Starting phenix.real_space_refine on Thu Feb 5 04:33:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9van_64902/02_2026/9van_64902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9van_64902/02_2026/9van_64902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9van_64902/02_2026/9van_64902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9van_64902/02_2026/9van_64902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9van_64902/02_2026/9van_64902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9van_64902/02_2026/9van_64902.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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 44 5.16 5 C 9180 2.51 5 N 2614 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14526 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 6569 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 565} Link IDs: {'PTRANS': 62, 'TRANS': 998} Chain breaks: 27 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 2030 Unresolved non-hydrogen angles: 2591 Unresolved non-hydrogen dihedrals: 1656 Unresolved non-hydrogen chiralities: 194 Planarities with less than four sites: {'GLN:plan1': 36, 'HIS:plan': 31, 'ARG:plan': 57, 'PHE:plan': 23, 'GLU:plan': 46, 'ASP:plan': 36, 'TRP:plan': 5, 'TYR:plan': 13, 'ASN:plan1': 15} Unresolved non-hydrogen planarities: 1195 Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2933 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 370} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3042 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 379} Chain breaks: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "D" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 1982 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 378} Chain breaks: 2 Unresolved non-hydrogen bonds: 1255 Unresolved non-hydrogen angles: 1600 Unresolved non-hydrogen dihedrals: 1071 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLU:plan': 26, 'GLN:plan1': 16, 'PHE:plan': 27, 'HIS:plan': 18, 'TYR:plan': 12, 'ASP:plan': 15, 'ASN:plan1': 13, 'ARG:plan': 13, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 698 Time building chain proxies: 3.56, per 1000 atoms: 0.25 Number of scatterers: 14526 At special positions: 0 Unit cell: (117.3, 175.1, 294.95, 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 44 16.00 O 2688 8.00 N 2614 7.00 C 9180 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: 1.36 Conformation dependent library (CDL) restraints added in 769.6 milliseconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 23 sheets defined 37.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 1716 through 1729 Processing helix chain 'A' and resid 1747 through 1751 removed outlier: 3.948A pdb=" N GLU A1750 " --> pdb=" O PHE A1747 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A1751 " --> pdb=" O GLY A1748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1747 through 1751' Processing helix chain 'A' and resid 1752 through 1763 Processing helix chain 'A' and resid 1943 through 1979 removed outlier: 4.513A pdb=" N GLU A1947 " --> pdb=" O GLY A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 1996 Processing helix chain 'A' and resid 2024 through 2031 removed outlier: 4.171A pdb=" N THR A2028 " --> pdb=" O TYR A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2062 through 2071 Processing helix chain 'A' and resid 2072 through 2075 removed outlier: 3.577A pdb=" N SER A2075 " --> pdb=" O ASN A2072 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2072 through 2075' Processing helix chain 'A' and resid 2170 through 2175 removed outlier: 3.737A pdb=" N ASP A2175 " --> pdb=" O PRO A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2175 through 2197 Processing helix chain 'A' and resid 2204 through 2212 Processing helix chain 'A' and resid 2227 through 2231 Processing helix chain 'A' and resid 2233 through 2246 removed outlier: 4.059A pdb=" N LEU A2246 " --> pdb=" O ARG A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2334 removed outlier: 3.761A pdb=" N THR A2334 " --> pdb=" O PHE A2330 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2390 removed outlier: 4.134A pdb=" N ALA A2377 " --> pdb=" O LYS A2373 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A2381 " --> pdb=" O ALA A2377 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A2383 " --> pdb=" O ARG A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2506 through 2511 removed outlier: 3.793A pdb=" N GLU A2511 " --> pdb=" O THR A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2525 Processing helix chain 'A' and resid 2529 through 2534 removed outlier: 3.946A pdb=" N VAL A2534 " --> pdb=" O MET A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2550 through 2552 No H-bonds generated for 'chain 'A' and resid 2550 through 2552' Processing helix chain 'A' and resid 2553 through 2569 Processing helix chain 'A' and resid 2614 through 2618 Processing helix chain 'A' and resid 2667 through 2700 Processing helix chain 'A' and resid 2728 through 2735 Processing helix chain 'A' and resid 2789 through 2806 removed outlier: 3.713A pdb=" N GLN A2796 " --> pdb=" O TYR A2792 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A2799 " --> pdb=" O GLN A2795 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A2804 " --> pdb=" O ILE A2800 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A2805 " --> pdb=" O LYS A2801 " (cutoff:3.500A) Processing helix chain 'A' and resid 2808 through 2822 removed outlier: 5.728A pdb=" N MET A2814 " --> pdb=" O ARG A2810 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A2815 " --> pdb=" O GLN A2811 " (cutoff:3.500A) Processing helix chain 'A' and resid 2833 through 2844 Processing helix chain 'A' and resid 2907 through 2926 Processing helix chain 'A' and resid 3024 through 3039 removed outlier: 3.663A pdb=" N LEU A3039 " --> pdb=" O LYS A3035 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3057 removed outlier: 3.571A pdb=" N SER A3046 " --> pdb=" O VAL A3042 " (cutoff:3.500A) Processing helix chain 'A' and resid 3070 through 3082 Processing helix chain 'A' and resid 3108 through 3117 Processing helix chain 'A' and resid 3118 through 3122 Processing helix chain 'A' and resid 3249 through 3266 removed outlier: 3.663A pdb=" N GLU A3254 " --> pdb=" O PRO A3250 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A3257 " --> pdb=" O ALA A3253 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A3259 " --> pdb=" O VAL A3255 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA A3260 " --> pdb=" O GLY A3256 " (cutoff:3.500A) Processing helix chain 'A' and resid 3302 through 3310 removed outlier: 3.694A pdb=" N ALA A3310 " --> pdb=" O GLU A3306 " (cutoff:3.500A) Processing helix chain 'A' and resid 3316 through 3320 Processing helix chain 'A' and resid 3321 through 3329 removed outlier: 4.137A pdb=" N CYS A3325 " --> pdb=" O GLN A3322 " (cutoff:3.500A) Processing helix chain 'A' and resid 3330 through 3345 Processing helix chain 'A' and resid 3410 through 3431 removed outlier: 3.570A pdb=" N LEU A3431 " --> pdb=" O LEU A3427 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.615A pdb=" N THR B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 411 removed outlier: 3.968A pdb=" N HIS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 431 Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.929A pdb=" N THR C 195 " --> pdb=" O PRO C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 396 through 420 removed outlier: 3.648A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 27 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 48 through 71 Processing helix chain 'D' and resid 91 through 107 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.940A pdb=" N GLY D 112 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 150 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.553A pdb=" N LEU D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 206 removed outlier: 3.577A pdb=" N LEU D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 242 removed outlier: 3.656A pdb=" N SER D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 273 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 282 through 293 removed outlier: 3.518A pdb=" N LYS D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 309 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 371 through 377 removed outlier: 3.687A pdb=" N SER D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 432 removed outlier: 3.710A pdb=" N ILE D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 removed outlier: 4.351A pdb=" N PHE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1768 through 1772 removed outlier: 3.518A pdb=" N VAL A1781 " --> pdb=" O LEU A1919 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU A1919 " --> pdb=" O VAL A1781 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A1929 " --> pdb=" O ARG A1922 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2040 through 2046 removed outlier: 3.717A pdb=" N GLN A2160 " --> pdb=" O LEU A2099 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2222 through 2225 Processing sheet with id=AA4, first strand: chain 'A' and resid 2279 through 2282 removed outlier: 3.925A pdb=" N VAL A2294 " --> pdb=" O LYS A2362 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A2362 " --> pdb=" O VAL A2294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2544 through 2545 Processing sheet with id=AA6, first strand: chain 'A' and resid 2848 through 2853 Processing sheet with id=AA7, first strand: chain 'A' and resid 3092 through 3098 Processing sheet with id=AA8, first strand: chain 'A' and resid 3312 through 3315 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 3 removed outlier: 7.135A pdb=" N ARG B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLN B 345 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS B 326 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 309 " --> pdb=" O CYS B 326 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 13 removed outlier: 4.336A pdb=" N LYS B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B 352 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 71 removed outlier: 3.822A pdb=" N PHE B 119 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 127 through 133 removed outlier: 4.326A pdb=" N VAL B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 152 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS B 176 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA B 154 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 190 removed outlier: 4.185A pdb=" N LEU B 198 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.570A pdb=" N THR B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 285 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B 300 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 287 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 14 through 21 removed outlier: 6.872A pdb=" N ILE C 392 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE C 19 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 390 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY C 389 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU C 381 " --> pdb=" O HIS C 371 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N HIS C 371 " --> pdb=" O GLU C 381 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA C 383 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET C 369 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 385 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 31 through 32 removed outlier: 4.329A pdb=" N VAL C 50 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 87 removed outlier: 5.564A pdb=" N ILE C 80 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 102 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 146 through 153 removed outlier: 8.485A pdb=" N THR C 159 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU C 175 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 172 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 181 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 201 through 208 removed outlier: 4.530A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP C 232 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL C 238 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 250 through 256 Processing sheet with id=AC4, first strand: chain 'C' and resid 310 through 316 removed outlier: 3.637A pdb=" N ALA C 329 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N CYS C 337 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 348 through 352 removed outlier: 6.070A pdb=" N ALA D 348 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE D 317 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE D 402 " --> pdb=" O PRO D 398 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5051 1.34 - 1.46: 2627 1.46 - 1.58: 7034 1.58 - 1.70: 0 1.70 - 1.81: 64 Bond restraints: 14776 Sorted by residual: bond pdb=" CA LEU A2325 " pdb=" CB LEU A2325 " ideal model delta sigma weight residual 1.542 1.529 0.013 8.90e-03 1.26e+04 2.24e+00 bond pdb=" CB TRP A2529 " pdb=" CG TRP A2529 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.57e+00 bond pdb=" CG LEU A2185 " pdb=" CD2 LEU A2185 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" CG LEU C 216 " pdb=" CD1 LEU C 216 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" C ARG A2810 " pdb=" N GLN A2811 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.41e-02 5.03e+03 1.35e+00 ... (remaining 14771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 20030 2.51 - 5.02: 234 5.02 - 7.53: 20 7.53 - 10.04: 4 10.04 - 12.55: 4 Bond angle restraints: 20292 Sorted by residual: angle pdb=" N GLN A2617 " pdb=" CA GLN A2617 " pdb=" C GLN A2617 " ideal model delta sigma weight residual 114.56 106.53 8.03 1.27e+00 6.20e-01 4.00e+01 angle pdb=" C LEU A2325 " pdb=" N ARG A2326 " pdb=" CA ARG A2326 " ideal model delta sigma weight residual 121.54 132.65 -11.11 1.91e+00 2.74e-01 3.39e+01 angle pdb=" N GLN A2527 " pdb=" CA GLN A2527 " pdb=" C GLN A2527 " ideal model delta sigma weight residual 114.62 108.26 6.36 1.14e+00 7.69e-01 3.11e+01 angle pdb=" N ARG A2619 " pdb=" CA ARG A2619 " pdb=" C ARG A2619 " ideal model delta sigma weight residual 114.04 108.27 5.77 1.24e+00 6.50e-01 2.16e+01 angle pdb=" N VAL C 318 " pdb=" CA VAL C 318 " pdb=" C VAL C 318 " ideal model delta sigma weight residual 111.91 107.82 4.09 8.90e-01 1.26e+00 2.11e+01 ... (remaining 20287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 7899 17.42 - 34.84: 619 34.84 - 52.27: 150 52.27 - 69.69: 27 69.69 - 87.11: 10 Dihedral angle restraints: 8705 sinusoidal: 2244 harmonic: 6461 Sorted by residual: dihedral pdb=" CA ALA A2539 " pdb=" C ALA A2539 " pdb=" N SER A2540 " pdb=" CA SER A2540 " ideal model delta harmonic sigma weight residual -180.00 -156.06 -23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ALA A2526 " pdb=" C ALA A2526 " pdb=" N GLN A2527 " pdb=" CA GLN A2527 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER C 133 " pdb=" C SER C 133 " pdb=" N CYS C 134 " pdb=" CA CYS C 134 " ideal model delta harmonic sigma weight residual -180.00 -158.16 -21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1957 0.050 - 0.099: 421 0.099 - 0.149: 98 0.149 - 0.198: 1 0.198 - 0.248: 1 Chirality restraints: 2478 Sorted by residual: chirality pdb=" CA PRO A2324 " pdb=" N PRO A2324 " pdb=" C PRO A2324 " pdb=" CB PRO A2324 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA VAL A2655 " pdb=" N VAL A2655 " pdb=" C VAL A2655 " pdb=" CB VAL A2655 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL A2368 " pdb=" N VAL A2368 " pdb=" C VAL A2368 " pdb=" CB VAL A2368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2475 not shown) Planarity restraints: 2708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 89 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO C 90 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A2601 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A2602 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A2602 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2602 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A2644 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO A2645 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A2645 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2645 " -0.030 5.00e-02 4.00e+02 ... (remaining 2705 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 114 2.62 - 3.19: 12271 3.19 - 3.76: 21519 3.76 - 4.33: 26640 4.33 - 4.90: 46414 Nonbonded interactions: 106958 Sorted by model distance: nonbonded pdb=" OH TYR B 207 " pdb=" OD2 ASP B 295 " model vdw 2.048 3.040 nonbonded pdb=" O TYR A2923 " pdb=" OG SER A2926 " model vdw 2.160 3.040 nonbonded pdb=" O MET B 1 " pdb=" NH2 ARG B 343 " model vdw 2.214 3.120 nonbonded pdb=" OG SER C 26 " pdb=" O ALA C 44 " model vdw 2.232 3.040 nonbonded pdb=" O LEU A2325 " pdb=" NH1 ARG A2326 " model vdw 2.232 3.120 ... (remaining 106953 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: 34.760 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: 0.460 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.780 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 : 0.005 0.041 14776 Z= 0.211 Angle : 0.671 12.550 20292 Z= 0.377 Chirality : 0.043 0.248 2478 Planarity : 0.005 0.057 2708 Dihedral : 14.568 87.108 4481 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.79 % Favored : 93.98 % Rotamer: Outliers : 0.20 % Allowed : 23.77 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 0.65 (0.20), residues: 2160 helix: 2.41 (0.20), residues: 753 sheet: -0.11 (0.22), residues: 631 loop : -1.08 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2528 TYR 0.009 0.001 TYR C 225 PHE 0.012 0.001 PHE C 86 TRP 0.019 0.002 TRP A2529 HIS 0.003 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00465 (14776) covalent geometry : angle 0.67069 (20292) hydrogen bonds : bond 0.12700 ( 883) hydrogen bonds : angle 5.53777 ( 2481) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.637 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 55 average time/residue: 0.3741 time to fit residues: 24.6308 Evaluate side-chains 49 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 50.0000 chunk 200 optimal weight: 50.0000 chunk 212 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2793 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.125239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093275 restraints weight = 53458.317| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.99 r_work: 0.3049 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 14776 Z= 0.409 Angle : 0.740 11.992 20292 Z= 0.382 Chirality : 0.047 0.221 2478 Planarity : 0.005 0.062 2708 Dihedral : 4.483 26.949 2286 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.76 % Favored : 93.06 % Rotamer: Outliers : 3.05 % Allowed : 24.56 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 0.51 (0.19), residues: 2160 helix: 2.34 (0.19), residues: 765 sheet: -0.21 (0.22), residues: 618 loop : -1.25 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2326 TYR 0.016 0.002 TYR C 225 PHE 0.018 0.002 PHE C 86 TRP 0.024 0.002 TRP A2684 HIS 0.005 0.001 HIS A3043 Details of bonding type rmsd covalent geometry : bond 0.00933 (14776) covalent geometry : angle 0.73951 (20292) hydrogen bonds : bond 0.04123 ( 883) hydrogen bonds : angle 4.71934 ( 2481) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 0.608 Fit side-chains REVERT: B 407 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8817 (tt) outliers start: 31 outliers final: 8 residues processed: 81 average time/residue: 0.2995 time to fit residues: 29.1602 Evaluate side-chains 56 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 124 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN C 246 GLN C 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.130442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096777 restraints weight = 54457.043| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 5.40 r_work: 0.3149 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14776 Z= 0.161 Angle : 0.574 13.154 20292 Z= 0.292 Chirality : 0.042 0.195 2478 Planarity : 0.004 0.056 2708 Dihedral : 4.129 24.841 2286 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.28 % Favored : 94.54 % Rotamer: Outliers : 3.63 % Allowed : 23.58 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 0.85 (0.19), residues: 2160 helix: 2.65 (0.19), residues: 763 sheet: 0.00 (0.22), residues: 623 loop : -1.09 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2326 TYR 0.011 0.001 TYR B 404 PHE 0.011 0.001 PHE C 86 TRP 0.020 0.002 TRP A2233 HIS 0.003 0.001 HIS A3057 Details of bonding type rmsd covalent geometry : bond 0.00369 (14776) covalent geometry : angle 0.57372 (20292) hydrogen bonds : bond 0.03178 ( 883) hydrogen bonds : angle 4.27809 ( 2481) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 2329 GLU cc_start: 0.6672 (mp0) cc_final: 0.6291 (mp0) REVERT: A 2333 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8895 (tm) outliers start: 37 outliers final: 10 residues processed: 86 average time/residue: 0.3032 time to fit residues: 31.4061 Evaluate side-chains 60 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2250 HIS Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2918 GLN Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 93 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 148 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.125589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093238 restraints weight = 54060.525| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.73 r_work: 0.3224 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14776 Z= 0.184 Angle : 0.580 11.235 20292 Z= 0.294 Chirality : 0.042 0.162 2478 Planarity : 0.004 0.064 2708 Dihedral : 4.058 25.792 2286 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.02 % Favored : 93.75 % Rotamer: Outliers : 3.93 % Allowed : 23.67 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 0.96 (0.19), residues: 2160 helix: 2.76 (0.19), residues: 768 sheet: 0.11 (0.22), residues: 611 loop : -1.13 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2326 TYR 0.011 0.001 TYR B 404 PHE 0.012 0.001 PHE C 86 TRP 0.024 0.002 TRP A2233 HIS 0.005 0.001 HIS C 391 Details of bonding type rmsd covalent geometry : bond 0.00424 (14776) covalent geometry : angle 0.58006 (20292) hydrogen bonds : bond 0.03132 ( 883) hydrogen bonds : angle 4.18926 ( 2481) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 49 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 2326 ARG cc_start: 0.7786 (ptt-90) cc_final: 0.7475 (ptp90) REVERT: A 2329 GLU cc_start: 0.6563 (mp0) cc_final: 0.6213 (mp0) REVERT: A 2333 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8909 (tm) outliers start: 40 outliers final: 18 residues processed: 87 average time/residue: 0.3629 time to fit residues: 37.5019 Evaluate side-chains 68 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2918 GLN Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3039 LEU Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 39 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 8 optimal weight: 40.0000 chunk 54 optimal weight: 0.9980 chunk 189 optimal weight: 50.0000 chunk 132 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3077 HIS C 246 GLN C 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.125711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093276 restraints weight = 53720.675| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 5.09 r_work: 0.3057 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14776 Z= 0.172 Angle : 0.562 11.136 20292 Z= 0.285 Chirality : 0.042 0.163 2478 Planarity : 0.004 0.057 2708 Dihedral : 3.991 24.272 2286 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.46 % Favored : 94.35 % Rotamer: Outliers : 4.13 % Allowed : 24.17 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2160 helix: 2.94 (0.19), residues: 767 sheet: 0.12 (0.22), residues: 612 loop : -1.09 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2326 TYR 0.010 0.001 TYR B 404 PHE 0.011 0.001 PHE C 86 TRP 0.025 0.002 TRP A2233 HIS 0.003 0.001 HIS A3055 Details of bonding type rmsd covalent geometry : bond 0.00397 (14776) covalent geometry : angle 0.56231 (20292) hydrogen bonds : bond 0.02996 ( 883) hydrogen bonds : angle 4.09088 ( 2481) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 52 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 2326 ARG cc_start: 0.7671 (ptt-90) cc_final: 0.7320 (ptt-90) REVERT: A 2329 GLU cc_start: 0.6619 (mp0) cc_final: 0.6237 (mp0) REVERT: A 2333 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8932 (tm) REVERT: A 3040 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8052 (mpt) REVERT: B 304 ASP cc_start: 0.9196 (p0) cc_final: 0.8956 (p0) outliers start: 42 outliers final: 21 residues processed: 91 average time/residue: 0.3241 time to fit residues: 35.1211 Evaluate side-chains 73 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2250 HIS Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2918 GLN Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3039 LEU Chi-restraints excluded: chain A residue 3040 MET Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain A residue 3167 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 375 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 75 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 chunk 129 optimal weight: 0.0980 chunk 183 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 211 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.125774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.093355 restraints weight = 54116.801| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.60 r_work: 0.3263 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14776 Z= 0.120 Angle : 0.538 11.102 20292 Z= 0.271 Chirality : 0.041 0.152 2478 Planarity : 0.004 0.055 2708 Dihedral : 3.818 23.871 2286 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 3.93 % Allowed : 24.36 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.24 (0.19), residues: 2160 helix: 3.08 (0.19), residues: 768 sheet: 0.24 (0.22), residues: 608 loop : -1.05 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2326 TYR 0.010 0.001 TYR B 404 PHE 0.010 0.001 PHE A2552 TRP 0.026 0.001 TRP A2233 HIS 0.003 0.000 HIS A3055 Details of bonding type rmsd covalent geometry : bond 0.00280 (14776) covalent geometry : angle 0.53841 (20292) hydrogen bonds : bond 0.02727 ( 883) hydrogen bonds : angle 3.94611 ( 2481) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 51 time to evaluate : 0.552 Fit side-chains REVERT: A 2326 ARG cc_start: 0.7725 (ptt-90) cc_final: 0.7286 (ptt-90) REVERT: A 2333 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8852 (tm) REVERT: A 2578 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: A 3040 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8047 (mpt) REVERT: B 304 ASP cc_start: 0.9220 (p0) cc_final: 0.8987 (p0) outliers start: 40 outliers final: 18 residues processed: 89 average time/residue: 0.3365 time to fit residues: 35.8893 Evaluate side-chains 71 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2250 HIS Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2578 GLU Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3039 LEU Chi-restraints excluded: chain A residue 3040 MET Chi-restraints excluded: chain A residue 3042 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 40.0000 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 50.0000 chunk 62 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 203 optimal weight: 50.0000 chunk 207 optimal weight: 50.0000 chunk 89 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 190 optimal weight: 40.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3077 HIS C 246 GLN C 391 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.125868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.093589 restraints weight = 53634.823| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.63 r_work: 0.3252 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14776 Z= 0.163 Angle : 0.563 11.146 20292 Z= 0.281 Chirality : 0.042 0.149 2478 Planarity : 0.004 0.049 2708 Dihedral : 3.862 23.921 2286 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.60 % Favored : 94.21 % Rotamer: Outliers : 3.93 % Allowed : 24.26 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.29 (0.20), residues: 2160 helix: 3.15 (0.19), residues: 768 sheet: 0.20 (0.22), residues: 616 loop : -1.00 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2326 TYR 0.010 0.001 TYR B 404 PHE 0.011 0.001 PHE C 86 TRP 0.030 0.002 TRP A2233 HIS 0.003 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00376 (14776) covalent geometry : angle 0.56285 (20292) hydrogen bonds : bond 0.02852 ( 883) hydrogen bonds : angle 3.96400 ( 2481) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 49 time to evaluate : 0.580 Fit side-chains REVERT: A 2326 ARG cc_start: 0.7738 (ptt-90) cc_final: 0.7331 (ptt-90) REVERT: A 2333 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8881 (tm) REVERT: A 3040 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8035 (mpt) REVERT: B 195 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9029 (mm) REVERT: B 304 ASP cc_start: 0.9201 (p0) cc_final: 0.8981 (p0) outliers start: 40 outliers final: 22 residues processed: 87 average time/residue: 0.3276 time to fit residues: 34.4119 Evaluate side-chains 74 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2250 HIS Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2771 ILE Chi-restraints excluded: chain A residue 2930 VAL Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3039 LEU Chi-restraints excluded: chain A residue 3040 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 32 optimal weight: 0.3980 chunk 188 optimal weight: 50.0000 chunk 83 optimal weight: 0.0570 chunk 171 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 22 optimal weight: 50.0000 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.125929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.093678 restraints weight = 53445.364| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.58 r_work: 0.3301 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14776 Z= 0.110 Angle : 0.537 11.238 20292 Z= 0.265 Chirality : 0.041 0.155 2478 Planarity : 0.004 0.048 2708 Dihedral : 3.709 23.747 2286 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.81 % Favored : 95.00 % Rotamer: Outliers : 3.14 % Allowed : 25.34 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.40 (0.20), residues: 2160 helix: 3.26 (0.19), residues: 766 sheet: 0.30 (0.22), residues: 612 loop : -0.98 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2326 TYR 0.010 0.001 TYR B 404 PHE 0.009 0.001 PHE B 90 TRP 0.031 0.002 TRP A2233 HIS 0.002 0.000 HIS A3057 Details of bonding type rmsd covalent geometry : bond 0.00255 (14776) covalent geometry : angle 0.53683 (20292) hydrogen bonds : bond 0.02577 ( 883) hydrogen bonds : angle 3.83351 ( 2481) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.602 Fit side-chains REVERT: A 2326 ARG cc_start: 0.7582 (ptt-90) cc_final: 0.7273 (ptt-90) REVERT: A 2333 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8842 (tm) REVERT: A 3040 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8013 (mpt) REVERT: B 120 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8864 (ttpp) REVERT: B 195 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9111 (mm) REVERT: B 291 MET cc_start: 0.8532 (ptm) cc_final: 0.7663 (ppp) REVERT: B 304 ASP cc_start: 0.9149 (p0) cc_final: 0.8906 (p0) outliers start: 32 outliers final: 17 residues processed: 80 average time/residue: 0.3644 time to fit residues: 34.5968 Evaluate side-chains 71 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3040 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 24 optimal weight: 10.0000 chunk 192 optimal weight: 0.4980 chunk 185 optimal weight: 50.0000 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 191 optimal weight: 50.0000 chunk 49 optimal weight: 0.5980 chunk 100 optimal weight: 50.0000 chunk 31 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.125993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.093690 restraints weight = 53716.933| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 5.08 r_work: 0.3081 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14776 Z= 0.151 Angle : 0.562 11.581 20292 Z= 0.278 Chirality : 0.042 0.172 2478 Planarity : 0.004 0.048 2708 Dihedral : 3.770 23.266 2286 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 3.14 % Allowed : 25.34 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.20), residues: 2160 helix: 3.27 (0.19), residues: 768 sheet: 0.22 (0.22), residues: 623 loop : -0.91 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2326 TYR 0.010 0.001 TYR B 404 PHE 0.011 0.001 PHE C 86 TRP 0.033 0.001 TRP A2233 HIS 0.003 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00350 (14776) covalent geometry : angle 0.56170 (20292) hydrogen bonds : bond 0.02747 ( 883) hydrogen bonds : angle 3.87286 ( 2481) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 50 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 2333 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8897 (tm) REVERT: A 3040 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8066 (mpt) REVERT: B 120 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8896 (ttpp) REVERT: B 195 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 291 MET cc_start: 0.8565 (ptm) cc_final: 0.7714 (ppp) REVERT: B 304 ASP cc_start: 0.9144 (p0) cc_final: 0.8883 (p0) outliers start: 32 outliers final: 19 residues processed: 79 average time/residue: 0.3370 time to fit residues: 31.9230 Evaluate side-chains 73 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3039 LEU Chi-restraints excluded: chain A residue 3040 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 31 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 203 optimal weight: 50.0000 chunk 109 optimal weight: 0.6980 chunk 23 optimal weight: 50.0000 chunk 44 optimal weight: 0.0060 chunk 154 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 192 optimal weight: 30.0000 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.125919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.093560 restraints weight = 54000.676| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.58 r_work: 0.3234 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14776 Z= 0.126 Angle : 0.549 13.707 20292 Z= 0.270 Chirality : 0.041 0.166 2478 Planarity : 0.004 0.048 2708 Dihedral : 3.721 22.928 2286 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 2.85 % Allowed : 25.54 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.45 (0.20), residues: 2160 helix: 3.30 (0.19), residues: 767 sheet: 0.30 (0.22), residues: 609 loop : -0.92 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2326 TYR 0.010 0.001 TYR B 404 PHE 0.009 0.001 PHE C 86 TRP 0.034 0.002 TRP A2233 HIS 0.002 0.000 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00292 (14776) covalent geometry : angle 0.54944 (20292) hydrogen bonds : bond 0.02636 ( 883) hydrogen bonds : angle 3.83184 ( 2481) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 2333 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8860 (tm) REVERT: A 2674 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 3040 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8091 (mpt) REVERT: B 120 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8881 (ttpp) REVERT: B 195 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9061 (mm) REVERT: B 291 MET cc_start: 0.8539 (ptm) cc_final: 0.7699 (ppp) REVERT: B 304 ASP cc_start: 0.9086 (p0) cc_final: 0.8827 (p0) outliers start: 29 outliers final: 21 residues processed: 77 average time/residue: 0.3296 time to fit residues: 30.5388 Evaluate side-chains 76 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2250 HIS Chi-restraints excluded: chain A residue 2333 LEU Chi-restraints excluded: chain A residue 2370 LEU Chi-restraints excluded: chain A residue 2556 SER Chi-restraints excluded: chain A residue 2659 LEU Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2980 THR Chi-restraints excluded: chain A residue 2991 ILE Chi-restraints excluded: chain A residue 3039 LEU Chi-restraints excluded: chain A residue 3040 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 CYS Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 104 optimal weight: 50.0000 chunk 122 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 176 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN C 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.126028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093748 restraints weight = 53789.708| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.74 r_work: 0.3260 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14776 Z= 0.128 Angle : 0.552 13.337 20292 Z= 0.271 Chirality : 0.041 0.186 2478 Planarity : 0.004 0.048 2708 Dihedral : 3.697 22.851 2286 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.37 % Favored : 94.49 % Rotamer: Outliers : 2.75 % Allowed : 25.74 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.49 (0.20), residues: 2160 helix: 3.34 (0.19), residues: 767 sheet: 0.27 (0.22), residues: 618 loop : -0.87 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2326 TYR 0.009 0.001 TYR B 404 PHE 0.009 0.001 PHE C 86 TRP 0.035 0.001 TRP A2233 HIS 0.002 0.001 HIS A2704 Details of bonding type rmsd covalent geometry : bond 0.00298 (14776) covalent geometry : angle 0.55208 (20292) hydrogen bonds : bond 0.02622 ( 883) hydrogen bonds : angle 3.78452 ( 2481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9653.45 seconds wall clock time: 164 minutes 15.85 seconds (9855.85 seconds total)