final: 40 residues processed: 119 average time/residue: 0.0888 time to fit residues: 17.6038 Evaluate side-chains 120 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 71 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2691 LEU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 2999 GLN Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3248 PHE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR 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 346 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 146 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** 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 = 0.4141 r_free = 0.4141 target = 0.079025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.058974 restraints weight = 80903.813| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 5.16 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13682 Z= 0.114 Angle : 0.608 10.372 18718 Z= 0.302 Chirality : 0.042 0.209 2225 Planarity : 0.006 0.106 2421 Dihedral : 5.563 58.265 2003 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.25 % Favored : 93.37 % Rotamer: Outliers : 4.17 % Allowed : 28.24 % Favored : 67.58 % 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: -0.72 (0.21), residues: 1840 helix: 1.22 (0.23), residues: 587 sheet: -0.54 (0.23), residues: 533 loop : -1.84 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.008 0.001 TYR A3361 PHE 0.012 0.001 PHE D 22 TRP 0.010 0.001 TRP A3428 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00289 (13682) covalent geometry : angle 0.60806 (18718) hydrogen bonds : bond 0.02804 ( 625) hydrogen bonds : angle 4.78368 ( 1764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 73 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 2578 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6855 (tm-30) REVERT: A 2768 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8315 (pp) REVERT: A 2814 MET cc_start: 0.6813 (tmm) cc_final: 0.6520 (tmm) REVERT: A 2861 TRP cc_start: 0.7940 (OUTLIER) cc_final: 0.7296 (m100) REVERT: A 3307 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5445 (tt) REVERT: A 3365 LEU cc_start: 0.9187 (tt) cc_final: 0.8844 (pp) REVERT: B 114 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.8895 (pt0) REVERT: B 375 ASN cc_start: 0.8986 (t0) cc_final: 0.8594 (t0) REVERT: D 168 MET cc_start: 0.9114 (pmm) cc_final: 0.8891 (pmm) REVERT: D 230 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6044 (m-80) REVERT: D 264 MET cc_start: 0.8603 (ptp) cc_final: 0.7941 (ppp) outliers start: 47 outliers final: 39 residues processed: 115 average time/residue: 0.0856 time to fit residues: 16.4678 Evaluate side-chains 118 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2574 VAL Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2691 LEU Chi-restraints excluded: chain A residue 2692 ILE Chi-restraints excluded: chain A residue 2768 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2791 THR Chi-restraints excluded: chain A residue 2861 TRP Chi-restraints excluded: chain A residue 3053 LEU Chi-restraints excluded: chain A residue 3142 VAL Chi-restraints excluded: chain A residue 3248 PHE Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3363 VAL Chi-restraints excluded: chain A residue 3410 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 122 HIS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 THR 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 346 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 230 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 171 optimal weight: 0.3980 chunk 154 optimal weight: 0.0370 chunk 128 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 52 optimal weight: 0.0040 overall best weight: 0.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN C 230 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.080519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.060928 restraints weight = 81295.653| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 4.78 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13682 Z= 0.102 Angle : 0.600 10.588 18718 Z= 0.295 Chirality : 0.042 0.207 2225 Planarity : 0.006 0.105 2421 Dihedral : 5.269 58.140 2003 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.60 % Favored : 94.08 % Rotamer: Outliers : 3.11 % Allowed : 29.22 % Favored : 67.67 % 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: -0.50 (0.21), residues: 1840 helix: 1.39 (0.23), residues: 582 sheet: -0.30 (0.23), residues: 529 loop : -1.79 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.008 0.001 TYR D 143 PHE 0.012 0.001 PHE A3003 TRP 0.017 0.001 TRP A3333 HIS 0.004 0.001 HIS C 171 Details of bonding type rmsd covalent geometry : bond 0.00260 (13682) covalent geometry : angle 0.59950 (18718) hydrogen bonds : bond 0.02648 ( 625) hydrogen bonds : angle 4.62486 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5584.97 seconds wall clock time: 95 minutes 49.54 seconds (5749.54 seconds total)