Starting phenix.real_space_refine on Sat Jan 25 23:43:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxw_42787/01_2025/8uxw_42787_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxw_42787/01_2025/8uxw_42787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uxw_42787/01_2025/8uxw_42787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxw_42787/01_2025/8uxw_42787.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxw_42787/01_2025/8uxw_42787_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxw_42787/01_2025/8uxw_42787_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.090 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: 7 Type Number sf(0) Gaussians P 21 5.49 5 Mg 10 5.21 5 S 230 5.16 5 C 24684 2.51 5 N 6643 2.21 5 O 7441 1.98 5 H 38330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 287 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 77359 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 6226 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 379} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 6153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6153 Classifications: {'peptide': 387} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5576 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 340} Chain breaks: 1 Chain: "D" Number of atoms: 5153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5153 Classifications: {'peptide': 316} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2746 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2781 Classifications: {'peptide': 168} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 2362 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "H" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5758 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.65, per 1000 atoms: 0.36 Number of scatterers: 77359 At special positions: 0 Unit cell: (129.216, 205.938, 227.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 230 16.00 P 21 15.00 Mg 10 11.99 O 7441 8.00 N 6643 7.00 C 24684 6.00 H 38330 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 217 " - pdb=" SG CYS N 257 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.15 Conformation dependent library (CDL) restraints added in 4.8 seconds 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 72 sheets defined 48.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.580A pdb=" N LYS A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 135 through 149 removed outlier: 3.565A pdb=" N ARG A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.542A pdb=" N ALA A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.556A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.679A pdb=" N TYR A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 341 through 366 removed outlier: 3.715A pdb=" N SER A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.585A pdb=" N GLU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.550A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.029A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.653A pdb=" N GLN B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.665A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.141A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 325 Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.044A pdb=" N ARG B 332 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 361 removed outlier: 3.608A pdb=" N ASP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.817A pdb=" N TRP B 368 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 378 removed outlier: 3.731A pdb=" N GLU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.613A pdb=" N LYS B 384 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 Processing helix chain 'C' and resid 316 through 330 Processing helix chain 'D' and resid 8 through 21 removed outlier: 3.660A pdb=" N SER D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.604A pdb=" N ASN D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 120 through 140 Processing helix chain 'D' and resid 143 through 155 removed outlier: 3.992A pdb=" N SER D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 removed outlier: 3.848A pdb=" N VAL D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 removed outlier: 6.696A pdb=" N ALA D 208 " --> pdb=" O ARG D 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN D 210 " --> pdb=" O PRO D 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 210' Processing helix chain 'D' and resid 223 through 227 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.604A pdb=" N VAL D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 297 removed outlier: 3.872A pdb=" N LYS D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 42 through 55 removed outlier: 4.386A pdb=" N ARG E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA E 53 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 84 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 125 through 150 removed outlier: 3.749A pdb=" N SER E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 168 through 172 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 36 through 41 removed outlier: 3.571A pdb=" N VAL F 40 " --> pdb=" O PRO F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 80 through 97 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 166 removed outlier: 5.007A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 168 No H-bonds generated for 'chain 'F' and resid 167 through 168' Processing helix chain 'G' and resid 2 through 6 removed outlier: 4.168A pdb=" N THR G 5 " --> pdb=" O THR G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.718A pdb=" N ILE G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 49 Proline residue: G 41 - end of helix removed outlier: 3.607A pdb=" N ILE G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 60 Processing helix chain 'G' and resid 69 through 87 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 100 through 116 Processing helix chain 'G' and resid 122 through 138 removed outlier: 3.691A pdb=" N LEU G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 148 Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 removed outlier: 3.892A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.865A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.586A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 204 through 217 Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 234 through 237 Processing helix chain 'H' and resid 252 through 263 Proline residue: H 258 - end of helix removed outlier: 4.590A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 291 removed outlier: 3.546A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.425A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.693A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 Processing helix chain 'I' and resid 55 through 62 Processing helix chain 'I' and resid 78 through 92 removed outlier: 4.047A pdb=" N LYS I 84 " --> pdb=" O ASP I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.003A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET I 123 " --> pdb=" O MET I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 143 removed outlier: 4.046A pdb=" N TYR I 143 " --> pdb=" O VAL I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.713A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 202 through 217 removed outlier: 3.789A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 260 Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 261 through 262 No H-bonds generated for 'chain 'I' and resid 261 through 262' Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'I' and resid 273 through 285 Processing helix chain 'I' and resid 288 through 295 removed outlier: 4.260A pdb=" N ASP I 292 " --> pdb=" O ILE I 289 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR I 294 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 4.142A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 351 through 355 removed outlier: 4.354A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 removed outlier: 5.688A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 373 removed outlier: 4.341A pdb=" N HIS I 371 " --> pdb=" O SER I 368 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 373 " --> pdb=" O VAL I 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 61 Processing helix chain 'M' and resid 78 through 92 Processing helix chain 'M' and resid 97 through 101 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.774A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 146 Processing helix chain 'M' and resid 181 through 193 Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 202 through 214 Processing helix chain 'M' and resid 222 through 231 Processing helix chain 'M' and resid 252 through 260 Proline residue: M 258 - end of helix Processing helix chain 'M' and resid 261 through 262 No H-bonds generated for 'chain 'M' and resid 261 through 262' Processing helix chain 'M' and resid 263 through 268 Processing helix chain 'M' and resid 273 through 285 Processing helix chain 'M' and resid 289 through 295 Processing helix chain 'M' and resid 301 through 306 removed outlier: 4.357A pdb=" N TYR M 306 " --> pdb=" O THR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 321 Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 337 through 349 Processing helix chain 'M' and resid 350 through 355 removed outlier: 3.592A pdb=" N GLN M 353 " --> pdb=" O SER M 350 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 removed outlier: 5.690A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 374 removed outlier: 3.735A pdb=" N ARG M 372 " --> pdb=" O SER M 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 78 through 92 Processing helix chain 'N' and resid 97 through 101 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.949A pdb=" N ARG N 116 " --> pdb=" O PRO N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 145 removed outlier: 3.649A pdb=" N SER N 141 " --> pdb=" O GLN N 137 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR N 143 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 194 removed outlier: 3.568A pdb=" N THR N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 197 No H-bonds generated for 'chain 'N' and resid 195 through 197' Processing helix chain 'N' and resid 202 through 217 removed outlier: 4.213A pdb=" N LYS N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS N 217 " --> pdb=" O LYS N 213 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 232 removed outlier: 3.547A pdb=" N ALA N 231 " --> pdb=" O MET N 227 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER N 232 " --> pdb=" O ALA N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 260 Proline residue: N 258 - end of helix Processing helix chain 'N' and resid 261 through 262 No H-bonds generated for 'chain 'N' and resid 261 through 262' Processing helix chain 'N' and resid 263 through 268 Processing helix chain 'N' and resid 273 through 285 Processing helix chain 'N' and resid 289 through 295 Processing helix chain 'N' and resid 301 through 305 Processing helix chain 'N' and resid 308 through 321 Processing helix chain 'N' and resid 337 through 347 Processing helix chain 'N' and resid 359 through 366 removed outlier: 3.677A pdb=" N GLU N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 374 removed outlier: 4.084A pdb=" N ARG N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 Processing helix chain 'O' and resid 78 through 92 Processing helix chain 'O' and resid 97 through 101 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.964A pdb=" N ARG O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 145 removed outlier: 3.581A pdb=" N TYR O 143 " --> pdb=" O VAL O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 197 removed outlier: 4.204A pdb=" N GLU O 195 " --> pdb=" O LYS O 191 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 217 removed outlier: 3.553A pdb=" N ILE O 208 " --> pdb=" O ALA O 204 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS O 215 " --> pdb=" O ASP O 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 232 Processing helix chain 'O' and resid 252 through 260 Proline residue: O 258 - end of helix Processing helix chain 'O' and resid 261 through 262 No H-bonds generated for 'chain 'O' and resid 261 through 262' Processing helix chain 'O' and resid 263 through 268 Processing helix chain 'O' and resid 273 through 285 Processing helix chain 'O' and resid 289 through 295 Processing helix chain 'O' and resid 301 through 305 Processing helix chain 'O' and resid 308 through 321 Processing helix chain 'O' and resid 337 through 347 Processing helix chain 'O' and resid 351 through 355 Processing helix chain 'O' and resid 359 through 366 Processing helix chain 'O' and resid 367 through 373 Processing helix chain 'P' and resid 55 through 61 Processing helix chain 'P' and resid 78 through 92 Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.890A pdb=" N ARG P 116 " --> pdb=" O PRO P 112 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET P 123 " --> pdb=" O MET P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 146 Processing helix chain 'P' and resid 181 through 194 removed outlier: 3.563A pdb=" N THR P 194 " --> pdb=" O MET P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 197 No H-bonds generated for 'chain 'P' and resid 195 through 197' Processing helix chain 'P' and resid 202 through 217 removed outlier: 3.581A pdb=" N GLU P 207 " --> pdb=" O THR P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 232 Processing helix chain 'P' and resid 252 through 260 Proline residue: P 258 - end of helix Processing helix chain 'P' and resid 261 through 262 No H-bonds generated for 'chain 'P' and resid 261 through 262' Processing helix chain 'P' and resid 263 through 268 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 289 through 295 Processing helix chain 'P' and resid 301 through 305 Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 334 through 336 No H-bonds generated for 'chain 'P' and resid 334 through 336' Processing helix chain 'P' and resid 337 through 349 Processing helix chain 'P' and resid 351 through 355 removed outlier: 4.371A pdb=" N GLN P 354 " --> pdb=" O THR P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 359 through 366 removed outlier: 3.794A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 369 through 374 Processing helix chain 'Q' and resid 55 through 61 Processing helix chain 'Q' and resid 78 through 92 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.918A pdb=" N ARG Q 116 " --> pdb=" O PRO Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 146 Processing helix chain 'Q' and resid 181 through 195 removed outlier: 4.020A pdb=" N GLU Q 195 " --> pdb=" O LYS Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 217 removed outlier: 3.753A pdb=" N GLU Q 207 " --> pdb=" O THR Q 203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 233 Processing helix chain 'Q' and resid 234 through 237 Processing helix chain 'Q' and resid 252 through 257 removed outlier: 3.510A pdb=" N CYS Q 257 " --> pdb=" O GLU Q 253 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 262 Processing helix chain 'Q' and resid 263 through 268 Processing helix chain 'Q' and resid 273 through 285 Processing helix chain 'Q' and resid 286 through 294 removed outlier: 3.655A pdb=" N ARG Q 290 " --> pdb=" O ASP Q 286 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS Q 291 " --> pdb=" O ILE Q 287 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP Q 292 " --> pdb=" O ASP Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 305 Processing helix chain 'Q' and resid 308 through 321 Processing helix chain 'Q' and resid 334 through 336 No H-bonds generated for 'chain 'Q' and resid 334 through 336' Processing helix chain 'Q' and resid 337 through 349 Processing helix chain 'Q' and resid 350 through 353 Processing helix chain 'Q' and resid 359 through 363 Processing helix chain 'Q' and resid 366 through 368 No H-bonds generated for 'chain 'Q' and resid 366 through 368' Processing helix chain 'Q' and resid 369 through 374 Processing helix chain 'R' and resid 55 through 61 Processing helix chain 'R' and resid 78 through 92 Processing helix chain 'R' and resid 97 through 101 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.919A pdb=" N ARG R 116 " --> pdb=" O PRO R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.729A pdb=" N SER R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 Processing helix chain 'R' and resid 195 through 197 No H-bonds generated for 'chain 'R' and resid 195 through 197' Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.957A pdb=" N GLU R 207 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE R 208 " --> pdb=" O ALA R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 230 Processing helix chain 'R' and resid 231 through 236 removed outlier: 6.877A pdb=" N SER R 234 " --> pdb=" O ALA R 231 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER R 235 " --> pdb=" O SER R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 260 Proline residue: R 258 - end of helix Processing helix chain 'R' and resid 261 through 262 No H-bonds generated for 'chain 'R' and resid 261 through 262' Processing helix chain 'R' and resid 263 through 268 Processing helix chain 'R' and resid 273 through 285 removed outlier: 3.582A pdb=" N CYS R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 295 Processing helix chain 'R' and resid 301 through 306 removed outlier: 4.342A pdb=" N TYR R 306 " --> pdb=" O THR R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 Processing helix chain 'R' and resid 337 through 349 Processing helix chain 'R' and resid 351 through 355 removed outlier: 4.280A pdb=" N GLN R 354 " --> pdb=" O THR R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 359 through 364 Processing helix chain 'R' and resid 366 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.459A pdb=" N ILE A 8 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR A 129 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N MET A 10 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 126 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA A 158 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 128 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.583A pdb=" N ILE A 330 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 271 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 30 removed outlier: 6.754A pdb=" N ILE B 6 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR B 106 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU B 8 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 9 removed outlier: 6.803A pdb=" N VAL C 372 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 362 " --> pdb=" O TYR C 353 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 349 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 16 through 19 removed outlier: 4.546A pdb=" N GLU C 16 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 35 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU C 37 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.602A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 79 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 103 through 108 removed outlier: 3.741A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.877A pdb=" N LYS C 169 " --> pdb=" O CYS C 165 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER C 174 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 198 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 208 through 213 removed outlier: 3.804A pdb=" N SER C 228 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 243 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 254 through 261 removed outlier: 6.588A pdb=" N ALA C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 278 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS C 286 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN C 280 " --> pdb=" O TRP C 284 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 162 removed outlier: 6.991A pdb=" N GLU D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AC6, first strand: chain 'F' and resid 47 through 56 removed outlier: 5.435A pdb=" N LYS F 49 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N SER F 65 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.629A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'I' and resid 29 through 32 removed outlier: 4.113A pdb=" N THR I 106 " --> pdb=" O CYS I 10 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'M' and resid 29 through 32 removed outlier: 4.732A pdb=" N ASN M 12 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'M' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'M' and resid 176 through 178 removed outlier: 6.340A pdb=" N ASN M 297 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 176 through 178 removed outlier: 3.612A pdb=" N GLN O 41 " --> pdb=" O ALA M 170 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.759A pdb=" N THR N 106 " --> pdb=" O CYS N 10 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN N 12 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'N' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'N' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'N' and resid 169 through 170 removed outlier: 6.395A pdb=" N ILE N 151 " --> pdb=" O VAL N 298 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N SER N 300 " --> pdb=" O ILE N 151 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU N 153 " --> pdb=" O SER N 300 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN N 297 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'O' and resid 29 through 32 removed outlier: 6.624A pdb=" N LEU O 8 " --> pdb=" O LEU O 104 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR O 106 " --> pdb=" O LEU O 8 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N CYS O 10 " --> pdb=" O THR O 106 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 53 through 54 Processing sheet with id=AF6, first strand: chain 'O' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'O' and resid 169 through 170 Processing sheet with id=AF8, first strand: chain 'O' and resid 169 through 170 removed outlier: 6.521A pdb=" N ILE O 151 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER O 300 " --> pdb=" O ILE O 151 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU O 153 " --> pdb=" O SER O 300 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN O 297 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 238 through 241 Processing sheet with id=AG1, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.734A pdb=" N LEU P 8 " --> pdb=" O LEU P 104 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR P 106 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N CYS P 10 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 53 through 54 Processing sheet with id=AG3, first strand: chain 'P' and resid 71 through 72 Processing sheet with id=AG4, first strand: chain 'P' and resid 169 through 170 Processing sheet with id=AG5, first strand: chain 'P' and resid 169 through 170 removed outlier: 6.445A pdb=" N ASN P 297 " --> pdb=" O ILE P 330 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 238 through 241 Processing sheet with id=AG7, first strand: chain 'Q' and resid 29 through 32 removed outlier: 6.767A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR Q 106 " --> pdb=" O LEU Q 8 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS Q 10 " --> pdb=" O THR Q 106 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AG9, first strand: chain 'Q' and resid 71 through 72 Processing sheet with id=AH1, first strand: chain 'Q' and resid 169 through 170 Processing sheet with id=AH2, first strand: chain 'Q' and resid 169 through 170 removed outlier: 6.470A pdb=" N ASN Q 297 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 238 through 241 Processing sheet with id=AH4, first strand: chain 'R' and resid 29 through 32 removed outlier: 6.523A pdb=" N LEU R 8 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR R 106 " --> pdb=" O LEU R 8 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N CYS R 10 " --> pdb=" O THR R 106 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 53 through 54 Processing sheet with id=AH6, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AH7, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AH8, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AH9, first strand: chain 'R' and resid 238 through 241 1933 hydrogen bonds defined for protein. 5043 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: 36.49 Time building geometry restraints manager: 18.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 0.98: 846 0.98 - 1.19: 37421 1.19 - 1.40: 14272 1.40 - 1.61: 25290 1.61 - 1.82: 396 Bond restraints: 78225 Sorted by residual: bond pdb=" NH2 ARG I 210 " pdb="HH21 ARG I 210 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR P 278 " pdb=" H THR P 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG D 162 " pdb="HH22 ARG D 162 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 TYR B 143 " pdb=" HE1 TYR B 143 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLU Q 107 " pdb=" H GLU Q 107 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 78220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 134924 4.61 - 9.22: 6257 9.22 - 13.84: 93 13.84 - 18.45: 4 18.45 - 23.06: 8 Bond angle restraints: 141286 Sorted by residual: angle pdb=" PA ATP B 902 " pdb=" O3A ATP B 902 " pdb=" PB ATP B 902 " ideal model delta sigma weight residual 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 125.32 14.55 1.00e+00 1.00e+00 2.12e+02 angle pdb=" O2B ADP M 802 " pdb=" PB ADP M 802 " pdb=" O3B ADP M 802 " ideal model delta sigma weight residual 119.90 96.84 23.06 3.00e+00 1.11e-01 5.91e+01 angle pdb=" O1B ADP I 802 " pdb=" PB ADP I 802 " pdb=" O2B ADP I 802 " ideal model delta sigma weight residual 119.90 96.90 23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O1B ADP P 802 " pdb=" PB ADP P 802 " pdb=" O3B ADP P 802 " ideal model delta sigma weight residual 119.90 97.12 22.78 3.00e+00 1.11e-01 5.77e+01 ... (remaining 141281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.11: 35098 31.11 - 62.22: 1573 62.22 - 93.33: 253 93.33 - 124.44: 8 124.44 - 155.54: 8 Dihedral angle restraints: 36940 sinusoidal: 20227 harmonic: 16713 Sorted by residual: dihedral pdb=" O1B ADP M 802 " pdb=" O3A ADP M 802 " pdb=" PB ADP M 802 " pdb=" PA ADP M 802 " ideal model delta sinusoidal sigma weight residual -60.00 95.54 -155.54 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP Q 802 " pdb=" O3A ADP Q 802 " pdb=" PA ADP Q 802 " pdb=" PB ADP Q 802 " ideal model delta sinusoidal sigma weight residual -60.00 93.12 -153.12 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" O1B ADP R 802 " pdb=" O3A ADP R 802 " pdb=" PB ADP R 802 " pdb=" PA ADP R 802 " ideal model delta sinusoidal sigma weight residual -60.00 92.18 -152.19 1 2.00e+01 2.50e-03 4.52e+01 ... (remaining 36937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4674 0.123 - 0.245: 1174 0.245 - 0.368: 130 0.368 - 0.491: 10 0.491 - 0.613: 2 Chirality restraints: 5990 Sorted by residual: chirality pdb=" CA ARG D 287 " pdb=" N ARG D 287 " pdb=" C ARG D 287 " pdb=" CB ARG D 287 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CA ARG Q 95 " pdb=" N ARG Q 95 " pdb=" C ARG Q 95 " pdb=" CB ARG Q 95 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA CYS F 167 " pdb=" N CYS F 167 " pdb=" C CYS F 167 " pdb=" CB CYS F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 5987 not shown) Planarity restraints: 11609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP O 340 " 0.324 2.00e-02 2.50e+03 1.21e-01 5.89e+02 pdb=" CG TRP O 340 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP O 340 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP O 340 " -0.124 2.00e-02 2.50e+03 pdb=" NE1 TRP O 340 " -0.135 2.00e-02 2.50e+03 pdb=" CE2 TRP O 340 " -0.098 2.00e-02 2.50e+03 pdb=" CE3 TRP O 340 " -0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 340 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 340 " -0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP O 340 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP O 340 " 0.087 2.00e-02 2.50e+03 pdb=" HE1 TRP O 340 " -0.059 2.00e-02 2.50e+03 pdb=" HE3 TRP O 340 " -0.126 2.00e-02 2.50e+03 pdb=" HZ2 TRP O 340 " 0.110 2.00e-02 2.50e+03 pdb=" HZ3 TRP O 340 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP O 340 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 340 " 0.335 2.00e-02 2.50e+03 1.21e-01 5.81e+02 pdb=" CG TRP M 340 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP M 340 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP M 340 " -0.105 2.00e-02 2.50e+03 pdb=" NE1 TRP M 340 " -0.137 2.00e-02 2.50e+03 pdb=" CE2 TRP M 340 " -0.081 2.00e-02 2.50e+03 pdb=" CE3 TRP M 340 " -0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 340 " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 340 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP M 340 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 TRP M 340 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TRP M 340 " -0.062 2.00e-02 2.50e+03 pdb=" HE3 TRP M 340 " -0.139 2.00e-02 2.50e+03 pdb=" HZ2 TRP M 340 " 0.118 2.00e-02 2.50e+03 pdb=" HZ3 TRP M 340 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP M 340 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " 0.309 2.00e-02 2.50e+03 1.18e-01 5.60e+02 pdb=" CG TRP A 387 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " -0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " -0.130 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " -0.044 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " 0.052 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP A 387 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TRP A 387 " -0.144 2.00e-02 2.50e+03 pdb=" HE3 TRP A 387 " -0.165 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 387 " 0.119 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 387 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP A 387 " 0.140 2.00e-02 2.50e+03 ... (remaining 11606 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 4779 2.17 - 2.78: 134319 2.78 - 3.38: 231288 3.38 - 3.99: 314703 3.99 - 4.60: 457706 Nonbonded interactions: 1142795 Sorted by model distance: nonbonded pdb=" HG SER B 275 " pdb=" OE1 GLU B 316 " model vdw 1.560 2.450 nonbonded pdb=" OD1 ASP C 328 " pdb=" HG1 THR O 351 " model vdw 1.584 2.450 nonbonded pdb=" HG SER B 311 " pdb=" OE1 GLU F 31 " model vdw 1.587 2.450 nonbonded pdb=" OE2 GLU A 106 " pdb=" HG SER A 149 " model vdw 1.590 2.450 nonbonded pdb=" OE1 GLU O 270 " pdb=" HG1 THR P 202 " model vdw 1.595 2.450 ... (remaining 1142790 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 'H' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'I' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'M' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = chain 'N' selection = (chain 'O' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'P' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'Q' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) selection = (chain 'R' and (resid 6 through 216 or (resid 217 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 218 through 256 or (resid 257 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 258 through 375 or resid 801 through 802)) } 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: 5.460 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: 0.980 Extract box with map and model: 2.300 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 136.060 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:17.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.013 0.141 39895 Z= 0.844 Angle : 1.916 23.059 54139 Z= 1.259 Chirality : 0.104 0.613 5990 Planarity : 0.017 0.387 6962 Dihedral : 15.354 155.545 14846 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 2.69 % Allowed : 5.81 % Favored : 91.50 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.11), residues: 4854 helix: -1.74 (0.10), residues: 1937 sheet: -0.26 (0.19), residues: 627 loop : 0.18 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.222 0.031 TRP M 340 HIS 0.016 0.004 HIS Q 371 PHE 0.117 0.013 PHE F 101 TYR 0.176 0.018 TYR B 127 ARG 0.017 0.002 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 1217 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1104 time to evaluate : 4.570 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: 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: 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: 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: 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 95 ARG cc_start: 0.6906 (mtt-85) cc_final: 0.6021 (mtm180) REVERT: A 226 ASP cc_start: 0.7315 (m-30) cc_final: 0.6885 (m-30) REVERT: A 228 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6766 (m-40) REVERT: A 235 LYS cc_start: 0.6483 (pttp) cc_final: 0.6270 (ptmt) REVERT: A 239 ARG cc_start: 0.6322 (mtt180) cc_final: 0.5822 (mtm-85) REVERT: A 253 LYS cc_start: 0.6842 (mppt) cc_final: 0.6306 (mptt) REVERT: A 297 GLU cc_start: 0.6379 (mt-10) cc_final: 0.5385 (mp0) REVERT: A 340 LYS cc_start: 0.7326 (tptp) cc_final: 0.6684 (tttt) REVERT: A 406 LYS cc_start: 0.7013 (pttp) cc_final: 0.6740 (ptpp) REVERT: B 6 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7337 (mt) REVERT: B 21 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7882 (mtmm) REVERT: B 68 LYS cc_start: 0.6426 (mtmt) cc_final: 0.6012 (mtmt) REVERT: B 72 GLU cc_start: 0.7770 (tt0) cc_final: 0.7441 (tt0) REVERT: B 73 ASN cc_start: 0.7177 (m-40) cc_final: 0.6589 (t0) REVERT: B 96 ILE cc_start: 0.7657 (mm) cc_final: 0.7184 (pt) REVERT: B 118 LYS cc_start: 0.6512 (ttpt) cc_final: 0.6250 (mtmm) REVERT: B 187 ARG cc_start: 0.6975 (mtt180) cc_final: 0.6758 (mtt90) REVERT: B 211 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6305 (mt-10) REVERT: B 224 GLU cc_start: 0.6699 (pt0) cc_final: 0.6488 (mt-10) REVERT: B 228 LYS cc_start: 0.6537 (ttpt) cc_final: 0.5940 (ttpp) REVERT: B 295 ARG cc_start: 0.6773 (mtp-110) cc_final: 0.6117 (mtt180) REVERT: C 22 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7126 (mp10) REVERT: C 73 CYS cc_start: 0.6303 (m) cc_final: 0.5780 (p) REVERT: C 83 GLU cc_start: 0.7140 (tt0) cc_final: 0.6262 (tp30) REVERT: C 91 LYS cc_start: 0.7445 (ttpt) cc_final: 0.6542 (tptm) REVERT: C 250 SER cc_start: 0.8246 (p) cc_final: 0.7953 (m) REVERT: C 251 GLN cc_start: 0.7848 (mt0) cc_final: 0.6647 (pp30) REVERT: C 252 LEU cc_start: 0.6943 (mm) cc_final: 0.6424 (mt) REVERT: C 327 MET cc_start: 0.7641 (mtp) cc_final: 0.7399 (mtp) REVERT: C 359 ASN cc_start: 0.6661 (m110) cc_final: 0.6178 (t0) REVERT: D 3 SER cc_start: 0.8362 (t) cc_final: 0.8156 (p) REVERT: D 23 ASN cc_start: 0.7655 (t0) cc_final: 0.7400 (t0) REVERT: D 28 ASP cc_start: 0.8003 (t0) cc_final: 0.7706 (t70) REVERT: D 47 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7238 (mttp) REVERT: D 56 MET cc_start: 0.8321 (ttm) cc_final: 0.8012 (ttm) REVERT: D 73 GLN cc_start: 0.7361 (tt0) cc_final: 0.7051 (mt0) REVERT: D 113 MET cc_start: 0.7281 (tpp) cc_final: 0.6767 (mmt) REVERT: D 143 ASN cc_start: 0.7243 (t0) cc_final: 0.7011 (t0) REVERT: D 157 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6795 (mtm) REVERT: D 172 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6420 (mt-10) REVERT: D 255 ARG cc_start: 0.5740 (mtm110) cc_final: 0.5483 (mtt90) REVERT: D 283 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7230 (mmt180) REVERT: D 284 MET cc_start: 0.7757 (mtt) cc_final: 0.7529 (mtt) REVERT: E 88 ASN cc_start: 0.5608 (t0) cc_final: 0.5395 (t0) REVERT: E 94 ARG cc_start: 0.7601 (mtp180) cc_final: 0.6996 (mtp180) REVERT: E 98 SER cc_start: 0.7067 (t) cc_final: 0.6655 (m) REVERT: F 31 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: F 57 GLU cc_start: 0.7241 (tp30) cc_final: 0.6876 (mp0) REVERT: F 58 GLN cc_start: 0.7552 (mp-120) cc_final: 0.6096 (tp-100) REVERT: F 81 GLU cc_start: 0.6930 (mp0) cc_final: 0.6126 (mm-30) REVERT: F 88 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6223 (ttm110) REVERT: F 97 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6893 (mmm160) REVERT: F 107 LYS cc_start: 0.7154 (mmmm) cc_final: 0.6900 (mptm) REVERT: F 148 GLU cc_start: 0.6881 (tt0) cc_final: 0.6680 (tt0) REVERT: G 18 GLU cc_start: 0.7433 (pt0) cc_final: 0.6381 (mm-30) REVERT: G 20 ASP cc_start: 0.7673 (m-30) cc_final: 0.7259 (t0) REVERT: G 71 GLU cc_start: 0.6050 (mp0) cc_final: 0.5649 (pm20) REVERT: G 82 ASP cc_start: 0.6164 (m-30) cc_final: 0.5824 (m-30) REVERT: G 102 GLU cc_start: 0.7015 (tt0) cc_final: 0.6373 (mp0) REVERT: G 132 LYS cc_start: 0.7202 (mttm) cc_final: 0.6871 (mtmm) REVERT: G 135 GLU cc_start: 0.7082 (tt0) cc_final: 0.6706 (tt0) REVERT: H 72 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: H 83 GLU cc_start: 0.6827 (pt0) cc_final: 0.6583 (tm-30) REVERT: H 121 GLN cc_start: 0.6607 (tt0) cc_final: 0.6276 (tm-30) REVERT: H 141 SER cc_start: 0.7935 (t) cc_final: 0.7706 (m) REVERT: H 165 ILE cc_start: 0.7578 (tt) cc_final: 0.7359 (mt) REVERT: H 191 LYS cc_start: 0.6548 (tttp) cc_final: 0.6092 (ttmt) REVERT: H 206 ARG cc_start: 0.6742 (ttm-80) cc_final: 0.5637 (ttm110) REVERT: H 225 ASN cc_start: 0.7570 (m-40) cc_final: 0.6875 (t0) REVERT: H 234 SER cc_start: 0.6728 (m) cc_final: 0.6404 (t) REVERT: H 269 MET cc_start: 0.8362 (ttm) cc_final: 0.8103 (ttp) REVERT: H 313 MET cc_start: 0.7697 (tpt) cc_final: 0.7474 (tpt) REVERT: H 328 LYS cc_start: 0.6863 (mmmm) cc_final: 0.6546 (mppt) REVERT: I 11 ASP cc_start: 0.6266 (t0) cc_final: 0.6038 (t0) REVERT: I 25 ASP cc_start: 0.6784 (m-30) cc_final: 0.6560 (p0) REVERT: I 50 LYS cc_start: 0.7482 (mmpt) cc_final: 0.7021 (mtpm) REVERT: I 68 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7237 (mttt) REVERT: I 92 ASN cc_start: 0.7425 (m-40) cc_final: 0.7170 (m-40) REVERT: I 122 ILE cc_start: 0.7580 (pt) cc_final: 0.7204 (mm) REVERT: I 169 TYR cc_start: 0.6596 (m-80) cc_final: 0.5396 (t80) REVERT: I 215 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7293 (mttp) REVERT: I 296 ASN cc_start: 0.7243 (t0) cc_final: 0.6879 (t0) REVERT: I 305 MET cc_start: 0.8155 (mmm) cc_final: 0.7826 (mmm) REVERT: I 336 LYS cc_start: 0.6832 (ptpp) cc_final: 0.6530 (ttpt) REVERT: I 362 TYR cc_start: 0.6950 (t80) cc_final: 0.6669 (t80) REVERT: M 78 ASN cc_start: 0.7435 (t0) cc_final: 0.6952 (t0) REVERT: M 96 VAL cc_start: 0.7487 (m) cc_final: 0.7275 (m) REVERT: M 194 THR cc_start: 0.8079 (m) cc_final: 0.7633 (p) REVERT: M 202 THR cc_start: 0.7555 (m) cc_final: 0.7220 (p) REVERT: M 224 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7414 (pm20) REVERT: M 263 GLN cc_start: 0.7739 (mt0) cc_final: 0.7315 (mt0) REVERT: N 47 MET cc_start: 0.1361 (ttp) cc_final: 0.0488 (ttm) REVERT: N 225 ASN cc_start: 0.6778 (t0) cc_final: 0.6478 (m-40) REVERT: N 276 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6980 (mt-10) REVERT: N 328 LYS cc_start: 0.7428 (tptt) cc_final: 0.6951 (tppp) REVERT: N 355 MET cc_start: 0.8059 (mtt) cc_final: 0.7802 (mtp) REVERT: N 360 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7123 (tp-100) REVERT: O 41 GLN cc_start: 0.6989 (tp40) cc_final: 0.6730 (mm-40) REVERT: O 68 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7691 (ptpp) REVERT: O 100 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7609 (mt-10) REVERT: O 113 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7240 (mmtp) REVERT: O 118 LYS cc_start: 0.7282 (mttm) cc_final: 0.6682 (mtpm) REVERT: O 206 ARG cc_start: 0.7598 (ttp-170) cc_final: 0.6586 (ttp-110) REVERT: O 276 GLU cc_start: 0.6904 (tt0) cc_final: 0.6431 (tt0) REVERT: O 284 LYS cc_start: 0.7966 (mttm) cc_final: 0.7534 (mtpm) REVERT: O 286 ASP cc_start: 0.6881 (t0) cc_final: 0.6518 (m-30) REVERT: O 326 LYS cc_start: 0.7368 (ptpp) cc_final: 0.6438 (mmmt) REVERT: O 328 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7084 (mttp) REVERT: O 359 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7672 (tptp) REVERT: P 82 MET cc_start: 0.7772 (tpt) cc_final: 0.6931 (tpt) REVERT: P 283 MET cc_start: 0.8200 (mmm) cc_final: 0.7974 (mmp) REVERT: P 326 LYS cc_start: 0.7660 (pttp) cc_final: 0.7454 (pttm) REVERT: P 359 LYS cc_start: 0.7195 (ptmm) cc_final: 0.6816 (tttt) REVERT: Q 6 THR cc_start: 0.8029 (p) cc_final: 0.7559 (t) REVERT: Q 34 ILE cc_start: 0.8353 (mt) cc_final: 0.7899 (pt) REVERT: Q 47 MET cc_start: 0.6248 (mmm) cc_final: 0.5405 (ptt) REVERT: Q 60 SER cc_start: 0.7986 (t) cc_final: 0.7690 (p) REVERT: Q 66 THR cc_start: 0.8303 (t) cc_final: 0.8056 (m) REVERT: Q 82 MET cc_start: 0.8272 (tpt) cc_final: 0.7748 (tpt) REVERT: Q 95 ARG cc_start: 0.6926 (ptp-170) cc_final: 0.6378 (ptp-110) REVERT: Q 167 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7331 (mm-30) REVERT: Q 190 MET cc_start: 0.7630 (mtm) cc_final: 0.7387 (mtp) REVERT: Q 215 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6949 (mmtp) REVERT: Q 224 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7795 (mp0) REVERT: Q 246 GLN cc_start: 0.7922 (mt0) cc_final: 0.7618 (mt0) REVERT: Q 291 LYS cc_start: 0.5649 (mttm) cc_final: 0.4643 (tmtm) REVERT: Q 314 GLN cc_start: 0.7972 (tt0) cc_final: 0.7624 (tt0) REVERT: Q 328 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6601 (ttpp) REVERT: Q 336 LYS cc_start: 0.7676 (tptm) cc_final: 0.7349 (tppp) REVERT: Q 354 GLN cc_start: 0.7645 (pm20) cc_final: 0.7059 (mm110) REVERT: R 25 ASP cc_start: 0.7944 (m-30) cc_final: 0.7599 (t70) REVERT: R 83 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7002 (mt-10) REVERT: R 100 GLU cc_start: 0.8143 (pt0) cc_final: 0.7825 (pt0) REVERT: R 167 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7248 (mm-30) REVERT: R 206 ARG cc_start: 0.6814 (tpp80) cc_final: 0.6356 (ttp-170) REVERT: R 215 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7301 (mptm) REVERT: R 234 SER cc_start: 0.5746 (OUTLIER) cc_final: 0.5418 (t) outliers start: 113 outliers final: 36 residues processed: 1162 average time/residue: 2.7227 time to fit residues: 3888.0237 Evaluate side-chains 725 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 681 time to evaluate : 4.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 359 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 234 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 383 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 313 ASN B 10 ASN B 48 GLN B 83 ASN B 173 HIS B 201 ASN B 335 ASN B 364 ASN C 209 HIS ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 292 GLN E 156 HIS F 10 ASN F 60 GLN F 120 ASN G 19 GLN G 106 ASN H 137 GLN I 41 GLN M 59 GLN N 137 GLN O 353 GLN O 360 GLN P 263 GLN Q 41 GLN Q 87 HIS Q 173 HIS R 49 GLN R 354 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111675 restraints weight = 130889.183| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.58 r_work: 0.3079 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39895 Z= 0.247 Angle : 0.737 9.141 54139 Z= 0.388 Chirality : 0.047 0.234 5990 Planarity : 0.006 0.088 6962 Dihedral : 11.045 145.131 5608 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.00 % Allowed : 13.77 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4854 helix: -0.70 (0.11), residues: 1945 sheet: -0.39 (0.17), residues: 876 loop : 0.64 (0.14), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 356 HIS 0.006 0.001 HIS C 140 PHE 0.027 0.001 PHE B 277 TYR 0.024 0.001 TYR B 88 ARG 0.007 0.001 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 845 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 719 time to evaluate : 5.525 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: 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: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: A 239 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7951 (mtm-85) REVERT: A 242 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 253 LYS cc_start: 0.7954 (mppt) cc_final: 0.7608 (mptt) REVERT: A 297 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6790 (mp0) REVERT: A 302 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: B 6 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8244 (mt) REVERT: B 96 ILE cc_start: 0.8315 (mm) cc_final: 0.7943 (pt) REVERT: B 152 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 295 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7343 (mpt-90) REVERT: B 364 ASN cc_start: 0.7588 (m-40) cc_final: 0.7335 (t0) REVERT: C 91 LYS cc_start: 0.8549 (ttpt) cc_final: 0.7957 (tttt) REVERT: C 359 ASN cc_start: 0.7535 (m110) cc_final: 0.7207 (t0) REVERT: D 47 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8043 (mttp) REVERT: D 185 ARG cc_start: 0.8515 (ptp-170) cc_final: 0.8308 (ptp-170) REVERT: D 229 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7654 (mm) REVERT: E 58 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7605 (ptm160) REVERT: E 61 GLU cc_start: 0.7717 (tt0) cc_final: 0.7267 (pt0) REVERT: E 94 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7620 (mtp180) REVERT: E 98 SER cc_start: 0.7776 (t) cc_final: 0.7504 (m) REVERT: F 58 GLN cc_start: 0.8462 (mp-120) cc_final: 0.7674 (tp-100) REVERT: F 81 GLU cc_start: 0.8441 (mp0) cc_final: 0.8162 (mm-30) REVERT: G 54 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7075 (tm-30) REVERT: H 25 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8134 (OUTLIER) REVERT: H 123 MET cc_start: 0.8859 (tpp) cc_final: 0.7910 (mmt) REVERT: H 206 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7324 (ttm110) REVERT: I 68 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8308 (mttt) REVERT: I 123 MET cc_start: 0.7436 (mmp) cc_final: 0.6981 (mmt) REVERT: I 169 TYR cc_start: 0.6709 (m-80) cc_final: 0.5516 (t80) REVERT: M 83 GLU cc_start: 0.6953 (tt0) cc_final: 0.6558 (tm-30) REVERT: M 194 THR cc_start: 0.8106 (m) cc_final: 0.7624 (p) REVERT: M 202 THR cc_start: 0.7420 (m) cc_final: 0.7132 (p) REVERT: M 206 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7222 (ttm110) REVERT: M 224 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7260 (pm20) REVERT: M 227 MET cc_start: 0.8342 (mmt) cc_final: 0.7846 (mmt) REVERT: N 41 GLN cc_start: 0.7012 (pt0) cc_final: 0.6772 (pm20) REVERT: N 47 MET cc_start: 0.1598 (ttp) cc_final: 0.0864 (ttm) REVERT: N 225 ASN cc_start: 0.7489 (t0) cc_final: 0.7170 (m-40) REVERT: N 299 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8668 (mtt) REVERT: O 206 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.8027 (ttp-110) REVERT: O 326 LYS cc_start: 0.7521 (ptpp) cc_final: 0.6992 (mmmt) REVERT: P 82 MET cc_start: 0.8952 (tpt) cc_final: 0.8042 (tpt) REVERT: P 180 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9034 (tp) REVERT: P 221 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8672 (tp) REVERT: P 355 MET cc_start: 0.8512 (mtm) cc_final: 0.8180 (mtt) REVERT: Q 47 MET cc_start: 0.7473 (mmm) cc_final: 0.6523 (ptt) REVERT: Q 190 MET cc_start: 0.8709 (mtm) cc_final: 0.8382 (mtp) REVERT: Q 291 LYS cc_start: 0.6697 (mttm) cc_final: 0.6035 (tmtm) REVERT: Q 313 MET cc_start: 0.8900 (tpt) cc_final: 0.8683 (mmm) REVERT: R 206 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7961 (ttp-170) outliers start: 126 outliers final: 49 residues processed: 794 average time/residue: 2.7426 time to fit residues: 2662.8929 Evaluate side-chains 641 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 582 time to evaluate : 4.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 250 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 51 ASP Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 199 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 345 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 chunk 462 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 426 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 320 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 433 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 172 ASN B 263 GLN D 254 ASN E 139 GLN F 120 ASN F 129 HIS G 19 GLN G 31 GLN H 162 ASN H 225 ASN I 41 GLN I 161 HIS M 88 HIS M 162 ASN M 173 HIS N 360 GLN ** O 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 173 HIS R 354 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107821 restraints weight = 131076.580| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.48 r_work: 0.3090 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39895 Z= 0.254 Angle : 0.649 7.862 54139 Z= 0.332 Chirality : 0.046 0.213 5990 Planarity : 0.005 0.068 6962 Dihedral : 9.868 153.455 5563 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.05 % Allowed : 15.22 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.12), residues: 4854 helix: -0.18 (0.12), residues: 1944 sheet: -0.50 (0.17), residues: 876 loop : 0.70 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 356 HIS 0.006 0.001 HIS O 161 PHE 0.018 0.001 PHE B 277 TYR 0.023 0.001 TYR A 402 ARG 0.006 0.001 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 733 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 605 time to evaluate : 4.684 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: 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 207 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8306 (tppt) REVERT: A 239 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7768 (mtm-85) REVERT: A 242 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 253 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7493 (mptt) REVERT: A 302 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: B 6 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8296 (mt) REVERT: B 96 ILE cc_start: 0.8338 (mm) cc_final: 0.8107 (pt) REVERT: B 147 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8304 (mt) REVERT: B 152 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8617 (p) REVERT: B 244 ASP cc_start: 0.7482 (m-30) cc_final: 0.7264 (m-30) REVERT: B 295 ARG cc_start: 0.7715 (mtp180) cc_final: 0.7222 (mpt-90) REVERT: B 364 ASN cc_start: 0.7648 (m-40) cc_final: 0.7337 (t0) REVERT: B 380 ARG cc_start: 0.8119 (tpp-160) cc_final: 0.7843 (tpp-160) REVERT: C 91 LYS cc_start: 0.8382 (ttpt) cc_final: 0.7804 (tptp) REVERT: C 359 ASN cc_start: 0.7651 (m110) cc_final: 0.7316 (t0) REVERT: D 47 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8087 (mttp) REVERT: D 84 MET cc_start: 0.8126 (mpp) cc_final: 0.7904 (tmm) REVERT: D 229 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7682 (mm) REVERT: E 61 GLU cc_start: 0.7799 (tt0) cc_final: 0.7058 (pt0) REVERT: E 94 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7568 (mtp180) REVERT: E 98 SER cc_start: 0.7806 (t) cc_final: 0.7478 (m) REVERT: F 58 GLN cc_start: 0.8473 (mp-120) cc_final: 0.7657 (tp-100) REVERT: F 74 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8277 (mp) REVERT: F 81 GLU cc_start: 0.8328 (mp0) cc_final: 0.7919 (mm-30) REVERT: F 88 ARG cc_start: 0.8660 (ttt-90) cc_final: 0.7975 (ttm110) REVERT: G 54 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7035 (tm-30) REVERT: H 28 ARG cc_start: 0.7866 (tpp-160) cc_final: 0.7484 (tpp80) REVERT: H 306 TYR cc_start: 0.9203 (m-80) cc_final: 0.8888 (m-80) REVERT: I 68 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8290 (mttt) REVERT: I 169 TYR cc_start: 0.6688 (m-80) cc_final: 0.5508 (t80) REVERT: I 305 MET cc_start: 0.8923 (mmm) cc_final: 0.8687 (mmm) REVERT: M 80 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6647 (t70) REVERT: M 83 GLU cc_start: 0.7107 (tt0) cc_final: 0.6549 (tm-30) REVERT: M 194 THR cc_start: 0.8120 (m) cc_final: 0.7682 (p) REVERT: M 202 THR cc_start: 0.7676 (m) cc_final: 0.7365 (p) REVERT: M 206 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7048 (ttm110) REVERT: M 224 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7282 (pm20) REVERT: M 227 MET cc_start: 0.8347 (mmt) cc_final: 0.8011 (mmt) REVERT: N 41 GLN cc_start: 0.7083 (pt0) cc_final: 0.6818 (pm20) REVERT: N 47 MET cc_start: 0.1547 (ttp) cc_final: 0.0763 (ttm) REVERT: N 211 ASP cc_start: 0.8005 (m-30) cc_final: 0.7745 (t70) REVERT: O 68 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8683 (ptpp) REVERT: O 206 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.7866 (ttm-80) REVERT: P 82 MET cc_start: 0.8920 (tpt) cc_final: 0.8120 (tpt) REVERT: P 355 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8135 (mtt) REVERT: Q 47 MET cc_start: 0.7511 (mmm) cc_final: 0.6554 (ptt) REVERT: Q 72 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: Q 190 MET cc_start: 0.8614 (mtm) cc_final: 0.8293 (mtp) REVERT: Q 291 LYS cc_start: 0.6523 (mttm) cc_final: 0.5992 (tmtm) REVERT: R 21 PHE cc_start: 0.7628 (m-10) cc_final: 0.7371 (m-80) REVERT: R 47 MET cc_start: 0.4747 (mmt) cc_final: 0.4503 (ppp) REVERT: R 72 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7893 (mt-10) REVERT: R 125 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7533 (mp0) REVERT: R 206 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7801 (ttm-80) outliers start: 128 outliers final: 51 residues processed: 689 average time/residue: 2.7837 time to fit residues: 2346.1584 Evaluate side-chains 619 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 555 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 41 GLN Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 263 optimal weight: 9.9990 chunk 430 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 464 optimal weight: 4.9990 chunk 320 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 336 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 254 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN ** O 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN Q 246 GLN R 137 GLN R 275 HIS R 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116442 restraints weight = 133752.984| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.57 r_work: 0.3323 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 39895 Z= 0.261 Angle : 0.624 7.674 54139 Z= 0.316 Chirality : 0.045 0.211 5990 Planarity : 0.005 0.089 6962 Dihedral : 9.491 161.371 5559 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.95 % Allowed : 15.51 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 4854 helix: 0.07 (0.12), residues: 1944 sheet: -0.56 (0.17), residues: 886 loop : 0.74 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.007 0.001 HIS O 161 PHE 0.018 0.001 PHE B 277 TYR 0.016 0.001 TYR B 88 ARG 0.009 0.000 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 710 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 586 time to evaluate : 4.800 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8240 (tppt) REVERT: A 242 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: A 253 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7380 (mptt) REVERT: A 257 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8188 (ttt180) REVERT: A 302 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: B 96 ILE cc_start: 0.8379 (mm) cc_final: 0.8147 (pt) REVERT: B 119 MET cc_start: 0.8085 (ttm) cc_final: 0.7825 (ttp) REVERT: B 244 ASP cc_start: 0.7363 (m-30) cc_final: 0.7117 (m-30) REVERT: B 295 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7009 (mpt-90) REVERT: B 364 ASN cc_start: 0.7632 (m-40) cc_final: 0.7261 (t0) REVERT: C 41 ASP cc_start: 0.6786 (t0) cc_final: 0.6309 (p0) REVERT: C 359 ASN cc_start: 0.7547 (m110) cc_final: 0.7188 (t0) REVERT: D 47 LYS cc_start: 0.8344 (mtmm) cc_final: 0.7989 (mttp) REVERT: D 68 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7930 (tt) REVERT: D 113 MET cc_start: 0.8870 (mmt) cc_final: 0.8486 (mmt) REVERT: D 229 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7674 (mm) REVERT: E 58 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7267 (ptm160) REVERT: E 61 GLU cc_start: 0.7775 (tt0) cc_final: 0.6991 (pt0) REVERT: E 94 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7560 (mtp180) REVERT: E 98 SER cc_start: 0.7734 (t) cc_final: 0.7397 (m) REVERT: F 58 GLN cc_start: 0.8402 (mp-120) cc_final: 0.7629 (tp-100) REVERT: F 81 GLU cc_start: 0.8161 (mp0) cc_final: 0.7643 (mm-30) REVERT: F 88 ARG cc_start: 0.8591 (ttt-90) cc_final: 0.7788 (ttm110) REVERT: G 54 GLN cc_start: 0.7597 (mm-40) cc_final: 0.6957 (tm-30) REVERT: H 28 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7462 (tpp80) REVERT: H 206 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.6977 (ttm110) REVERT: H 306 TYR cc_start: 0.9213 (m-80) cc_final: 0.8922 (m-80) REVERT: I 68 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8206 (mttt) REVERT: M 78 ASN cc_start: 0.7454 (t0) cc_final: 0.6965 (t0) REVERT: M 194 THR cc_start: 0.8088 (m) cc_final: 0.7676 (p) REVERT: M 195 GLU cc_start: 0.6626 (tm-30) cc_final: 0.6376 (tm-30) REVERT: M 202 THR cc_start: 0.7700 (m) cc_final: 0.7390 (p) REVERT: M 206 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7165 (ttm110) REVERT: M 224 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7276 (pm20) REVERT: M 227 MET cc_start: 0.8309 (mmt) cc_final: 0.7929 (mmt) REVERT: N 47 MET cc_start: 0.1357 (ttp) cc_final: 0.0619 (ttm) REVERT: N 305 MET cc_start: 0.8662 (mtp) cc_final: 0.8265 (mmt) REVERT: N 355 MET cc_start: 0.8214 (mtp) cc_final: 0.7880 (mtt) REVERT: O 68 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8655 (ptpp) REVERT: O 206 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.7713 (ttm-80) REVERT: P 82 MET cc_start: 0.8906 (tpt) cc_final: 0.8187 (tpt) REVERT: P 180 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8758 (tp) REVERT: P 355 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8008 (mtt) REVERT: Q 47 MET cc_start: 0.7486 (mmm) cc_final: 0.6493 (ptt) REVERT: Q 72 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: Q 190 MET cc_start: 0.8578 (mtm) cc_final: 0.8255 (mtp) REVERT: Q 291 LYS cc_start: 0.6373 (mttm) cc_final: 0.5880 (tmtm) REVERT: Q 368 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8655 (t) REVERT: R 72 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7851 (mt-10) REVERT: R 99 GLU cc_start: 0.7933 (pm20) cc_final: 0.7615 (pm20) REVERT: R 107 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: R 206 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7653 (ttm-80) REVERT: R 314 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7922 (tt0) outliers start: 124 outliers final: 58 residues processed: 665 average time/residue: 2.8048 time to fit residues: 2293.1614 Evaluate side-chains 621 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 548 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 357 ILE Chi-restraints excluded: chain M residue 360 GLN Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 314 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 226 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 329 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 453 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 227 HIS D 160 HIS ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN N 296 ASN ** O 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 ASN R 137 GLN R 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.146030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113772 restraints weight = 133572.803| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.48 r_work: 0.3289 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 39895 Z= 0.328 Angle : 0.643 8.238 54139 Z= 0.323 Chirality : 0.046 0.219 5990 Planarity : 0.005 0.099 6962 Dihedral : 9.334 171.845 5556 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.83 % Allowed : 16.25 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 4854 helix: 0.14 (0.12), residues: 1946 sheet: -0.36 (0.16), residues: 937 loop : 0.68 (0.15), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 387 HIS 0.008 0.001 HIS O 161 PHE 0.019 0.002 PHE F 101 TYR 0.040 0.002 TYR B 377 ARG 0.009 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 667 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 548 time to evaluate : 4.682 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8256 (tppt) REVERT: A 238 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: A 242 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: A 253 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7373 (mptt) REVERT: A 302 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: B 21 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8057 (mtmm) REVERT: B 75 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8168 (pt) REVERT: B 96 ILE cc_start: 0.8426 (mm) cc_final: 0.8126 (pt) REVERT: B 119 MET cc_start: 0.8049 (ttm) cc_final: 0.7764 (ttp) REVERT: B 244 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: B 295 ARG cc_start: 0.7655 (mtp180) cc_final: 0.6974 (mpt-90) REVERT: B 364 ASN cc_start: 0.7678 (m-40) cc_final: 0.7291 (t0) REVERT: C 359 ASN cc_start: 0.7599 (m110) cc_final: 0.7269 (t0) REVERT: D 47 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7952 (mttp) REVERT: D 102 GLU cc_start: 0.7172 (mp0) cc_final: 0.6741 (mp0) REVERT: D 106 GLN cc_start: 0.7832 (pt0) cc_final: 0.7459 (mt0) REVERT: D 143 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7022 (t0) REVERT: D 163 ASP cc_start: 0.7187 (p0) cc_final: 0.6978 (p0) REVERT: D 186 GLU cc_start: 0.7618 (tp30) cc_final: 0.7358 (mm-30) REVERT: D 229 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7675 (mm) REVERT: D 269 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8581 (mp) REVERT: D 287 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7250 (mtp180) REVERT: E 58 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7343 (ptm160) REVERT: E 94 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7517 (mtp180) REVERT: E 98 SER cc_start: 0.7653 (t) cc_final: 0.7320 (m) REVERT: F 58 GLN cc_start: 0.8426 (mp-120) cc_final: 0.7626 (tp-100) REVERT: F 81 GLU cc_start: 0.8192 (mp0) cc_final: 0.7629 (mm-30) REVERT: F 145 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: G 98 GLU cc_start: 0.7647 (pp20) cc_final: 0.7445 (pp20) REVERT: H 28 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7523 (tpp80) REVERT: H 68 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8304 (mttm) REVERT: H 206 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.6976 (ttm110) REVERT: H 306 TYR cc_start: 0.9250 (m-80) cc_final: 0.8921 (m-80) REVERT: I 68 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8208 (mttt) REVERT: I 152 VAL cc_start: 0.7624 (OUTLIER) cc_final: 0.7406 (p) REVERT: I 305 MET cc_start: 0.8899 (mmm) cc_final: 0.8697 (mmm) REVERT: M 194 THR cc_start: 0.8005 (m) cc_final: 0.7662 (p) REVERT: M 202 THR cc_start: 0.7677 (m) cc_final: 0.7360 (p) REVERT: M 224 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7266 (pm20) REVERT: N 47 MET cc_start: 0.1315 (ttp) cc_final: 0.0551 (ttm) REVERT: N 206 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7036 (ttm110) REVERT: N 305 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8286 (mmt) REVERT: O 68 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8659 (ptpp) REVERT: O 206 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.7703 (ttm-80) REVERT: P 82 MET cc_start: 0.8876 (tpt) cc_final: 0.8208 (tpt) REVERT: P 206 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7992 (ttm110) REVERT: P 355 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8243 (mpp) REVERT: Q 47 MET cc_start: 0.7597 (mmm) cc_final: 0.6509 (ptt) REVERT: Q 72 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: Q 190 MET cc_start: 0.8553 (mtm) cc_final: 0.8248 (mtp) REVERT: Q 225 ASN cc_start: 0.7989 (t0) cc_final: 0.7709 (m110) REVERT: Q 291 LYS cc_start: 0.6354 (mttm) cc_final: 0.5829 (tmtm) REVERT: R 72 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7841 (mt-10) REVERT: R 99 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: R 107 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: R 206 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7634 (ttm-80) outliers start: 119 outliers final: 54 residues processed: 626 average time/residue: 2.9335 time to fit residues: 2255.6022 Evaluate side-chains 603 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 526 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 12 ASN Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 368 SER Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 82 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 418 optimal weight: 0.9990 chunk 343 optimal weight: 0.9980 chunk 357 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 73 GLN F 56 ASN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 162 ASN O 225 ASN R 137 GLN R 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110668 restraints weight = 133658.121| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.55 r_work: 0.3242 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39895 Z= 0.237 Angle : 0.602 7.642 54139 Z= 0.301 Chirality : 0.044 0.211 5990 Planarity : 0.005 0.098 6962 Dihedral : 9.120 177.302 5554 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 17.10 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.12), residues: 4854 helix: 0.27 (0.12), residues: 1947 sheet: -0.33 (0.16), residues: 945 loop : 0.72 (0.15), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.006 0.001 HIS A 404 PHE 0.017 0.001 PHE B 277 TYR 0.015 0.001 TYR B 88 ARG 0.010 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 649 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 547 time to evaluate : 4.686 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8274 (tppt) REVERT: A 242 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 253 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7431 (mptt) REVERT: A 302 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6993 (m-30) REVERT: B 21 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8041 (mtmm) REVERT: B 75 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8236 (pt) REVERT: B 96 ILE cc_start: 0.8403 (mm) cc_final: 0.8166 (pt) REVERT: B 119 MET cc_start: 0.8095 (ttm) cc_final: 0.7823 (ttp) REVERT: B 244 ASP cc_start: 0.7324 (m-30) cc_final: 0.7069 (m-30) REVERT: B 295 ARG cc_start: 0.7697 (mtp180) cc_final: 0.7019 (mpt-90) REVERT: B 364 ASN cc_start: 0.7658 (m-40) cc_final: 0.7248 (t0) REVERT: C 359 ASN cc_start: 0.7611 (m110) cc_final: 0.7228 (t0) REVERT: D 47 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7952 (mttp) REVERT: D 106 GLN cc_start: 0.7867 (pt0) cc_final: 0.7544 (mt0) REVERT: D 143 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6989 (t0) REVERT: D 186 GLU cc_start: 0.7695 (tp30) cc_final: 0.7470 (mm-30) REVERT: D 229 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7684 (mm) REVERT: D 269 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8603 (mp) REVERT: D 287 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7309 (mtp180) REVERT: E 45 ASP cc_start: 0.7163 (m-30) cc_final: 0.6941 (m-30) REVERT: E 58 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7363 (ptm160) REVERT: E 94 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7567 (mtp180) REVERT: E 98 SER cc_start: 0.7656 (t) cc_final: 0.7330 (m) REVERT: F 58 GLN cc_start: 0.8420 (mp-120) cc_final: 0.7651 (tp-100) REVERT: F 81 GLU cc_start: 0.8258 (mp0) cc_final: 0.7703 (mm-30) REVERT: F 145 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: H 28 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7531 (tpp80) REVERT: H 47 MET cc_start: 0.8065 (tpp) cc_final: 0.7224 (mmp) REVERT: H 68 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8336 (mttm) REVERT: H 206 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.7066 (ttm110) REVERT: H 306 TYR cc_start: 0.9249 (m-80) cc_final: 0.8987 (m-80) REVERT: I 68 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8277 (mttt) REVERT: I 152 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7439 (p) REVERT: M 194 THR cc_start: 0.8031 (m) cc_final: 0.7705 (p) REVERT: M 202 THR cc_start: 0.7722 (m) cc_final: 0.7436 (p) REVERT: M 224 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7286 (pm20) REVERT: N 47 MET cc_start: 0.1422 (ttp) cc_final: 0.0617 (ttm) REVERT: N 206 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7082 (ttm110) REVERT: N 211 ASP cc_start: 0.7959 (m-30) cc_final: 0.7743 (t70) REVERT: N 236 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7943 (mp) REVERT: N 355 MET cc_start: 0.8217 (mtp) cc_final: 0.7862 (mtt) REVERT: O 68 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8636 (ptpp) REVERT: O 72 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7820 (mp0) REVERT: O 206 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.7770 (ttp-110) REVERT: P 82 MET cc_start: 0.8868 (tpt) cc_final: 0.8307 (tpt) REVERT: P 355 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (mpp) REVERT: Q 47 MET cc_start: 0.7623 (mmm) cc_final: 0.6569 (ptt) REVERT: Q 72 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: Q 82 MET cc_start: 0.9164 (tpt) cc_final: 0.8936 (tpt) REVERT: Q 190 MET cc_start: 0.8570 (mtm) cc_final: 0.8330 (mtp) REVERT: Q 225 ASN cc_start: 0.8020 (t0) cc_final: 0.7740 (m110) REVERT: Q 291 LYS cc_start: 0.6455 (mttm) cc_final: 0.5948 (tmtm) REVERT: R 99 GLU cc_start: 0.7943 (pm20) cc_final: 0.7657 (pm20) REVERT: R 206 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7680 (ttm-80) REVERT: R 314 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7914 (tt0) outliers start: 102 outliers final: 51 residues processed: 615 average time/residue: 2.9384 time to fit residues: 2234.5873 Evaluate side-chains 593 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 523 time to evaluate : 4.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 257 CYS Chi-restraints excluded: chain R residue 314 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 316 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 406 optimal weight: 1.9990 chunk 474 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 73 GLN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN R 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108362 restraints weight = 133246.730| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.58 r_work: 0.3204 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 39895 Z= 0.373 Angle : 0.643 8.337 54139 Z= 0.323 Chirality : 0.046 0.237 5990 Planarity : 0.005 0.100 6962 Dihedral : 9.051 176.044 5547 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.76 % Allowed : 17.03 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 4854 helix: 0.18 (0.12), residues: 1946 sheet: -0.21 (0.17), residues: 857 loop : 0.54 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 387 HIS 0.008 0.001 HIS I 173 PHE 0.018 0.002 PHE B 351 TYR 0.016 0.002 TYR B 88 ARG 0.010 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 656 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 540 time to evaluate : 4.678 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8269 (tppt) REVERT: A 238 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: A 242 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: A 253 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7430 (mptt) REVERT: A 302 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7060 (m-30) REVERT: B 10 ASN cc_start: 0.7879 (p0) cc_final: 0.7657 (p0) REVERT: B 21 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8048 (mtmm) REVERT: B 75 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8222 (pt) REVERT: B 96 ILE cc_start: 0.8433 (mm) cc_final: 0.8228 (pt) REVERT: B 119 MET cc_start: 0.8132 (ttm) cc_final: 0.7869 (ttp) REVERT: B 244 ASP cc_start: 0.7415 (m-30) cc_final: 0.7155 (m-30) REVERT: B 295 ARG cc_start: 0.7719 (mtp180) cc_final: 0.7051 (mpt-90) REVERT: B 364 ASN cc_start: 0.7720 (m-40) cc_final: 0.7238 (t0) REVERT: C 359 ASN cc_start: 0.7670 (m110) cc_final: 0.7310 (t0) REVERT: D 47 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7936 (mttp) REVERT: D 106 GLN cc_start: 0.7853 (pt0) cc_final: 0.7591 (mt0) REVERT: D 186 GLU cc_start: 0.7743 (tp30) cc_final: 0.7504 (mm-30) REVERT: D 229 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7690 (mm) REVERT: D 269 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8626 (mp) REVERT: D 287 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7368 (mtp180) REVERT: E 58 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7389 (ptm160) REVERT: E 94 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7595 (mtp180) REVERT: E 98 SER cc_start: 0.7700 (t) cc_final: 0.7349 (m) REVERT: F 58 GLN cc_start: 0.8410 (mp-120) cc_final: 0.7661 (tp-100) REVERT: F 81 GLU cc_start: 0.8332 (mp0) cc_final: 0.7751 (mm-30) REVERT: F 145 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: G 132 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8285 (mppt) REVERT: H 28 ARG cc_start: 0.7842 (tpp-160) cc_final: 0.7569 (tpp80) REVERT: H 47 MET cc_start: 0.8068 (tpp) cc_final: 0.7198 (mmp) REVERT: H 68 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8365 (mttm) REVERT: H 206 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7122 (ttm110) REVERT: H 306 TYR cc_start: 0.9261 (m-80) cc_final: 0.8963 (m-80) REVERT: I 68 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8266 (mttt) REVERT: I 152 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7420 (p) REVERT: M 83 GLU cc_start: 0.7238 (tt0) cc_final: 0.6631 (tm-30) REVERT: M 194 THR cc_start: 0.8018 (m) cc_final: 0.7701 (p) REVERT: M 195 GLU cc_start: 0.6651 (tm-30) cc_final: 0.6434 (tm-30) REVERT: M 202 THR cc_start: 0.7735 (m) cc_final: 0.7447 (p) REVERT: M 224 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7297 (pm20) REVERT: N 47 MET cc_start: 0.1231 (ttp) cc_final: 0.0472 (ttm) REVERT: N 206 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7120 (ttm110) REVERT: N 211 ASP cc_start: 0.7961 (m-30) cc_final: 0.7753 (t70) REVERT: N 236 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7903 (mp) REVERT: N 305 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8267 (mmt) REVERT: N 355 MET cc_start: 0.8237 (mtp) cc_final: 0.7869 (mtt) REVERT: O 68 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8665 (ptpp) REVERT: O 72 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: O 206 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.7779 (ttm-80) REVERT: P 82 MET cc_start: 0.8884 (tpt) cc_final: 0.8254 (tpt) REVERT: P 206 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8121 (ttm110) REVERT: P 241 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: P 355 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (mpp) REVERT: Q 47 MET cc_start: 0.7772 (mmm) cc_final: 0.6599 (ptt) REVERT: Q 72 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: Q 190 MET cc_start: 0.8597 (mtm) cc_final: 0.8358 (mtp) REVERT: Q 225 ASN cc_start: 0.8053 (t0) cc_final: 0.7741 (m110) REVERT: Q 291 LYS cc_start: 0.6451 (mttm) cc_final: 0.5928 (tmtm) REVERT: R 99 GLU cc_start: 0.7946 (pm20) cc_final: 0.7656 (pm20) REVERT: R 107 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.6606 (tp30) REVERT: R 206 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7700 (ttm-80) outliers start: 116 outliers final: 60 residues processed: 619 average time/residue: 2.8516 time to fit residues: 2155.3505 Evaluate side-chains 611 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 527 time to evaluate : 4.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 336 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain O residue 149 THR Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 241 GLU Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 391 optimal weight: 2.9990 chunk 475 optimal weight: 1.9990 chunk 286 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 456 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 73 GLN ** G 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN Q 162 ASN R 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110403 restraints weight = 133717.089| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.55 r_work: 0.3238 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39895 Z= 0.229 Angle : 0.592 7.779 54139 Z= 0.295 Chirality : 0.044 0.200 5990 Planarity : 0.005 0.112 6962 Dihedral : 8.755 167.562 5547 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.24 % Allowed : 17.84 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 4854 helix: 0.35 (0.12), residues: 1947 sheet: -0.17 (0.17), residues: 869 loop : 0.61 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.010 0.001 HIS I 173 PHE 0.015 0.001 PHE B 277 TYR 0.018 0.001 TYR I 279 ARG 0.012 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 635 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 541 time to evaluate : 4.638 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: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8250 (tppt) REVERT: A 242 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: A 253 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7419 (mptt) REVERT: A 302 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: B 21 LYS cc_start: 0.8536 (mtmt) cc_final: 0.7971 (mtmm) REVERT: B 75 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8277 (pt) REVERT: B 244 ASP cc_start: 0.7332 (m-30) cc_final: 0.7065 (m-30) REVERT: B 295 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7017 (mpt-90) REVERT: B 364 ASN cc_start: 0.7694 (m-40) cc_final: 0.7228 (t0) REVERT: C 359 ASN cc_start: 0.7649 (m110) cc_final: 0.7238 (t0) REVERT: D 47 LYS cc_start: 0.8276 (mtmm) cc_final: 0.7932 (mttp) REVERT: D 269 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8616 (mp) REVERT: D 287 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: E 58 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7396 (ptm160) REVERT: E 61 GLU cc_start: 0.7912 (tt0) cc_final: 0.7379 (mt-10) REVERT: E 94 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7636 (mtp180) REVERT: E 98 SER cc_start: 0.7713 (t) cc_final: 0.7381 (m) REVERT: F 58 GLN cc_start: 0.8352 (mp-120) cc_final: 0.7565 (tp-100) REVERT: F 81 GLU cc_start: 0.8273 (mp0) cc_final: 0.7694 (mm-30) REVERT: F 97 ARG cc_start: 0.8448 (mmm160) cc_final: 0.8048 (mmm-85) REVERT: F 145 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: G 132 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8310 (mppt) REVERT: H 28 ARG cc_start: 0.7829 (tpp-160) cc_final: 0.7559 (tpp80) REVERT: H 30 VAL cc_start: 0.9082 (m) cc_final: 0.8858 (t) REVERT: H 47 MET cc_start: 0.8073 (tpp) cc_final: 0.7145 (mmp) REVERT: H 68 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8355 (mttm) REVERT: H 165 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7985 (mt) REVERT: H 206 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7117 (ttm110) REVERT: H 306 TYR cc_start: 0.9243 (m-80) cc_final: 0.8998 (m-80) REVERT: I 68 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8279 (mttt) REVERT: I 152 VAL cc_start: 0.7636 (OUTLIER) cc_final: 0.7400 (p) REVERT: M 194 THR cc_start: 0.8029 (m) cc_final: 0.7741 (p) REVERT: M 195 GLU cc_start: 0.6634 (tm-30) cc_final: 0.6426 (tm-30) REVERT: M 202 THR cc_start: 0.7754 (m) cc_final: 0.7452 (p) REVERT: M 206 ARG cc_start: 0.7716 (ttp80) cc_final: 0.6769 (ttm110) REVERT: M 224 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7291 (pm20) REVERT: N 47 MET cc_start: 0.1227 (ttp) cc_final: 0.0471 (ttm) REVERT: N 206 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7101 (ttm110) REVERT: N 305 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8307 (mmt) REVERT: N 355 MET cc_start: 0.8203 (mtp) cc_final: 0.7816 (mtt) REVERT: O 68 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8584 (ptpp) REVERT: O 72 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: O 206 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.7771 (ttm-80) REVERT: P 82 MET cc_start: 0.8856 (tpt) cc_final: 0.8280 (tpt) REVERT: P 206 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8108 (ttm110) REVERT: P 355 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8311 (mpp) REVERT: Q 47 MET cc_start: 0.7722 (mmm) cc_final: 0.6611 (ptt) REVERT: Q 72 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: Q 190 MET cc_start: 0.8571 (mtm) cc_final: 0.8315 (mtp) REVERT: Q 225 ASN cc_start: 0.8024 (t0) cc_final: 0.7739 (m110) REVERT: Q 291 LYS cc_start: 0.6417 (mttm) cc_final: 0.5975 (tmtm) REVERT: R 99 GLU cc_start: 0.7964 (pm20) cc_final: 0.7665 (pm20) REVERT: R 206 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7656 (ttm-80) REVERT: R 297 ASN cc_start: 0.8733 (m110) cc_final: 0.8423 (m-40) outliers start: 94 outliers final: 47 residues processed: 602 average time/residue: 2.7778 time to fit residues: 2033.6924 Evaluate side-chains 595 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 528 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 206 ARG Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain O residue 12 ASN Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 88 optimal weight: 2.9990 chunk 407 optimal weight: 4.9990 chunk 417 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 366 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 260 optimal weight: 7.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN G 130 HIS I 12 ASN O 225 ASN P 297 ASN ** Q 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 GLN R 297 ASN R 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112871 restraints weight = 133531.245| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.55 r_work: 0.3280 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39895 Z= 0.162 Angle : 0.560 6.789 54139 Z= 0.277 Chirality : 0.043 0.183 5990 Planarity : 0.004 0.114 6962 Dihedral : 8.304 171.255 5544 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.64 % Allowed : 18.53 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 4854 helix: 0.63 (0.12), residues: 1952 sheet: -0.20 (0.17), residues: 877 loop : 0.71 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.008 0.001 HIS I 173 PHE 0.019 0.001 PHE D 10 TYR 0.017 0.001 TYR I 279 ARG 0.014 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 627 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 558 time to evaluate : 4.544 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8194 (tppt) REVERT: A 253 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7289 (mptt) REVERT: A 302 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: B 21 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7884 (mtmm) REVERT: B 75 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8149 (pt) REVERT: B 152 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8632 (p) REVERT: B 224 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 244 ASP cc_start: 0.7161 (m-30) cc_final: 0.6871 (m-30) REVERT: B 295 ARG cc_start: 0.7589 (mtp180) cc_final: 0.6867 (mpt-90) REVERT: B 364 ASN cc_start: 0.7653 (m-40) cc_final: 0.7115 (t0) REVERT: C 41 ASP cc_start: 0.6850 (t0) cc_final: 0.6270 (p0) REVERT: C 359 ASN cc_start: 0.7567 (m110) cc_final: 0.7088 (t0) REVERT: D 47 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7807 (mttp) REVERT: D 143 ASN cc_start: 0.7197 (m-40) cc_final: 0.6997 (t0) REVERT: E 58 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8008 (ptt180) REVERT: E 61 GLU cc_start: 0.7947 (tt0) cc_final: 0.7401 (mt-10) REVERT: E 94 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7583 (mtp180) REVERT: E 98 SER cc_start: 0.7668 (t) cc_final: 0.7330 (m) REVERT: F 23 GLU cc_start: 0.8170 (tt0) cc_final: 0.7963 (tt0) REVERT: F 58 GLN cc_start: 0.8265 (mp-120) cc_final: 0.7301 (tp-100) REVERT: F 81 GLU cc_start: 0.8229 (mp0) cc_final: 0.7585 (mm-30) REVERT: G 132 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8180 (mppt) REVERT: H 28 ARG cc_start: 0.7869 (tpp-160) cc_final: 0.7576 (tpp80) REVERT: H 47 MET cc_start: 0.7972 (tpp) cc_final: 0.7307 (mmp) REVERT: H 68 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8252 (mttm) REVERT: H 165 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7865 (mt) REVERT: H 206 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.6973 (ttm110) REVERT: H 306 TYR cc_start: 0.9204 (m-80) cc_final: 0.8971 (m-80) REVERT: I 68 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8190 (mttt) REVERT: M 194 THR cc_start: 0.7910 (m) cc_final: 0.7646 (p) REVERT: M 202 THR cc_start: 0.7646 (m) cc_final: 0.7349 (p) REVERT: M 206 ARG cc_start: 0.7711 (ttp80) cc_final: 0.6764 (ttm110) REVERT: M 224 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7279 (pm20) REVERT: M 237 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6966 (mt-10) REVERT: N 47 MET cc_start: 0.1080 (ttp) cc_final: 0.0389 (ttm) REVERT: N 51 ASP cc_start: 0.7869 (m-30) cc_final: 0.7648 (p0) REVERT: O 68 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8492 (ptpp) REVERT: O 72 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: O 82 MET cc_start: 0.9271 (tpt) cc_final: 0.8838 (tpt) REVERT: O 113 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8195 (mmtp) REVERT: O 206 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.7619 (ttm-80) REVERT: P 82 MET cc_start: 0.8795 (tpt) cc_final: 0.8192 (tpt) REVERT: P 355 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: Q 47 MET cc_start: 0.7615 (mmm) cc_final: 0.6530 (ptt) REVERT: Q 72 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: Q 225 ASN cc_start: 0.8007 (t0) cc_final: 0.7663 (m110) REVERT: Q 291 LYS cc_start: 0.6333 (mttm) cc_final: 0.5877 (tmtm) REVERT: R 47 MET cc_start: 0.6123 (ppp) cc_final: 0.5681 (ppp) REVERT: R 99 GLU cc_start: 0.7934 (pm20) cc_final: 0.7637 (pm20) REVERT: R 206 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7587 (ttm-80) REVERT: R 297 ASN cc_start: 0.8661 (m-40) cc_final: 0.8377 (m-40) outliers start: 69 outliers final: 41 residues processed: 603 average time/residue: 2.7578 time to fit residues: 2023.6843 Evaluate side-chains 586 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 531 time to evaluate : 4.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 191 LYS Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 329 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 284 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 305 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN Q 12 ASN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN R 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112403 restraints weight = 133381.032| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.55 r_work: 0.3270 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 39895 Z= 0.220 Angle : 0.666 59.155 54139 Z= 0.352 Chirality : 0.044 0.448 5990 Planarity : 0.005 0.146 6962 Dihedral : 8.293 171.078 5542 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.12 % Favored : 97.86 % Rotamer: Outliers : 1.36 % Allowed : 19.22 % Favored : 79.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 4854 helix: 0.64 (0.12), residues: 1952 sheet: -0.19 (0.17), residues: 877 loop : 0.71 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 102 HIS 0.008 0.001 HIS I 173 PHE 0.017 0.001 PHE D 10 TYR 0.015 0.001 TYR I 279 ARG 0.008 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 66 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Evaluate side-chains 589 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 532 time to evaluate : 4.704 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8237 (tppt) REVERT: A 253 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7352 (mptt) REVERT: A 302 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: B 21 LYS cc_start: 0.8509 (mtmt) cc_final: 0.7921 (mtmm) REVERT: B 75 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8212 (pt) REVERT: B 152 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8641 (p) REVERT: B 224 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 244 ASP cc_start: 0.7177 (m-30) cc_final: 0.6884 (m-30) REVERT: B 295 ARG cc_start: 0.7623 (mtp180) cc_final: 0.6952 (mpt-90) REVERT: B 364 ASN cc_start: 0.7654 (m-40) cc_final: 0.7151 (t0) REVERT: C 41 ASP cc_start: 0.6826 (t0) cc_final: 0.6274 (p0) REVERT: C 359 ASN cc_start: 0.7602 (m110) cc_final: 0.7170 (t0) REVERT: D 47 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7845 (mttp) REVERT: E 58 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8037 (ptt180) REVERT: E 94 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7612 (mtp180) REVERT: E 98 SER cc_start: 0.7721 (t) cc_final: 0.7384 (m) REVERT: F 58 GLN cc_start: 0.8271 (mp-120) cc_final: 0.7387 (tp-100) REVERT: F 81 GLU cc_start: 0.8268 (mp0) cc_final: 0.7659 (mm-30) REVERT: G 132 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8256 (mppt) REVERT: H 28 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7581 (tpp80) REVERT: H 47 MET cc_start: 0.7980 (tpp) cc_final: 0.7337 (mmp) REVERT: H 68 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8282 (mttm) REVERT: H 165 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7917 (mt) REVERT: H 206 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7052 (ttm110) REVERT: H 306 TYR cc_start: 0.9210 (m-80) cc_final: 0.8985 (m-80) REVERT: I 11 ASP cc_start: 0.7359 (t0) cc_final: 0.6994 (t70) REVERT: I 68 LYS cc_start: 0.8579 (mmmt) cc_final: 0.8253 (mttt) REVERT: M 194 THR cc_start: 0.7959 (m) cc_final: 0.7694 (p) REVERT: M 202 THR cc_start: 0.7698 (m) cc_final: 0.7408 (p) REVERT: M 206 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6804 (ttm110) REVERT: M 224 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7296 (pm20) REVERT: M 237 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6971 (mt-10) REVERT: N 47 MET cc_start: 0.1108 (ttp) cc_final: 0.0413 (ttm) REVERT: O 68 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8498 (ptpp) REVERT: O 72 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: O 82 MET cc_start: 0.9272 (tpt) cc_final: 0.8849 (tpt) REVERT: O 113 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8232 (mmtp) REVERT: O 206 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.7696 (ttm-80) REVERT: P 82 MET cc_start: 0.8815 (tpt) cc_final: 0.8221 (tpt) REVERT: P 355 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8311 (mpp) REVERT: Q 47 MET cc_start: 0.7633 (mmm) cc_final: 0.6565 (ptt) REVERT: Q 72 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: Q 225 ASN cc_start: 0.8033 (t0) cc_final: 0.7725 (m110) REVERT: Q 291 LYS cc_start: 0.6386 (mttm) cc_final: 0.5948 (tmtm) REVERT: R 47 MET cc_start: 0.6127 (ppp) cc_final: 0.5680 (ppp) REVERT: R 99 GLU cc_start: 0.7951 (pm20) cc_final: 0.7682 (pm20) REVERT: R 206 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7661 (ttm-80) outliers start: 57 outliers final: 40 residues processed: 570 average time/residue: 2.8275 time to fit residues: 1962.2820 Evaluate side-chains 585 residues out of total 4203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 531 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 161 TYR Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain I residue 18 LYS Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 72 GLU Chi-restraints excluded: chain O residue 113 LYS Chi-restraints excluded: chain O residue 324 THR Chi-restraints excluded: chain O residue 375 PHE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 355 MET Chi-restraints excluded: chain Q residue 44 MET Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 191 LYS Chi-restraints excluded: chain R residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 403 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 365 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 356 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 143 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN Q 12 ASN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 ASN R 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112237 restraints weight = 133878.936| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.57 r_work: 0.3267 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 39895 Z= 0.218 Angle : 0.664 59.200 54139 Z= 0.351 Chirality : 0.044 0.403 5990 Planarity : 0.005 0.143 6962 Dihedral : 8.293 171.078 5542 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.31 % Allowed : 19.27 % Favored : 79.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 4854 helix: 0.64 (0.12), residues: 1952 sheet: -0.19 (0.17), residues: 877 loop : 0.71 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 102 HIS 0.008 0.001 HIS I 173 PHE 0.017 0.001 PHE D 10 TYR 0.015 0.001 TYR I 279 ARG 0.008 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: