Starting phenix.real_space_refine on Mon Sep 14 10:37:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9on3_70628/09_2026/9on3_70628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9on3_70628/09_2026/9on3_70628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9on3_70628/09_2026/9on3_70628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9on3_70628/09_2026/9on3_70628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9on3_70628/09_2026/9on3_70628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9on3_70628/09_2026/9on3_70628.map" } resolution = 3.4 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= 0.075 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 107 5.16 5 C 18125 2.51 5 N 4940 2.21 5 O 5439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28611 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 22154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2734, 22154 Classifications: {'peptide': 2734} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 114, 'TRANS': 2619} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3126 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 373} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3071 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 364} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.01, per 1000 atoms: 0.21 Number of scatterers: 28611 At special positions: 0 Unit cell: (114.4, 150.7, 259.6, 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 107 16.00 O 5439 8.00 N 4940 7.00 C 18125 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A1626 " - pdb=" SG CYS A1634 " distance=2.03 Simple disulfide: pdb=" SG CYS A2223 " - pdb=" SG CYS A2255 " distance=2.03 Simple disulfide: pdb=" SG CYS A2340 " - pdb=" SG CYS A2346 " distance=2.04 Simple disulfide: pdb=" SG CYS A2392 " - pdb=" SG CYS A2406 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS C 116 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A3401 " - " ASN A1184 " " NAG A3402 " - " ASN A 629 " " NAG B 501 " - " ASN B 95 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A2143 " " NAG F 1 " - " ASN A2064 " " NAG G 1 " - " ASN A1990 " " NAG H 1 " - " ASN A1261 " " NAG I 1 " - " ASN A1165 " " NAG J 1 " - " ASN A 282 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6646 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 44 sheets defined 29.2% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 110 through 113 removed outlier: 4.035A pdb=" N HIS A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 282 through 288 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.780A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 556 through 560 Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.758A pdb=" N PHE A 691 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 692 " --> pdb=" O THR A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 862 through 864 No H-bonds generated for 'chain 'A' and resid 862 through 864' Processing helix chain 'A' and resid 876 through 888 removed outlier: 3.742A pdb=" N ASP A 880 " --> pdb=" O ASN A 876 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 905 removed outlier: 3.686A pdb=" N ASP A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1011 Processing helix chain 'A' and resid 1014 through 1044 Processing helix chain 'A' and resid 1082 through 1087 removed outlier: 3.786A pdb=" N MET A1086 " --> pdb=" O ASP A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1202 removed outlier: 3.808A pdb=" N LYS A1201 " --> pdb=" O PHE A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1348 No H-bonds generated for 'chain 'A' and resid 1346 through 1348' Processing helix chain 'A' and resid 1529 through 1536 Processing helix chain 'A' and resid 1777 through 1781 removed outlier: 3.596A pdb=" N CYS A1780 " --> pdb=" O HIS A1777 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1831 removed outlier: 3.535A pdb=" N ALA A1828 " --> pdb=" O ILE A1824 " (cutoff:3.500A) Processing helix chain 'A' and resid 1891 through 1899 removed outlier: 3.657A pdb=" N HIS A1895 " --> pdb=" O PRO A1891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1924 Processing helix chain 'A' and resid 1992 through 2003 removed outlier: 3.865A pdb=" N CYS A1996 " --> pdb=" O THR A1992 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A2001 " --> pdb=" O TYR A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2207 through 2211 Processing helix chain 'A' and resid 2216 through 2231 Processing helix chain 'A' and resid 2252 through 2256 removed outlier: 3.927A pdb=" N GLY A2256 " --> pdb=" O PHE A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2257 through 2269 Processing helix chain 'A' and resid 2298 through 2303 removed outlier: 3.669A pdb=" N LEU A2301 " --> pdb=" O LEU A2298 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A2302 " --> pdb=" O GLU A2299 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A2303 " --> pdb=" O GLU A2300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2298 through 2303' Processing helix chain 'A' and resid 2319 through 2333 removed outlier: 3.534A pdb=" N GLU A2332 " --> pdb=" O ASP A2328 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS A2333 " --> pdb=" O ALA A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2357 through 2362 Processing helix chain 'A' and resid 2365 through 2379 Processing helix chain 'A' and resid 2384 through 2396 Processing helix chain 'A' and resid 2403 through 2415 removed outlier: 3.921A pdb=" N THR A2407 " --> pdb=" O LEU A2403 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A2415 " --> pdb=" O GLU A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2425 through 2430 Processing helix chain 'A' and resid 2431 through 2438 Processing helix chain 'A' and resid 2439 through 2443 removed outlier: 3.709A pdb=" N LYS A2442 " --> pdb=" O GLN A2439 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER A2443 " --> pdb=" O ARG A2440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2439 through 2443' Processing helix chain 'A' and resid 2444 through 2458 Processing helix chain 'A' and resid 2721 through 2725 Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 77 through 104 removed outlier: 3.693A pdb=" N LEU B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.753A pdb=" N PHE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 172 removed outlier: 3.541A pdb=" N LEU B 120 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 removed outlier: 4.635A pdb=" N ASP B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 196 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.821A pdb=" N ASP B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 254 Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 261 through 274 removed outlier: 4.059A pdb=" N ALA B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 4.014A pdb=" N ALA B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 315 through 322 removed outlier: 3.846A pdb=" N GLN B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.592A pdb=" N TRP B 334 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B 335 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 341 through 347 removed outlier: 4.436A pdb=" N ASN B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 367 removed outlier: 3.678A pdb=" N ARG B 367 " --> pdb=" O GLN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 392 removed outlier: 4.443A pdb=" N TYR B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.503A pdb=" N LYS B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 77 through 105 removed outlier: 3.831A pdb=" N TRP C 82 " --> pdb=" O CYS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 185 removed outlier: 3.891A pdb=" N GLU C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.929A pdb=" N LEU C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 234 Processing helix chain 'C' and resid 237 through 255 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 261 through 274 removed outlier: 3.962A pdb=" N ALA C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 281 through 302 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 315 through 322 removed outlier: 3.795A pdb=" N GLN C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 322 " --> pdb=" O HIS C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 328 Processing helix chain 'C' and resid 330 through 335 removed outlier: 4.358A pdb=" N ARG C 335 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 removed outlier: 3.889A pdb=" N VAL C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 349 through 366 Processing helix chain 'C' and resid 371 through 393 removed outlier: 4.442A pdb=" N TYR C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 393 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 410 removed outlier: 3.504A pdb=" N PHE C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 418 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 4.008A pdb=" N PHE A 7 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.501A pdb=" N LYS A 15 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 364 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 344 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 359 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.590A pdb=" N GLU A 27 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.590A pdb=" N GLU A 27 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.789A pdb=" N LEU A 107 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG A 97 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU A 105 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN A 99 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 125 through 128 removed outlier: 3.899A pdb=" N ILE A 137 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AA8, first strand: chain 'A' and resid 180 through 184 Processing sheet with id=AA9, first strand: chain 'A' and resid 235 through 236 removed outlier: 3.890A pdb=" N THR A 250 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 253 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A 270 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 258 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS A 268 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 290 through 292 Processing sheet with id=AB2, first strand: chain 'A' and resid 402 through 403 removed outlier: 7.143A pdb=" N TYR A 402 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N ASN A 636 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR A 590 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE A 605 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 588 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU A 607 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR A 586 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 577 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N TYR A 591 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 11.712A pdb=" N TYR A 575 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 576 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY A 540 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.566A pdb=" N LEU A 495 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N TYR A 484 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 11.712A pdb=" N TYR A 575 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N TYR A 591 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 577 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR A 586 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU A 607 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 588 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE A 605 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR A 590 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 638 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 648 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 642 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N TRP A 645 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N ASP A 660 " --> pdb=" O TRP A 645 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LYS A 647 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS A 658 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 649 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 668 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TRP A 667 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 676 " --> pdb=" O ARG A1212 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 682 " --> pdb=" O PHE A1206 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N PHE A1206 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 684 " --> pdb=" O SER A1204 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N SER A1204 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR A1207 " --> pdb=" O TYR A1223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 428 through 435 removed outlier: 3.640A pdb=" N LEU A 432 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A 445 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 434 " --> pdb=" O VAL A 443 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 443 " --> pdb=" O GLU A 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB6, first strand: chain 'A' and resid 695 through 696 removed outlier: 3.523A pdb=" N VAL A1190 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 702 through 705 removed outlier: 5.656A pdb=" N ILE A 726 " --> pdb=" O GLU A 741 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 741 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 752 through 755 removed outlier: 3.693A pdb=" N LEU A 762 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 772 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASP A 792 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLN A 778 " --> pdb=" O GLU A 786 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLU A 786 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR A 780 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 798 through 801 removed outlier: 3.538A pdb=" N VAL A 798 " --> pdb=" O CYS A 809 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 809 " --> pdb=" O VAL A 798 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 800 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 815 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 814 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AC2, first strand: chain 'A' and resid 907 through 909 removed outlier: 4.010A pdb=" N LEU A 933 " --> pdb=" O ILE A 914 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 916 " --> pdb=" O PHE A 931 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 947 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 907 through 909 removed outlier: 4.010A pdb=" N LEU A 933 " --> pdb=" O ILE A 914 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 916 " --> pdb=" O PHE A 931 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 926 " --> pdb=" O ILE A 953 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 961 through 964 removed outlier: 7.077A pdb=" N VAL A 970 " --> pdb=" O MET A 989 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET A 989 " --> pdb=" O VAL A 970 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 972 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1056 through 1057 removed outlier: 4.144A pdb=" N VAL A1062 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A1079 " --> pdb=" O GLN A1068 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 3.571A pdb=" N ALA A1102 " --> pdb=" O LYS A1111 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A1111 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1112 " --> pdb=" O VAL A1121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.536A pdb=" N GLU A1158 " --> pdb=" O PHE A1153 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1230 through 1233 Processing sheet with id=AC9, first strand: chain 'A' and resid 1256 through 1260 Processing sheet with id=AD1, first strand: chain 'A' and resid 1301 through 1303 removed outlier: 3.595A pdb=" N ILE A1312 " --> pdb=" O ILE A1302 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1325 through 1327 removed outlier: 3.632A pdb=" N ARG A1387 " --> pdb=" O ASP A1465 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1325 through 1327 removed outlier: 6.550A pdb=" N TYR A1433 " --> pdb=" O HIS A1425 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A1437 " --> pdb=" O GLY A1421 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLY A1421 " --> pdb=" O THR A1437 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N ASP A1439 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 10.809A pdb=" N LEU A1419 " --> pdb=" O ASP A1439 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A1421 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU A1404 " --> pdb=" O GLY A1421 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N LYS A1423 " --> pdb=" O ASN A1402 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N ASN A1402 " --> pdb=" O LYS A1423 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N HIS A1425 " --> pdb=" O MET A1400 " (cutoff:3.500A) removed outlier: 11.313A pdb=" N MET A1400 " --> pdb=" O HIS A1425 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1480 through 1483 removed outlier: 3.623A pdb=" N ALA A1492 " --> pdb=" O VAL A1482 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG A1491 " --> pdb=" O ASN A1503 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A1513 " --> pdb=" O LEU A1504 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1524 through 1527 removed outlier: 7.109A pdb=" N VAL A1699 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A1715 " --> pdb=" O VAL A1699 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1701 " --> pdb=" O VAL A1713 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A1713 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A1703 " --> pdb=" O VAL A1711 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL A1711 " --> pdb=" O ILE A1727 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A1737 " --> pdb=" O ILE A1728 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1524 through 1527 removed outlier: 7.109A pdb=" N VAL A1699 " --> pdb=" O VAL A1715 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A1715 " --> pdb=" O VAL A1699 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1701 " --> pdb=" O VAL A1713 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL A1713 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A1703 " --> pdb=" O VAL A1711 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL A1711 " --> pdb=" O ILE A1727 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1549 through 1552 removed outlier: 3.635A pdb=" N TYR A1549 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1693 " --> pdb=" O THR A1551 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A1686 " --> pdb=" O TYR A1576 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1549 through 1552 removed outlier: 3.635A pdb=" N TYR A1549 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1693 " --> pdb=" O THR A1551 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU A1690 " --> pdb=" O VAL A1603 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A1603 " --> pdb=" O GLU A1690 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A1662 " --> pdb=" O VAL A1654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A1656 " --> pdb=" O LEU A1660 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1620 through 1623 Processing sheet with id=AE1, first strand: chain 'A' and resid 1761 through 1762 removed outlier: 3.560A pdb=" N GLN A1761 " --> pdb=" O SER A1770 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1817 through 1819 removed outlier: 6.119A pdb=" N ILE A1849 " --> pdb=" O TRP A1865 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TRP A1865 " --> pdb=" O ILE A1849 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A1851 " --> pdb=" O LYS A1863 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS A1863 " --> pdb=" O ALA A1851 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A1853 " --> pdb=" O VAL A1861 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A1861 " --> pdb=" O TYR A1877 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A1876 " --> pdb=" O VAL A1889 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A1889 " --> pdb=" O THR A1876 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR A1878 " --> pdb=" O ILE A1887 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE A1887 " --> pdb=" O TYR A1927 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1925 " --> pdb=" O VAL A1889 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER A1926 " --> pdb=" O LYS A1937 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A1937 " --> pdb=" O SER A1926 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU A1928 " --> pdb=" O ILE A1935 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1944 through 1949 removed outlier: 6.801A pdb=" N THR A1944 " --> pdb=" O HIS A1960 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS A1960 " --> pdb=" O THR A1944 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU A1946 " --> pdb=" O SER A1958 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A1958 " --> pdb=" O GLU A1946 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A1948 " --> pdb=" O ARG A1956 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ARG A1956 " --> pdb=" O PHE A1975 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A1971 " --> pdb=" O HIS A1960 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A1972 " --> pdb=" O VAL A1989 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N MET A1984 " --> pdb=" O SER A2014 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A1988 " --> pdb=" O ASP A2010 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP A2010 " --> pdb=" O LEU A1988 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A2032 " --> pdb=" O GLU A2043 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A2036 " --> pdb=" O ASN A2039 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N GLN A2040 " --> pdb=" O VAL A2060 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N VAL A2060 " --> pdb=" O GLN A2040 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N MET A2042 " --> pdb=" O PHE A2058 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE A2058 " --> pdb=" O MET A2042 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A2044 " --> pdb=" O LYS A2056 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A2056 " --> pdb=" O SER A2044 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A2046 " --> pdb=" O ILE A2054 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A2054 " --> pdb=" O TYR A2071 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A2070 " --> pdb=" O ARG A2082 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLU A2074 " --> pdb=" O LEU A2078 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU A2078 " --> pdb=" O GLU A2074 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LYS A2077 " --> pdb=" O TYR A2098 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N TYR A2098 " --> pdb=" O LYS A2077 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N HIS A2079 " --> pdb=" O TYR A2096 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A2106 " --> pdb=" O ASP A2097 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A2107 " --> pdb=" O PHE A2117 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A2117 " --> pdb=" O ILE A2107 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE A2153 " --> pdb=" O VAL A2164 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A2187 " --> pdb=" O SER A2165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A2188 " --> pdb=" O HIS A2279 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A2277 " --> pdb=" O PHE A2190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A2278 " --> pdb=" O PHE A2295 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A2295 " --> pdb=" O GLY A2278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 2281 through 2283 removed outlier: 7.140A pdb=" N ILE A2290 " --> pdb=" O SER A2469 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A2469 " --> pdb=" O ILE A2290 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET A2480 " --> pdb=" O TYR A2470 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A2472 " --> pdb=" O HIS A2478 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS A2478 " --> pdb=" O ILE A2472 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG A2479 " --> pdb=" O LEU A2490 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG A2487 " --> pdb=" O ARG A2504 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG A2504 " --> pdb=" O ARG A2487 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A2489 " --> pdb=" O LEU A2502 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A2502 " --> pdb=" O ARG A2489 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU A2491 " --> pdb=" O THR A2500 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR A2500 " --> pdb=" O MET A2519 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 2336 through 2337 removed outlier: 3.513A pdb=" N THR A2337 " --> pdb=" O ARG A2349 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 2535 through 2541 removed outlier: 6.528A pdb=" N ILE A2535 " --> pdb=" O MET A2552 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET A2552 " --> pdb=" O ILE A2535 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N HIS A2537 " --> pdb=" O ILE A2550 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE A2550 " --> pdb=" O HIS A2537 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA A2539 " --> pdb=" O SER A2548 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N ARG A2546 " --> pdb=" O TYR A2562 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N TYR A2562 " --> pdb=" O ARG A2546 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N SER A2548 " --> pdb=" O TYR A2560 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR A2569 " --> pdb=" O TYR A2585 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A2585 " --> pdb=" O THR A2569 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS A2571 " --> pdb=" O GLU A2583 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU A2583 " --> pdb=" O LYS A2571 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A2573 " --> pdb=" O MET A2581 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A2625 " --> pdb=" O ILE A2617 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS A2619 " --> pdb=" O LEU A2623 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A2623 " --> pdb=" O LYS A2619 " (cutoff:3.500A) removed outlier: 12.457A pdb=" N GLN A2622 " --> pdb=" O THR A2637 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N THR A2637 " --> pdb=" O GLN A2622 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A2624 " --> pdb=" O VAL A2635 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ARG A2644 " --> pdb=" O ALA A2655 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A2655 " --> pdb=" O ARG A2644 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A2646 " --> pdb=" O VAL A2653 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A2655 " --> pdb=" O PHE A2668 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A2657 " --> pdb=" O ARG A2666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 2684 through 2686 removed outlier: 3.761A pdb=" N GLU A2684 " --> pdb=" O ASN A2693 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A2691 " --> pdb=" O GLU A2686 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 55 through 59 removed outlier: 3.905A pdb=" N VAL C 59 " --> pdb=" O CYS B 55 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 57 " --> pdb=" O ILE C 57 " (cutoff:3.500A) 1220 hydrogen bonds defined for protein. 3363 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: 13.00 Time building geometry restraints manager: 3.35 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: 9387 1.34 - 1.46: 6313 1.46 - 1.58: 13366 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 29250 Sorted by residual: bond pdb=" N ILE A1140 " pdb=" CA ILE A1140 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.12e+01 bond pdb=" N ILE A1132 " pdb=" CA ILE A1132 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N VAL A1134 " pdb=" CA VAL A1134 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.63e+00 bond pdb=" N ASN A1335 " pdb=" CA ASN A1335 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.33e-02 5.65e+03 7.81e+00 bond pdb=" N TYR A1139 " pdb=" CA TYR A1139 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.16e-02 7.43e+03 7.73e+00 ... (remaining 29245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 38582 1.44 - 2.89: 822 2.89 - 4.33: 134 4.33 - 5.78: 24 5.78 - 7.22: 10 Bond angle restraints: 39572 Sorted by residual: angle pdb=" N PRO A1137 " pdb=" CA PRO A1137 " pdb=" C PRO A1137 " ideal model delta sigma weight residual 112.47 105.49 6.98 2.06e+00 2.36e-01 1.15e+01 angle pdb=" CA GLU A1435 " pdb=" C GLU A1435 " pdb=" O GLU A1435 " ideal model delta sigma weight residual 121.58 117.88 3.70 1.16e+00 7.43e-01 1.02e+01 angle pdb=" N VAL A1135 " pdb=" CA VAL A1135 " pdb=" C VAL A1135 " ideal model delta sigma weight residual 112.80 109.23 3.57 1.15e+00 7.56e-01 9.61e+00 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 108.88 115.30 -6.42 2.16e+00 2.14e-01 8.84e+00 angle pdb=" CA SER A 442 " pdb=" C SER A 442 " pdb=" O SER A 442 " ideal model delta sigma weight residual 121.56 118.02 3.54 1.21e+00 6.83e-01 8.55e+00 ... (remaining 39567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16144 17.91 - 35.81: 1501 35.81 - 53.72: 237 53.72 - 71.62: 47 71.62 - 89.53: 20 Dihedral angle restraints: 17949 sinusoidal: 7621 harmonic: 10328 Sorted by residual: dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS C 78 " pdb=" CB CYS C 78 " ideal model delta sinusoidal sigma weight residual -86.00 -160.27 74.27 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS A2223 " pdb=" SG CYS A2223 " pdb=" SG CYS A2255 " pdb=" CB CYS A2255 " ideal model delta sinusoidal sigma weight residual 93.00 138.09 -45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS B 99 " pdb=" SG CYS B 99 " pdb=" SG CYS C 99 " pdb=" CB CYS C 99 " ideal model delta sinusoidal sigma weight residual 93.00 48.76 44.24 1 1.00e+01 1.00e-02 2.72e+01 ... (remaining 17946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4283 0.137 - 0.275: 24 0.275 - 0.412: 1 0.412 - 0.549: 1 0.549 - 0.686: 1 Chirality restraints: 4310 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A1990 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG A3401 " pdb=" ND2 ASN A1184 " pdb=" C2 NAG A3401 " pdb=" O5 NAG A3401 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1165 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 4307 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1990 " 0.003 2.00e-02 2.50e+03 2.86e-02 1.03e+01 pdb=" CG ASN A1990 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A1990 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A1990 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1138 " 0.282 9.50e-02 1.11e+02 1.27e-01 9.84e+00 pdb=" NE ARG A1138 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A1138 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A1138 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1138 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1718 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO A1719 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A1719 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1719 " 0.032 5.00e-02 4.00e+02 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2322 2.74 - 3.28: 26709 3.28 - 3.82: 44916 3.82 - 4.36: 51506 4.36 - 4.90: 92359 Nonbonded interactions: 217812 Sorted by model distance: nonbonded pdb=" OG1 THR B 77 " pdb=" OD1 ASP B 79 " model vdw 2.204 3.040 nonbonded pdb=" O TYR B 245 " pdb=" OH TYR B 267 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR C 278 " pdb=" OD1 ASP C 286 " model vdw 2.240 3.040 nonbonded pdb=" O PHE B 213 " pdb=" NH1 ARG B 224 " model vdw 2.250 3.120 nonbonded pdb=" OE2 GLU B 293 " pdb=" OG SER B 325 " model vdw 2.260 3.040 ... (remaining 217807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 54 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 431)) selection = (chain 'C' and (resid 54 through 169 or (resid 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 through 175 or (resid 176 through 184 a \ nd (name N or name CA or name C or name O or name CB )) or resid 185 through 431 \ )) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' } 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: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 34.920 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29278 Z= 0.145 Angle : 0.554 11.880 39647 Z= 0.298 Chirality : 0.046 0.686 4310 Planarity : 0.004 0.127 5127 Dihedral : 13.869 89.526 11276 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.20 % Allowed : 0.36 % Favored : 99.45 % 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: -0.67 (0.14), residues: 3494 helix: 1.21 (0.17), residues: 900 sheet: -0.62 (0.18), residues: 969 loop : -1.25 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 727 TYR 0.017 0.001 TYR A1337 PHE 0.015 0.001 PHE A 626 TRP 0.017 0.001 TRP A 281 HIS 0.007 0.001 HIS A1468 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (29250) covalent geometry : angle 0.53612 / 0.29 (39572) SS BOND : bond 0.00228 / 0.15 ( 9) SS BOND : angle 1.01865 / 0.52 ( 18) hydrogen bonds : bond 0.14915 / 9.76 ( 1152) hydrogen bonds : angle 6.72815 / 4.58 ( 3363) link_BETA1-4 : bond 0.00512 / 0.35 ( 9) link_BETA1-4 : angle 2.37102 / 1.85 ( 27) link_NAG-ASN : bond 0.00849 / 0.44 ( 10) link_NAG-ASN : angle 4.50549 / 3.76 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 427 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6579 (mtp-110) REVERT: A 69 SER cc_start: 0.7821 (p) cc_final: 0.7217 (m) REVERT: A 80 TYR cc_start: 0.7263 (m-80) cc_final: 0.7058 (m-10) REVERT: A 239 ASP cc_start: 0.7588 (p0) cc_final: 0.7325 (p0) REVERT: A 337 MET cc_start: 0.9061 (mmt) cc_final: 0.8706 (mmt) REVERT: A 616 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8170 (ttpt) REVERT: A 642 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 667 TRP cc_start: 0.7657 (p-90) cc_final: 0.7153 (p-90) REVERT: A 768 TYR cc_start: 0.7669 (m-80) cc_final: 0.7409 (m-80) REVERT: A 814 LEU cc_start: 0.8041 (tt) cc_final: 0.7624 (tt) REVERT: A 859 THR cc_start: 0.8091 (t) cc_final: 0.7891 (p) REVERT: A 864 ASN cc_start: 0.8553 (m110) cc_final: 0.7882 (t0) REVERT: A 910 TYR cc_start: 0.7811 (t80) cc_final: 0.7289 (t80) REVERT: A 929 LYS cc_start: 0.7711 (mttm) cc_final: 0.7293 (tppt) REVERT: A 1078 GLN cc_start: 0.8235 (mp10) cc_final: 0.7955 (mp10) REVERT: A 1114 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7712 (tm-30) REVERT: A 1182 HIS cc_start: 0.7001 (p-80) cc_final: 0.6528 (p-80) REVERT: A 1340 ASP cc_start: 0.7095 (m-30) cc_final: 0.6829 (m-30) REVERT: A 1769 MET cc_start: 0.9027 (ttm) cc_final: 0.8622 (ttm) REVERT: A 2215 MET cc_start: 0.7192 (tpp) cc_final: 0.6857 (tpp) REVERT: A 2356 PHE cc_start: 0.7447 (m-80) cc_final: 0.7192 (m-80) REVERT: A 2552 MET cc_start: 0.8700 (mmm) cc_final: 0.8439 (mmm) REVERT: B 168 ASP cc_start: 0.7748 (m-30) cc_final: 0.7392 (m-30) REVERT: B 227 ASN cc_start: 0.6795 (m-40) cc_final: 0.6314 (m110) outliers start: 6 outliers final: 2 residues processed: 432 average time/residue: 0.1881 time to fit residues: 129.7204 Evaluate side-chains 268 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1138 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 GLN A1426 HIS A1503 ASN B 131 HIS B 279 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 249 GLN C 258 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.171832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.133089 restraints weight = 49816.203| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.81 r_work: 0.3459 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29278 Z= 0.120 Angle : 0.561 11.828 39647 Z= 0.292 Chirality : 0.045 0.557 4310 Planarity : 0.004 0.054 5127 Dihedral : 4.921 46.305 4292 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.04 % Allowed : 6.54 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3494 helix: 1.48 (0.17), residues: 895 sheet: -0.37 (0.18), residues: 949 loop : -1.20 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1539 TYR 0.024 0.001 TYR B 220 PHE 0.021 0.001 PHE A1352 TRP 0.014 0.001 TRP A 667 HIS 0.006 0.001 HIS A1468 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (29250) covalent geometry : angle 0.54625 / 0.29 (39572) SS BOND : bond 0.00280 / 0.17 ( 9) SS BOND : angle 0.78986 / 0.44 ( 18) hydrogen bonds : bond 0.04434 / 2.93 ( 1152) hydrogen bonds : angle 5.47355 / 3.73 ( 3363) link_BETA1-4 : bond 0.00517 / 0.34 ( 9) link_BETA1-4 : angle 2.27741 / 1.75 ( 27) link_NAG-ASN : bond 0.00766 / 0.47 ( 10) link_NAG-ASN : angle 4.13666 / 3.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.6919 (ttt90) cc_final: 0.6468 (mtp-110) REVERT: A 69 SER cc_start: 0.7675 (p) cc_final: 0.7215 (m) REVERT: A 337 MET cc_start: 0.9012 (mmt) cc_final: 0.8717 (mmt) REVERT: A 616 LYS cc_start: 0.8257 (ttpt) cc_final: 0.8029 (ttpt) REVERT: A 814 LEU cc_start: 0.8032 (tt) cc_final: 0.7765 (tt) REVERT: A 864 ASN cc_start: 0.8352 (m110) cc_final: 0.7957 (t0) REVERT: A 910 TYR cc_start: 0.7950 (t80) cc_final: 0.7345 (t80) REVERT: A 929 LYS cc_start: 0.8107 (mttm) cc_final: 0.7404 (tptt) REVERT: A 1078 GLN cc_start: 0.8158 (mp10) cc_final: 0.7922 (mp10) REVERT: A 1149 LEU cc_start: 0.7863 (tp) cc_final: 0.7617 (tp) REVERT: A 1182 HIS cc_start: 0.6982 (p-80) cc_final: 0.6527 (p-80) REVERT: A 1340 ASP cc_start: 0.6935 (m-30) cc_final: 0.6732 (m-30) REVERT: A 2215 MET cc_start: 0.7426 (tpp) cc_final: 0.7112 (tpp) REVERT: A 2552 MET cc_start: 0.8666 (mmm) cc_final: 0.8412 (mmm) REVERT: B 95 ASN cc_start: 0.8142 (m-40) cc_final: 0.7339 (m-40) REVERT: B 208 GLU cc_start: 0.8359 (pt0) cc_final: 0.7993 (mm-30) REVERT: B 227 ASN cc_start: 0.7758 (m-40) cc_final: 0.7498 (m110) REVERT: B 246 GLN cc_start: 0.7513 (mt0) cc_final: 0.6844 (pp30) REVERT: C 342 PRO cc_start: 0.4326 (Cg_exo) cc_final: 0.4118 (Cg_endo) outliers start: 32 outliers final: 23 residues processed: 305 average time/residue: 0.1757 time to fit residues: 89.3398 Evaluate side-chains 274 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1162 GLN Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain A residue 2729 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 249 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 224 optimal weight: 0.7980 chunk 320 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN B 195 ASN B 317 GLN B 318 HIS C 68 HIS C 249 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.172125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133123 restraints weight = 50178.583| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.62 r_work: 0.3479 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.002 0.076 29278 Z= 0.114 Angle : 0.548 19.494 39647 Z= 0.279 Chirality : 0.044 0.382 4310 Planarity : 0.004 0.051 5127 Dihedral : 5.811 106.260 4287 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.40 % Allowed : 8.43 % Favored : 90.17 % 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: -0.33 (0.15), residues: 3494 helix: 1.55 (0.17), residues: 900 sheet: -0.30 (0.18), residues: 944 loop : -1.15 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 353 TYR 0.021 0.001 TYR A 789 PHE 0.024 0.001 PHE B 231 TRP 0.014 0.001 TRP A 557 HIS 0.012 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (29250) covalent geometry : angle 0.52795 / 0.27 (39572) SS BOND : bond 0.00221 / 0.14 ( 9) SS BOND : angle 0.69551 / 0.39 ( 18) hydrogen bonds : bond 0.03972 / 2.63 ( 1152) hydrogen bonds : angle 5.09574 / 3.48 ( 3363) link_BETA1-4 : bond 0.00390 / 0.25 ( 9) link_BETA1-4 : angle 2.18420 / 1.66 ( 27) link_NAG-ASN : bond 0.01703 / 1.18 ( 10) link_NAG-ASN : angle 5.02046 / 3.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 SER cc_start: 0.7660 (p) cc_final: 0.7203 (m) REVERT: A 337 MET cc_start: 0.8993 (mmt) cc_final: 0.8734 (mmt) REVERT: A 616 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8073 (ttmt) REVERT: A 747 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8015 (mm-40) REVERT: A 814 LEU cc_start: 0.7932 (tt) cc_final: 0.7602 (tt) REVERT: A 864 ASN cc_start: 0.8237 (m110) cc_final: 0.7949 (t0) REVERT: A 910 TYR cc_start: 0.7888 (t80) cc_final: 0.7411 (t80) REVERT: A 929 LYS cc_start: 0.7911 (mttm) cc_final: 0.7168 (mmmt) REVERT: A 1078 GLN cc_start: 0.8227 (mp10) cc_final: 0.7910 (mp10) REVERT: A 1182 HIS cc_start: 0.6959 (p-80) cc_final: 0.6521 (p-80) REVERT: A 1340 ASP cc_start: 0.6897 (m-30) cc_final: 0.6691 (m-30) REVERT: A 2040 GLN cc_start: 0.7363 (tp40) cc_final: 0.7074 (tp40) REVERT: A 2215 MET cc_start: 0.7413 (tpp) cc_final: 0.7090 (tpp) REVERT: A 2552 MET cc_start: 0.8622 (mmm) cc_final: 0.8379 (mmm) REVERT: B 95 ASN cc_start: 0.7950 (m-40) cc_final: 0.7657 (m-40) REVERT: B 208 GLU cc_start: 0.8287 (pt0) cc_final: 0.7919 (mm-30) REVERT: C 127 MET cc_start: 0.8445 (tmm) cc_final: 0.8184 (tmm) REVERT: C 143 HIS cc_start: 0.8207 (m170) cc_final: 0.7988 (m170) REVERT: C 155 MET cc_start: 0.8829 (tmm) cc_final: 0.8409 (tmm) REVERT: C 342 PRO cc_start: 0.4272 (Cg_exo) cc_final: 0.4071 (Cg_endo) outliers start: 43 outliers final: 22 residues processed: 289 average time/residue: 0.1708 time to fit residues: 83.0368 Evaluate side-chains 269 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 2021 SER Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2400 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 201 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN A1412 ASN A1767 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.168672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129816 restraints weight = 49994.251| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.83 r_work: 0.3410 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29278 Z= 0.207 Angle : 0.606 15.223 39647 Z= 0.314 Chirality : 0.045 0.335 4310 Planarity : 0.004 0.053 5127 Dihedral : 6.026 117.700 4287 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.66 % Allowed : 9.93 % Favored : 88.42 % 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: -0.46 (0.15), residues: 3494 helix: 1.59 (0.17), residues: 899 sheet: -0.45 (0.18), residues: 937 loop : -1.28 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1539 TYR 0.027 0.002 TYR A1337 PHE 0.032 0.002 PHE A 626 TRP 0.020 0.002 TRP A 281 HIS 0.012 0.001 HIS A1468 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (29250) covalent geometry : angle 0.59113 / 0.31 (39572) SS BOND : bond 0.00310 / 0.21 ( 9) SS BOND : angle 0.77738 / 0.45 ( 18) hydrogen bonds : bond 0.04302 / 2.86 ( 1152) hydrogen bonds : angle 5.06785 / 3.46 ( 3363) link_BETA1-4 : bond 0.00565 / 0.40 ( 9) link_BETA1-4 : angle 2.22622 / 1.69 ( 27) link_NAG-ASN : bond 0.00840 / 0.57 ( 10) link_NAG-ASN : angle 4.50351 / 3.29 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6716 (mp0) REVERT: A 69 SER cc_start: 0.7709 (p) cc_final: 0.7326 (m) REVERT: A 193 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8677 (mp) REVERT: A 337 MET cc_start: 0.8908 (mmt) cc_final: 0.8675 (mmt) REVERT: A 616 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7869 (ttpt) REVERT: A 814 LEU cc_start: 0.8013 (tt) cc_final: 0.7735 (tt) REVERT: A 910 TYR cc_start: 0.8088 (t80) cc_final: 0.7823 (t80) REVERT: A 929 LYS cc_start: 0.7887 (mttm) cc_final: 0.7190 (mmmt) REVERT: A 2215 MET cc_start: 0.7450 (tpp) cc_final: 0.7158 (tpp) REVERT: B 95 ASN cc_start: 0.8109 (m-40) cc_final: 0.7808 (m-40) REVERT: B 113 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7542 (p) REVERT: C 143 HIS cc_start: 0.8172 (m-70) cc_final: 0.7864 (m170) REVERT: C 155 MET cc_start: 0.8830 (tmm) cc_final: 0.8346 (tmm) outliers start: 51 outliers final: 32 residues processed: 289 average time/residue: 0.1752 time to fit residues: 85.4473 Evaluate side-chains 279 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1809 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1954 ILE Chi-restraints excluded: chain A residue 2021 SER Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2319 ASP Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 285 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN A1141 GLN A1412 ASN B 318 HIS ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.170399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131917 restraints weight = 50041.407| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.48 r_work: 0.3432 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29278 Z= 0.127 Angle : 0.544 14.277 39647 Z= 0.281 Chirality : 0.044 0.363 4310 Planarity : 0.004 0.053 5127 Dihedral : 5.843 117.054 4287 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.56 % Allowed : 11.16 % Favored : 87.28 % 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: -0.33 (0.15), residues: 3494 helix: 1.65 (0.17), residues: 900 sheet: -0.37 (0.18), residues: 947 loop : -1.18 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.020 0.001 TYR A 789 PHE 0.018 0.001 PHE A 626 TRP 0.013 0.001 TRP A2685 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (29250) covalent geometry : angle 0.52817 / 0.28 (39572) SS BOND : bond 0.00254 / 0.16 ( 9) SS BOND : angle 0.72222 / 0.39 ( 18) hydrogen bonds : bond 0.03824 / 2.53 ( 1152) hydrogen bonds : angle 4.89783 / 3.35 ( 3363) link_BETA1-4 : bond 0.00564 / 0.39 ( 9) link_BETA1-4 : angle 2.16492 / 1.60 ( 27) link_NAG-ASN : bond 0.00759 / 0.48 ( 10) link_NAG-ASN : angle 4.32850 / 3.22 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6518 (mp0) REVERT: A 69 SER cc_start: 0.7731 (p) cc_final: 0.7314 (m) REVERT: A 80 TYR cc_start: 0.7370 (m-80) cc_final: 0.7005 (m-10) REVERT: A 337 MET cc_start: 0.8982 (mmt) cc_final: 0.8721 (mmt) REVERT: A 616 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7809 (ttpt) REVERT: A 814 LEU cc_start: 0.8018 (tt) cc_final: 0.7744 (tt) REVERT: A 864 ASN cc_start: 0.8403 (m110) cc_final: 0.7902 (t0) REVERT: A 929 LYS cc_start: 0.7914 (mttm) cc_final: 0.7207 (mmmt) REVERT: A 1077 GLN cc_start: 0.8061 (pt0) cc_final: 0.7318 (pt0) REVERT: A 1168 MET cc_start: 0.7658 (ptm) cc_final: 0.7334 (ptm) REVERT: A 1182 HIS cc_start: 0.6744 (p-80) cc_final: 0.6357 (p90) REVERT: A 1340 ASP cc_start: 0.6878 (m-30) cc_final: 0.6606 (m-30) REVERT: A 1393 MET cc_start: 0.8289 (ppp) cc_final: 0.8010 (ppp) REVERT: A 2051 GLU cc_start: 0.7855 (tp30) cc_final: 0.7569 (tp30) REVERT: A 2215 MET cc_start: 0.7452 (tpp) cc_final: 0.7079 (tpp) REVERT: B 95 ASN cc_start: 0.8267 (m-40) cc_final: 0.7988 (m-40) REVERT: C 155 MET cc_start: 0.8880 (tmm) cc_final: 0.8397 (tmm) outliers start: 48 outliers final: 32 residues processed: 286 average time/residue: 0.1661 time to fit residues: 79.9988 Evaluate side-chains 271 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 845 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2021 SER Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2729 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 9 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 0.0970 chunk 242 optimal weight: 10.0000 chunk 1 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2248 ASN C 68 HIS ** C 90 HIS ** 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 = 0.4269 r_free = 0.4269 target = 0.170272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131147 restraints weight = 50076.637| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.80 r_work: 0.3443 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29278 Z= 0.125 Angle : 0.544 13.489 39647 Z= 0.279 Chirality : 0.044 0.348 4310 Planarity : 0.004 0.051 5127 Dihedral : 5.800 117.721 4287 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.92 % Allowed : 11.58 % Favored : 86.50 % 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: -0.28 (0.15), residues: 3494 helix: 1.69 (0.17), residues: 899 sheet: -0.36 (0.18), residues: 950 loop : -1.14 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1170 TYR 0.024 0.001 TYR A 789 PHE 0.019 0.001 PHE A 626 TRP 0.014 0.001 TRP C 82 HIS 0.014 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (29250) covalent geometry : angle 0.52811 / 0.28 (39572) SS BOND : bond 0.00314 / 0.17 ( 9) SS BOND : angle 0.93953 / 0.47 ( 18) hydrogen bonds : bond 0.03727 / 2.47 ( 1152) hydrogen bonds : angle 4.80229 / 3.29 ( 3363) link_BETA1-4 : bond 0.00568 / 0.40 ( 9) link_BETA1-4 : angle 2.18608 / 1.59 ( 27) link_NAG-ASN : bond 0.00702 / 0.46 ( 10) link_NAG-ASN : angle 4.28409 / 3.21 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 260 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6447 (mp0) REVERT: A 69 SER cc_start: 0.7717 (p) cc_final: 0.7301 (m) REVERT: A 80 TYR cc_start: 0.7368 (m-80) cc_final: 0.7071 (m-10) REVERT: A 337 MET cc_start: 0.8926 (mmt) cc_final: 0.8675 (mmt) REVERT: A 616 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7769 (ttpt) REVERT: A 814 LEU cc_start: 0.8028 (tt) cc_final: 0.7800 (tt) REVERT: A 864 ASN cc_start: 0.8164 (m110) cc_final: 0.7761 (t0) REVERT: A 929 LYS cc_start: 0.7902 (mttm) cc_final: 0.7193 (mmmt) REVERT: A 946 LYS cc_start: 0.8644 (mppt) cc_final: 0.8207 (mmtm) REVERT: A 1077 GLN cc_start: 0.8074 (pt0) cc_final: 0.7317 (pt0) REVERT: A 1168 MET cc_start: 0.7532 (ptm) cc_final: 0.7075 (ptm) REVERT: A 1182 HIS cc_start: 0.6702 (p-80) cc_final: 0.6306 (p90) REVERT: A 1340 ASP cc_start: 0.6650 (m-30) cc_final: 0.6393 (m-30) REVERT: A 2051 GLU cc_start: 0.7814 (tp30) cc_final: 0.7558 (tp30) REVERT: A 2215 MET cc_start: 0.7406 (tpp) cc_final: 0.7085 (tpp) REVERT: B 95 ASN cc_start: 0.8159 (m-40) cc_final: 0.7886 (m-40) REVERT: C 143 HIS cc_start: 0.8157 (m-70) cc_final: 0.7885 (m170) REVERT: C 155 MET cc_start: 0.8776 (tmm) cc_final: 0.8363 (tmm) outliers start: 59 outliers final: 39 residues processed: 296 average time/residue: 0.1688 time to fit residues: 84.0632 Evaluate side-chains 281 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1809 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1990 ASN Chi-restraints excluded: chain A residue 2021 SER Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 242 optimal weight: 0.0670 chunk 84 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 274 optimal weight: 0.8980 chunk 333 optimal weight: 30.0000 chunk 219 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 HIS A 744 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN A1078 GLN C 68 HIS ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.169387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.130569 restraints weight = 49904.578| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.79 r_work: 0.3431 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29278 Z= 0.155 Angle : 0.567 12.756 39647 Z= 0.292 Chirality : 0.044 0.369 4310 Planarity : 0.004 0.051 5127 Dihedral : 5.868 118.278 4287 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.92 % Allowed : 12.17 % Favored : 85.91 % 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: -0.32 (0.15), residues: 3494 helix: 1.68 (0.17), residues: 901 sheet: -0.37 (0.18), residues: 945 loop : -1.17 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1170 TYR 0.022 0.001 TYR A1337 PHE 0.024 0.002 PHE A 626 TRP 0.015 0.001 TRP C 82 HIS 0.015 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (29250) covalent geometry : angle 0.55290 / 0.29 (39572) SS BOND : bond 0.00273 / 0.19 ( 9) SS BOND : angle 0.78104 / 0.43 ( 18) hydrogen bonds : bond 0.03843 / 2.54 ( 1152) hydrogen bonds : angle 4.80203 / 3.29 ( 3363) link_BETA1-4 : bond 0.00606 / 0.44 ( 9) link_BETA1-4 : angle 2.22643 / 1.61 ( 27) link_NAG-ASN : bond 0.00678 / 0.43 ( 10) link_NAG-ASN : angle 4.17229 / 3.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 257 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.7384 (m-80) cc_final: 0.7111 (m-10) REVERT: A 616 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7747 (ttpt) REVERT: A 814 LEU cc_start: 0.7974 (tt) cc_final: 0.7743 (tt) REVERT: A 864 ASN cc_start: 0.8211 (m110) cc_final: 0.7750 (t0) REVERT: A 929 LYS cc_start: 0.7762 (mttm) cc_final: 0.7043 (mmmt) REVERT: A 946 LYS cc_start: 0.8626 (mppt) cc_final: 0.8200 (mmtm) REVERT: A 1077 GLN cc_start: 0.7917 (pt0) cc_final: 0.7588 (pp30) REVERT: A 1182 HIS cc_start: 0.6791 (p-80) cc_final: 0.6379 (p90) REVERT: A 1796 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6747 (tm-30) REVERT: A 2051 GLU cc_start: 0.7822 (tp30) cc_final: 0.7571 (tp30) REVERT: A 2215 MET cc_start: 0.7420 (tpp) cc_final: 0.7118 (tpp) REVERT: B 95 ASN cc_start: 0.8252 (m-40) cc_final: 0.8000 (m-40) REVERT: B 231 PHE cc_start: 0.6678 (t80) cc_final: 0.6427 (t80) REVERT: C 143 HIS cc_start: 0.8059 (m-70) cc_final: 0.7777 (m170) REVERT: C 155 MET cc_start: 0.8675 (tmm) cc_final: 0.8300 (tmm) outliers start: 59 outliers final: 46 residues processed: 293 average time/residue: 0.1786 time to fit residues: 87.4596 Evaluate side-chains 290 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1185 GLU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1809 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 1990 ASN Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 132 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 256 optimal weight: 0.5980 chunk 257 optimal weight: 0.9980 chunk 283 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN C 68 HIS ** C 90 HIS ** 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 = 0.4268 r_free = 0.4268 target = 0.170032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131187 restraints weight = 50045.232| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.73 r_work: 0.3432 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29278 Z= 0.127 Angle : 0.550 12.231 39647 Z= 0.284 Chirality : 0.044 0.359 4310 Planarity : 0.004 0.052 5127 Dihedral : 5.802 118.253 4287 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.76 % Allowed : 12.82 % Favored : 85.42 % 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: -0.22 (0.15), residues: 3494 helix: 1.80 (0.17), residues: 892 sheet: -0.36 (0.18), residues: 961 loop : -1.10 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.023 0.001 TYR C 134 PHE 0.026 0.001 PHE A 745 TRP 0.017 0.001 TRP C 82 HIS 0.019 0.001 HIS A 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (29250) covalent geometry : angle 0.53549 / 0.28 (39572) SS BOND : bond 0.00241 / 0.15 ( 9) SS BOND : angle 0.73451 / 0.41 ( 18) hydrogen bonds : bond 0.03689 / 2.45 ( 1152) hydrogen bonds : angle 4.74299 / 3.25 ( 3363) link_BETA1-4 : bond 0.00574 / 0.41 ( 9) link_BETA1-4 : angle 2.16361 / 1.57 ( 27) link_NAG-ASN : bond 0.00686 / 0.43 ( 10) link_NAG-ASN : angle 4.05088 / 3.06 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.7362 (m-80) cc_final: 0.7114 (m-10) REVERT: A 616 LYS cc_start: 0.8140 (ttpt) cc_final: 0.7736 (ttpt) REVERT: A 814 LEU cc_start: 0.7963 (tt) cc_final: 0.7736 (tt) REVERT: A 864 ASN cc_start: 0.8356 (m110) cc_final: 0.7772 (t0) REVERT: A 946 LYS cc_start: 0.8641 (mppt) cc_final: 0.8202 (mmtm) REVERT: A 1182 HIS cc_start: 0.6850 (p-80) cc_final: 0.6349 (p90) REVERT: A 1796 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6771 (tm-30) REVERT: A 2051 GLU cc_start: 0.7709 (tp30) cc_final: 0.7494 (tp30) REVERT: A 2215 MET cc_start: 0.7439 (tpp) cc_final: 0.7106 (tpp) REVERT: B 95 ASN cc_start: 0.8298 (m-40) cc_final: 0.8031 (m-40) REVERT: B 231 PHE cc_start: 0.6663 (t80) cc_final: 0.6291 (t80) REVERT: C 143 HIS cc_start: 0.8114 (m-70) cc_final: 0.7874 (m170) REVERT: C 155 MET cc_start: 0.8781 (tmm) cc_final: 0.8377 (tmm) outliers start: 54 outliers final: 47 residues processed: 288 average time/residue: 0.1768 time to fit residues: 85.3861 Evaluate side-chains 289 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 744 HIS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1809 THR Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1954 ILE Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2018 GLU Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 208 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 180 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 86 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 307 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 744 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** 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 = 0.4280 r_free = 0.4280 target = 0.171113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132121 restraints weight = 49825.007| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.94 r_work: 0.3449 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29278 Z= 0.112 Angle : 0.562 17.373 39647 Z= 0.286 Chirality : 0.052 1.799 4310 Planarity : 0.004 0.051 5127 Dihedral : 5.945 118.065 4287 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.59 % Allowed : 13.34 % Favored : 85.06 % Cbeta Deviations : 0.03 % 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: -0.13 (0.15), residues: 3494 helix: 1.86 (0.17), residues: 893 sheet: -0.29 (0.18), residues: 961 loop : -1.04 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1170 TYR 0.029 0.001 TYR B 285 PHE 0.028 0.001 PHE B 213 TRP 0.018 0.001 TRP C 82 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (29250) covalent geometry : angle 0.53961 / 0.28 (39572) SS BOND : bond 0.00236 / 0.14 ( 9) SS BOND : angle 0.70731 / 0.40 ( 18) hydrogen bonds : bond 0.03512 / 2.33 ( 1152) hydrogen bonds : angle 4.66467 / 3.19 ( 3363) link_BETA1-4 : bond 0.00572 / 0.40 ( 9) link_BETA1-4 : angle 2.50195 / 1.69 ( 27) link_NAG-ASN : bond 0.00994 / 0.51 ( 10) link_NAG-ASN : angle 5.30293 / 4.30 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.7459 (m-80) cc_final: 0.7129 (m-10) REVERT: A 616 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7718 (ttpt) REVERT: A 814 LEU cc_start: 0.7893 (tt) cc_final: 0.7645 (tt) REVERT: A 864 ASN cc_start: 0.8338 (m110) cc_final: 0.7729 (t0) REVERT: A 946 LYS cc_start: 0.8637 (mppt) cc_final: 0.8210 (mmtm) REVERT: A 1182 HIS cc_start: 0.6826 (p-80) cc_final: 0.6301 (p90) REVERT: A 1340 ASP cc_start: 0.6771 (m-30) cc_final: 0.6515 (m-30) REVERT: A 1796 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6799 (tm-30) REVERT: A 1969 MET cc_start: 0.7572 (tpp) cc_final: 0.7315 (tpp) REVERT: A 2051 GLU cc_start: 0.7936 (tp30) cc_final: 0.7616 (tp30) REVERT: A 2215 MET cc_start: 0.7436 (tpp) cc_final: 0.7098 (tpp) REVERT: A 2707 TYR cc_start: 0.8001 (m-10) cc_final: 0.7737 (m-10) REVERT: B 95 ASN cc_start: 0.8279 (m-40) cc_final: 0.8002 (m-40) REVERT: C 83 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: C 143 HIS cc_start: 0.8090 (m-70) cc_final: 0.7877 (m90) REVERT: C 155 MET cc_start: 0.8725 (tmm) cc_final: 0.8364 (tmm) outliers start: 49 outliers final: 41 residues processed: 287 average time/residue: 0.1814 time to fit residues: 87.0862 Evaluate side-chains 285 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2021 SER Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain A residue 2637 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 187 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 328 optimal weight: 20.0000 chunk 344 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 276 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 744 HIS ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS ** C 90 HIS ** 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 = 0.4247 r_free = 0.4247 target = 0.168187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.129446 restraints weight = 49657.300| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.59 r_work: 0.3392 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29278 Z= 0.211 Angle : 0.633 18.206 39647 Z= 0.327 Chirality : 0.052 1.539 4310 Planarity : 0.004 0.054 5127 Dihedral : 6.321 118.670 4287 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.63 % Allowed : 13.28 % Favored : 85.10 % 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: -0.39 (0.15), residues: 3494 helix: 1.74 (0.17), residues: 896 sheet: -0.48 (0.18), residues: 958 loop : -1.25 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1470 TYR 0.028 0.002 TYR A1337 PHE 0.033 0.002 PHE A 626 TRP 0.019 0.002 TRP C 82 HIS 0.013 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (29250) covalent geometry : angle 0.61413 / 0.32 (39572) SS BOND : bond 0.00310 / 0.21 ( 9) SS BOND : angle 0.82358 / 0.46 ( 18) hydrogen bonds : bond 0.04088 / 2.70 ( 1152) hydrogen bonds : angle 4.86712 / 3.33 ( 3363) link_BETA1-4 : bond 0.00528 / 0.36 ( 9) link_BETA1-4 : angle 2.36342 / 1.71 ( 27) link_NAG-ASN : bond 0.00986 / 0.50 ( 10) link_NAG-ASN : angle 5.17837 / 4.27 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6988 Ramachandran restraints generated. 3494 Oldfield, 0 Emsley, 3494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 TYR cc_start: 0.7421 (m-80) cc_final: 0.7171 (m-10) REVERT: A 616 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7789 (ttpt) REVERT: A 814 LEU cc_start: 0.7930 (tt) cc_final: 0.7647 (tt) REVERT: A 864 ASN cc_start: 0.8355 (m110) cc_final: 0.7708 (t0) REVERT: A 946 LYS cc_start: 0.8618 (mppt) cc_final: 0.8392 (mppt) REVERT: A 1182 HIS cc_start: 0.7012 (p-80) cc_final: 0.6341 (p90) REVERT: A 1796 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 2051 GLU cc_start: 0.7812 (tp30) cc_final: 0.7532 (tp30) REVERT: A 2215 MET cc_start: 0.7492 (tpp) cc_final: 0.7143 (tpp) REVERT: B 95 ASN cc_start: 0.8273 (m-40) cc_final: 0.7999 (m-40) REVERT: C 155 MET cc_start: 0.8812 (tmm) cc_final: 0.8379 (tmm) outliers start: 50 outliers final: 44 residues processed: 280 average time/residue: 0.1640 time to fit residues: 78.6088 Evaluate side-chains 285 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1397 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain A residue 1453 ILE Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1747 HIS Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 2011 LEU Chi-restraints excluded: chain A residue 2018 GLU Chi-restraints excluded: chain A residue 2085 MET Chi-restraints excluded: chain A residue 2310 THR Chi-restraints excluded: chain A residue 2372 MET Chi-restraints excluded: chain A residue 2564 VAL Chi-restraints excluded: chain A residue 2637 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 25 optimal weight: 1.9990 chunk 296 optimal weight: 0.0470 chunk 279 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 236 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 329 optimal weight: 6.9990 overall best weight: 0.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 744 HIS ** A 753 HIS ** 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 = 0.4272 r_free = 0.4272 target = 0.170362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131904 restraints weight = 49931.125| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.48 r_work: 0.3420 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29278 Z= 0.119 Angle : 0.571 16.331 39647 Z= 0.293 Chirality : 0.048 1.302 4310 Planarity : 0.004 0.055 5127 Dihedral : 6.185 118.227 4287 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.46 % Allowed : 13.67 % Favored : 84.87 % 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: -0.20 (0.15), residues: 3494 helix: 1.90 (0.17), residues: 887 sheet: -0.38 (0.18), residues: 963 loop : -1.10 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1117 TYR 0.022 0.001 TYR B 285 PHE 0.037 0.001 PHE B 213 TRP 0.019 0.001 TRP C 82 HIS 0.012 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29250) covalent geometry : angle 0.55263 / 0.29 (39572) SS BOND : bond 0.00252 / 0.16 ( 9) SS BOND : angle 0.70125 / 0.41 ( 18) hydrogen bonds : bond 0.03601 / 2.37 ( 1152) hydrogen bonds : angle 4.72504 / 3.23 ( 3363) link_BETA1-4 : bond 0.00591 / 0.42 ( 9) link_BETA1-4 : angle 2.21018 / 1.58 ( 27) link_NAG-ASN : bond 0.00991 / 0.50 ( 10) link_NAG-ASN : angle 4.88356 / 3.98 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7221.05 seconds wall clock time: 124 minutes 30.81 seconds (7470.81 seconds total)