Starting phenix.real_space_refine on Sun Aug 9 10:32:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yaq_72734/08_2026/9yaq_72734.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yaq_72734/08_2026/9yaq_72734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yaq_72734/08_2026/9yaq_72734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yaq_72734/08_2026/9yaq_72734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yaq_72734/08_2026/9yaq_72734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yaq_72734/08_2026/9yaq_72734.map" } resolution = 4.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.213 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 Ca 3 9.91 5 P 8 5.49 5 Mg 4 5.21 5 S 198 5.16 5 C 21390 2.51 5 N 5806 2.21 5 O 6557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33966 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1304 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "F" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1304 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'TRANS': 159} Chain: "G" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 278 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "H" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 278 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "I" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 595 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "J" Number of atoms: 6461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6461 Classifications: {'peptide': 802} Link IDs: {'PTRANS': 30, 'TRANS': 771} Chain breaks: 1 Chain: "K" Number of atoms: 6475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6475 Classifications: {'peptide': 805} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 773} Chain: "L" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "M" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1217 Classifications: {'peptide': 153} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 146} Chain: "N" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1274 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Chain: "O" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 643 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} 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: 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: "C" 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: "D" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.79, per 1000 atoms: 0.20 Number of scatterers: 33966 At special positions: 0 Unit cell: (176.28, 151.872, 277.98, 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) Ca 3 19.99 S 198 16.00 P 8 15.00 Mg 4 11.99 O 6557 8.00 N 5806 7.00 C 21390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 187 helices and 31 sheets defined 52.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.674A pdb=" N LYS A 118 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.711A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.583A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.811A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 295' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 359 through 362 No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.863A pdb=" N ARG B 62 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY B 63 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.847A pdb=" N LYS B 118 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 125 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 4.216A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.798A pdb=" N GLU B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 216 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.544A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.997A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.558A pdb=" N LYS B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 373' Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.605A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 192 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 203 through 216 removed outlier: 4.314A pdb=" N GLU C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 216 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.561A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.518A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 295 removed outlier: 3.841A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.738A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 341 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.620A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Proline residue: C 367 - end of helix removed outlier: 5.212A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.615A pdb=" N ALA D 58 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.552A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.817A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.174A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.944A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.545A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.630A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 290 through 295' Processing helix chain 'D' and resid 302 through 305 removed outlier: 3.617A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 302 through 305' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.631A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 4.151A pdb=" N GLN D 354 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 355' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'E' and resid 126 through 283 removed outlier: 3.515A pdb=" N SER E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 283 removed outlier: 4.171A pdb=" N SER F 283 " --> pdb=" O ASN F 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 34 Processing helix chain 'H' and resid 2 through 34 Processing helix chain 'I' and resid 86 through 149 Processing helix chain 'J' and resid 6 through 8 No H-bonds generated for 'chain 'J' and resid 6 through 8' Processing helix chain 'J' and resid 10 through 16 removed outlier: 3.819A pdb=" N ALA J 13 " --> pdb=" O GLY J 10 " (cutoff:3.500A) Proline residue: J 14 - end of helix No H-bonds generated for 'chain 'J' and resid 10 through 16' Processing helix chain 'J' and resid 20 through 26 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 82 through 84 No H-bonds generated for 'chain 'J' and resid 82 through 84' Processing helix chain 'J' and resid 90 through 92 No H-bonds generated for 'chain 'J' and resid 90 through 92' Processing helix chain 'J' and resid 98 through 109 Processing helix chain 'J' and resid 132 through 134 No H-bonds generated for 'chain 'J' and resid 132 through 134' Processing helix chain 'J' and resid 136 through 142 removed outlier: 4.048A pdb=" N TYR J 142 " --> pdb=" O VAL J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 168 Processing helix chain 'J' and resid 185 through 201 removed outlier: 3.848A pdb=" N LYS J 189 " --> pdb=" O THR J 185 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 194 " --> pdb=" O ARG J 190 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA J 199 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE J 201 " --> pdb=" O VAL J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 209 No H-bonds generated for 'chain 'J' and resid 207 through 209' Processing helix chain 'J' and resid 211 through 213 No H-bonds generated for 'chain 'J' and resid 211 through 213' Processing helix chain 'J' and resid 216 through 231 Proline residue: J 225 - end of helix removed outlier: 3.770A pdb=" N PHE J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 273 No H-bonds generated for 'chain 'J' and resid 271 through 273' Processing helix chain 'J' and resid 284 through 290 Processing helix chain 'J' and resid 295 through 300 Processing helix chain 'J' and resid 327 through 339 Processing helix chain 'J' and resid 343 through 361 removed outlier: 3.983A pdb=" N ASN J 347 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY J 360 " --> pdb=" O ILE J 356 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN J 361 " --> pdb=" O MET J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 388 Processing helix chain 'J' and resid 392 through 400 removed outlier: 3.667A pdb=" N LYS J 397 " --> pdb=" O ALA J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 447 removed outlier: 3.917A pdb=" N LEU J 447 " --> pdb=" O ILE J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 503 Processing helix chain 'J' and resid 513 through 525 removed outlier: 3.733A pdb=" N GLN J 518 " --> pdb=" O MET J 515 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA J 519 " --> pdb=" O ASP J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 539 removed outlier: 3.598A pdb=" N CYS J 538 " --> pdb=" O LEU J 534 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET J 539 " --> pdb=" O GLU J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 556 Processing helix chain 'J' and resid 593 through 597 Processing helix chain 'J' and resid 603 through 610 Processing helix chain 'J' and resid 615 through 620 Processing helix chain 'J' and resid 647 through 664 removed outlier: 4.072A pdb=" N SER J 664 " --> pdb=" O THR J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 687 through 695 removed outlier: 4.810A pdb=" N GLN J 692 " --> pdb=" O LEU J 688 " (cutoff:3.500A) Processing helix chain 'J' and resid 698 through 707 Processing helix chain 'J' and resid 715 through 718 No H-bonds generated for 'chain 'J' and resid 715 through 718' Processing helix chain 'J' and resid 723 through 725 No H-bonds generated for 'chain 'J' and resid 723 through 725' Processing helix chain 'J' and resid 738 through 749 Processing helix chain 'J' and resid 753 through 755 No H-bonds generated for 'chain 'J' and resid 753 through 755' Processing helix chain 'J' and resid 769 through 807 removed outlier: 3.733A pdb=" N ALA J 790 " --> pdb=" O THR J 786 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU J 806 " --> pdb=" O LYS J 802 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG J 807 " --> pdb=" O LYS J 803 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 16 No H-bonds generated for 'chain 'K' and resid 13 through 16' Processing helix chain 'K' and resid 20 through 27 Processing helix chain 'K' and resid 82 through 84 No H-bonds generated for 'chain 'K' and resid 82 through 84' Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 98 through 110 removed outlier: 3.534A pdb=" N ASN K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 136 through 141 Processing helix chain 'K' and resid 154 through 168 Processing helix chain 'K' and resid 181 through 199 removed outlier: 3.541A pdb=" N ALA K 199 " --> pdb=" O PHE K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 231 removed outlier: 3.623A pdb=" N ASN K 224 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Proline residue: K 225 - end of helix removed outlier: 3.811A pdb=" N ALA K 229 " --> pdb=" O PRO K 225 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 290 Processing helix chain 'K' and resid 296 through 301 Processing helix chain 'K' and resid 311 through 314 No H-bonds generated for 'chain 'K' and resid 311 through 314' Processing helix chain 'K' and resid 325 through 338 removed outlier: 4.049A pdb=" N ASP K 333 " --> pdb=" O LEU K 329 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN K 334 " --> pdb=" O MET K 330 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 361 removed outlier: 3.909A pdb=" N GLY K 360 " --> pdb=" O ILE K 356 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN K 361 " --> pdb=" O MET K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 388 Processing helix chain 'K' and resid 392 through 400 Processing helix chain 'K' and resid 417 through 447 removed outlier: 3.562A pdb=" N LEU K 447 " --> pdb=" O ILE K 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 473 through 504 Processing helix chain 'K' and resid 515 through 523 removed outlier: 4.230A pdb=" N CYS K 520 " --> pdb=" O ASP K 516 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP K 522 " --> pdb=" O GLN K 518 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU K 523 " --> pdb=" O ALA K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 537 Processing helix chain 'K' and resid 545 through 554 Processing helix chain 'K' and resid 593 through 597 Processing helix chain 'K' and resid 603 through 610 Processing helix chain 'K' and resid 615 through 620 Processing helix chain 'K' and resid 647 through 663 Processing helix chain 'K' and resid 686 through 696 Processing helix chain 'K' and resid 698 through 706 Processing helix chain 'K' and resid 715 through 722 Processing helix chain 'K' and resid 738 through 747 Processing helix chain 'K' and resid 753 through 755 No H-bonds generated for 'chain 'K' and resid 753 through 755' Processing helix chain 'K' and resid 769 through 807 Processing helix chain 'L' and resid 49 through 62 removed outlier: 3.519A pdb=" N GLU L 57 " --> pdb=" O GLU L 53 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE L 62 " --> pdb=" O ALA L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 83 removed outlier: 4.887A pdb=" N ALA L 83 " --> pdb=" O ASP L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 96 No H-bonds generated for 'chain 'L' and resid 93 through 96' Processing helix chain 'L' and resid 102 through 105 No H-bonds generated for 'chain 'L' and resid 102 through 105' Processing helix chain 'L' and resid 112 through 124 Proline residue: L 117 - end of helix removed outlier: 3.537A pdb=" N LYS L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 137 Processing helix chain 'L' and resid 151 through 157 removed outlier: 4.249A pdb=" N ARG L 155 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS L 156 " --> pdb=" O ALA L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 176 removed outlier: 3.612A pdb=" N LEU L 173 " --> pdb=" O GLU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 194 Processing helix chain 'M' and resid 49 through 60 removed outlier: 3.716A pdb=" N GLU M 54 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET M 60 " --> pdb=" O LYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 81 removed outlier: 3.633A pdb=" N CYS M 77 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY M 78 " --> pdb=" O GLY M 75 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU M 81 " --> pdb=" O GLY M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 96 removed outlier: 3.718A pdb=" N LEU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 90 through 96' Processing helix chain 'M' and resid 102 through 105 No H-bonds generated for 'chain 'M' and resid 102 through 105' Processing helix chain 'M' and resid 112 through 123 Proline residue: M 117 - end of helix Processing helix chain 'M' and resid 131 through 141 removed outlier: 3.615A pdb=" N GLU M 136 " --> pdb=" O GLU M 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 160 removed outlier: 3.607A pdb=" N ALA M 159 " --> pdb=" O ARG M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 176 removed outlier: 4.652A pdb=" N GLY M 176 " --> pdb=" O LYS M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 194 removed outlier: 3.994A pdb=" N HIS M 192 " --> pdb=" O ALA M 188 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE M 193 " --> pdb=" O PHE M 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET M 194 " --> pdb=" O VAL M 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 188 through 194' Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 14 through 28 Processing helix chain 'N' and resid 38 through 48 removed outlier: 3.555A pdb=" N LEU N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 64 removed outlier: 3.996A pdb=" N VAL N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 85 removed outlier: 3.557A pdb=" N MET N 85 " --> pdb=" O MET N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 104 Processing helix chain 'N' and resid 114 through 123 removed outlier: 3.669A pdb=" N ALA N 123 " --> pdb=" O ILE N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 140 Processing helix chain 'N' and resid 150 through 156 Processing helix chain 'O' and resid 44 through 80 Processing helix chain 'O' and resid 91 through 136 Processing helix chain 'O' and resid 152 through 159 Processing helix chain 'P' and resid 200 through 212 Processing helix chain 'P' and resid 223 through 268 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.912A pdb=" N CYS A 10 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 104 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 299 removed outlier: 6.303A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 240 Processing sheet with id= E, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.837A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.517A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.483A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 240 Processing sheet with id= I, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.535A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 65 through 69 removed outlier: 3.525A pdb=" N GLY C 36 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 104 through 107 removed outlier: 6.677A pdb=" N TYR C 133 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLU C 107 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA C 135 " --> pdb=" O GLU C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 8.047A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= N, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.680A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 18 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 34 through 38 removed outlier: 3.619A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.164A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP D 154 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 238 through 240 Processing sheet with id= R, first strand: chain 'J' and resid 36 through 39 removed outlier: 6.650A pdb=" N THR J 60 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL J 69 " --> pdb=" O ALA J 61 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 115 through 118 removed outlier: 6.381A pdb=" N ARG J 671 " --> pdb=" O THR J 124 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 666 through 669 removed outlier: 3.580A pdb=" N GLN J 172 " --> pdb=" O PHE J 456 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER J 260 " --> pdb=" O HIS J 251 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 364 through 366 Processing sheet with id= V, first strand: chain 'J' and resid 404 through 406 Processing sheet with id= W, first strand: chain 'J' and resid 577 through 581 removed outlier: 3.625A pdb=" N PHE J 577 " --> pdb=" O TYR J 588 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 711 through 714 removed outlier: 3.530A pdb=" N VAL J 763 " --> pdb=" O ILE J 713 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 76 through 78 removed outlier: 6.797A pdb=" N THR K 60 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ARG K 54 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA K 61 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL K 69 " --> pdb=" O ALA K 61 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 115 through 118 removed outlier: 3.545A pdb=" N GLN K 172 " --> pdb=" O PHE K 456 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER K 260 " --> pdb=" O HIS K 251 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 364 through 366 Processing sheet with id= AB, first strand: chain 'K' and resid 402 through 406 Processing sheet with id= AC, first strand: chain 'K' and resid 577 through 581 removed outlier: 4.283A pdb=" N PHE K 577 " --> pdb=" O TYR K 588 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 711 through 714 Processing sheet with id= AE, first strand: chain 'M' and resid 148 through 150 1602 hydrogen bonds defined for protein. 4437 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: 6.65 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11311 1.34 - 1.46: 5831 1.46 - 1.58: 17064 1.58 - 1.69: 12 1.69 - 1.81: 348 Bond restraints: 34566 Sorted by residual: bond pdb=" C ALA J 13 " pdb=" N PRO J 14 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.19e-02 7.06e+03 3.37e+00 bond pdb=" CA VAL K 406 " pdb=" CB VAL K 406 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.11e-02 8.12e+03 1.32e+00 bond pdb=" CA ILE D 357 " pdb=" CB ILE D 357 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.05e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 34561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 46287 2.68 - 5.36: 232 5.36 - 8.03: 27 8.03 - 10.71: 1 10.71 - 13.39: 2 Bond angle restraints: 46549 Sorted by residual: angle pdb=" C GLY M 182 " pdb=" N CYS M 183 " pdb=" CA CYS M 183 " ideal model delta sigma weight residual 121.70 135.09 -13.39 1.80e+00 3.09e-01 5.53e+01 angle pdb=" C GLY L 182 " pdb=" N CYS L 183 " pdb=" CA CYS L 183 " ideal model delta sigma weight residual 121.70 134.43 -12.73 1.80e+00 3.09e-01 5.00e+01 angle pdb=" N ILE J 274 " pdb=" CA ILE J 274 " pdb=" C ILE J 274 " ideal model delta sigma weight residual 113.71 109.46 4.25 9.50e-01 1.11e+00 2.00e+01 angle pdb=" N ILE J 313 " pdb=" CA ILE J 313 " pdb=" C ILE J 313 " ideal model delta sigma weight residual 113.71 109.81 3.90 9.50e-01 1.11e+00 1.68e+01 angle pdb=" N VAL L 80 " pdb=" CA VAL L 80 " pdb=" C VAL L 80 " ideal model delta sigma weight residual 113.42 108.83 4.59 1.17e+00 7.31e-01 1.54e+01 ... (remaining 46544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19556 17.97 - 35.94: 1251 35.94 - 53.91: 296 53.91 - 71.87: 83 71.87 - 89.84: 42 Dihedral angle restraints: 21228 sinusoidal: 8896 harmonic: 12332 Sorted by residual: dihedral pdb=" CA ASP J 628 " pdb=" C ASP J 628 " pdb=" N THR J 629 " pdb=" CA THR J 629 " ideal model delta harmonic sigma weight residual -180.00 -106.59 -73.41 0 5.00e+00 4.00e-02 2.16e+02 dihedral pdb=" CA GLU A 3 " pdb=" C GLU A 3 " pdb=" N GLU A 4 " pdb=" CA GLU A 4 " ideal model delta harmonic sigma weight residual -180.00 -154.35 -25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA GLY K 626 " pdb=" C GLY K 626 " pdb=" N ALA K 627 " pdb=" CA ALA K 627 " ideal model delta harmonic sigma weight residual 180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 21225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3185 0.029 - 0.058: 1245 0.058 - 0.087: 400 0.087 - 0.116: 216 0.116 - 0.145: 39 Chirality restraints: 5085 Sorted by residual: chirality pdb=" CA ILE J 730 " pdb=" N ILE J 730 " pdb=" C ILE J 730 " pdb=" CB ILE J 730 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE K 674 " pdb=" N ILE K 674 " pdb=" C ILE K 674 " pdb=" CB ILE K 674 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE J 736 " pdb=" N ILE J 736 " pdb=" C ILE J 736 " pdb=" CB ILE J 736 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 5082 not shown) Planarity restraints: 6051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 306 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 307 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 224 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO K 225 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO K 225 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 225 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO B 112 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.021 5.00e-02 4.00e+02 ... (remaining 6048 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 185 2.51 - 3.10: 24747 3.10 - 3.70: 51568 3.70 - 4.30: 70611 4.30 - 4.90: 117095 Nonbonded interactions: 264206 Sorted by model distance: nonbonded pdb=" OD2 ASP D 11 " pdb="MG MG D 402 " model vdw 1.907 2.170 nonbonded pdb=" OD1 ASP A 11 " pdb="MG MG A 402 " model vdw 1.923 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 1.947 2.170 nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 402 " model vdw 2.000 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.036 2.170 ... (remaining 264201 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = (chain 'K' and (resid 4 through 624 or resid 628 through 808)) } ncs_group { reference = chain 'L' selection = chain 'M' } 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 group one per residue 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: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 : 0.002 0.026 34566 Z= 0.111 Angle : 0.540 13.389 46549 Z= 0.298 Chirality : 0.039 0.145 5085 Planarity : 0.004 0.045 6051 Dihedral : 13.642 89.842 13268 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.15 % Rotamer: Outliers : 3.04 % Allowed : 6.40 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4205 helix: 1.30 (0.11), residues: 2181 sheet: -0.64 (0.25), residues: 429 loop : -0.87 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 147 TYR 0.014 0.001 TYR L 186 PHE 0.017 0.001 PHE J 644 TRP 0.008 0.001 TRP D 79 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (34566) covalent geometry : angle 0.54008 / 0.30 (46549) hydrogen bonds : bond 0.14761 / 10.21 ( 1602) hydrogen bonds : angle 4.79175 / 3.35 ( 4437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 999 time to evaluate : 1.149 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: A 123 MET cc_start: 0.7309 (mmm) cc_final: 0.6964 (mmm) REVERT: A 132 MET cc_start: 0.9242 (ppp) cc_final: 0.8897 (ppp) REVERT: A 188 TYR cc_start: 0.8408 (t80) cc_final: 0.8121 (t80) REVERT: A 305 MET cc_start: 0.8188 (mmm) cc_final: 0.7652 (mmt) REVERT: A 337 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: B 111 ASN cc_start: 0.8072 (m-40) cc_final: 0.7617 (t0) REVERT: B 140 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 157 ASP cc_start: 0.7178 (t70) cc_final: 0.6568 (t0) REVERT: B 169 TYR cc_start: 0.7614 (m-80) cc_final: 0.7003 (m-80) REVERT: B 193 LEU cc_start: 0.8140 (mt) cc_final: 0.7746 (tp) REVERT: B 305 MET cc_start: 0.8749 (mmm) cc_final: 0.7787 (mmm) REVERT: B 337 TYR cc_start: 0.8936 (m-80) cc_final: 0.8328 (m-10) REVERT: B 346 LEU cc_start: 0.9389 (tp) cc_final: 0.9036 (tt) REVERT: C 43 VAL cc_start: 0.9192 (m) cc_final: 0.8804 (p) REVERT: C 81 ASP cc_start: 0.7300 (m-30) cc_final: 0.6822 (m-30) REVERT: C 149 THR cc_start: 0.8493 (p) cc_final: 0.8284 (p) REVERT: C 151 ILE cc_start: 0.8816 (tt) cc_final: 0.8529 (tt) REVERT: C 176 MET cc_start: 0.7595 (mmm) cc_final: 0.7284 (tpp) REVERT: C 192 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8447 (mm) REVERT: C 253 GLU cc_start: 0.7790 (mp0) cc_final: 0.7342 (mm-30) REVERT: C 267 ILE cc_start: 0.9030 (pt) cc_final: 0.8718 (mm) REVERT: C 274 ILE cc_start: 0.8283 (pt) cc_final: 0.8080 (pt) REVERT: C 303 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8070 (p) REVERT: C 305 MET cc_start: 0.7784 (mmm) cc_final: 0.7158 (mmm) REVERT: C 306 TYR cc_start: 0.8794 (m-80) cc_final: 0.8030 (m-80) REVERT: D 123 MET cc_start: 0.8814 (mmm) cc_final: 0.6883 (mmm) REVERT: D 190 MET cc_start: 0.8560 (tmm) cc_final: 0.8311 (tmm) REVERT: D 227 MET cc_start: 0.8318 (mmm) cc_final: 0.8102 (tpp) REVERT: D 305 MET cc_start: 0.7721 (mmm) cc_final: 0.7427 (tpt) REVERT: D 335 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7621 (mtt180) REVERT: D 340 TRP cc_start: 0.8101 (t60) cc_final: 0.7261 (t60) REVERT: D 355 MET cc_start: 0.8209 (mmm) cc_final: 0.7853 (mmt) REVERT: E 253 ILE cc_start: 0.7392 (tp) cc_final: 0.7176 (tp) REVERT: E 254 ASP cc_start: 0.7027 (m-30) cc_final: 0.6666 (t0) REVERT: F 181 GLU cc_start: 0.5617 (mt-10) cc_final: 0.5204 (tm-30) REVERT: F 218 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6380 (pt0) REVERT: J 38 TYR cc_start: 0.5931 (m-80) cc_final: 0.5723 (m-80) REVERT: J 95 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6123 (m-10) REVERT: J 112 TRP cc_start: 0.8065 (m100) cc_final: 0.7641 (m100) REVERT: J 257 LYS cc_start: 0.6363 (mmtm) cc_final: 0.5915 (mmmt) REVERT: J 333 ASP cc_start: 0.6490 (OUTLIER) cc_final: 0.5831 (t0) REVERT: J 349 MET cc_start: 0.8610 (mmm) cc_final: 0.6528 (mmt) REVERT: J 380 GLU cc_start: 0.6110 (mm-30) cc_final: 0.5876 (mm-30) REVERT: J 435 MET cc_start: 0.8387 (ttp) cc_final: 0.7246 (ttp) REVERT: J 508 TRP cc_start: 0.8176 (t-100) cc_final: 0.7833 (t-100) REVERT: J 517 LEU cc_start: 0.8938 (mt) cc_final: 0.8699 (mp) REVERT: J 567 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6609 (mmp80) REVERT: J 655 LEU cc_start: 0.8375 (tp) cc_final: 0.8114 (tp) REVERT: J 719 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.5364 (ppt170) REVERT: K 112 TRP cc_start: 0.8130 (m100) cc_final: 0.7815 (m-90) REVERT: K 116 THR cc_start: 0.9411 (m) cc_final: 0.9197 (m) REVERT: K 165 MET cc_start: 0.7719 (ttp) cc_final: 0.7489 (ttp) REVERT: K 266 TYR cc_start: 0.6316 (m-80) cc_final: 0.5561 (m-80) REVERT: K 303 ILE cc_start: 0.7047 (pt) cc_final: 0.6791 (mp) REVERT: K 313 ILE cc_start: 0.7865 (tt) cc_final: 0.7593 (tt) REVERT: K 337 ASP cc_start: 0.8004 (m-30) cc_final: 0.7746 (m-30) REVERT: K 350 TYR cc_start: 0.8574 (m-10) cc_final: 0.8308 (m-10) REVERT: K 356 ILE cc_start: 0.8141 (mt) cc_final: 0.7808 (mm) REVERT: K 531 MET cc_start: 0.8542 (mmt) cc_final: 0.8278 (mmm) REVERT: K 533 ILE cc_start: 0.8957 (pt) cc_final: 0.8432 (pt) REVERT: K 629 THR cc_start: 0.3696 (OUTLIER) cc_final: 0.3370 (t) REVERT: K 669 PHE cc_start: 0.7924 (m-80) cc_final: 0.7350 (m-80) REVERT: K 713 ILE cc_start: 0.8655 (tt) cc_final: 0.8430 (mp) REVERT: L 50 GLU cc_start: 0.6793 (pt0) cc_final: 0.6584 (pp20) REVERT: L 60 MET cc_start: 0.5357 (ppp) cc_final: 0.5055 (ppp) REVERT: L 164 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7759 (mmm160) REVERT: L 190 VAL cc_start: 0.3916 (p) cc_final: 0.3627 (p) REVERT: M 53 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8349 (pp20) REVERT: M 109 MET cc_start: 0.7131 (mmt) cc_final: 0.6918 (tpt) REVERT: M 144 GLU cc_start: 0.6069 (tp30) cc_final: 0.5798 (tm-30) REVERT: N 26 ILE cc_start: 0.6337 (mm) cc_final: 0.5775 (tp) REVERT: O 86 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5530 (pt) REVERT: O 108 VAL cc_start: 0.6180 (m) cc_final: 0.5968 (m) REVERT: O 118 LYS cc_start: 0.6692 (mtpp) cc_final: 0.6023 (mttm) REVERT: P 212 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8361 (mmm160) outliers start: 111 outliers final: 29 residues processed: 1081 average time/residue: 0.2087 time to fit residues: 359.2462 Evaluate side-chains 612 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 572 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS B 59 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN C 41 GLN C 49 GLN C 275 HIS D 275 HIS E 144 GLN E 263 GLN F 216 GLN F 263 GLN G 17 ASN J 75 GLN J 104 ASN J 160 ASN J 222 GLN J 238 ASN J 358 HIS J 401 HIS J 454 GLN J 486 GLN J 562 ASN J 654 ASN J 711 ASN J 760 HIS J 789 GLN K 172 GLN K 276 GLN K 451 GLN K 475 GLN ** K 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 555 ASN K 595 GLN K 602 ASN K 789 GLN L 156 HIS O 49 GLN O 56 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 222 ASN P 225 GLN P 235 GLN P 254 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095693 restraints weight = 114533.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.096517 restraints weight = 80165.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096769 restraints weight = 60713.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097237 restraints weight = 52683.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.097275 restraints weight = 47235.567| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34566 Z= 0.235 Angle : 0.733 11.077 46549 Z= 0.378 Chirality : 0.046 0.288 5085 Planarity : 0.005 0.052 6051 Dihedral : 5.703 44.067 4645 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 4205 helix: 0.94 (0.11), residues: 2158 sheet: -0.54 (0.27), residues: 384 loop : -1.01 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 198 TYR 0.025 0.002 TYR K 422 PHE 0.027 0.003 PHE J 801 TRP 0.026 0.002 TRP K 508 HIS 0.016 0.002 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (34566) covalent geometry : angle 0.73341 / 0.38 (46549) hydrogen bonds : bond 0.05000 / 3.34 ( 1602) hydrogen bonds : angle 4.47831 / 3.16 ( 4437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 694 time to evaluate : 1.326 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: A 9 VAL cc_start: 0.8687 (t) cc_final: 0.8113 (t) REVERT: A 123 MET cc_start: 0.8234 (mmm) cc_final: 0.7159 (mmm) REVERT: A 132 MET cc_start: 0.9396 (ppp) cc_final: 0.9118 (ppp) REVERT: A 246 GLN cc_start: 0.5296 (pt0) cc_final: 0.5022 (pt0) REVERT: A 340 TRP cc_start: 0.9005 (t60) cc_final: 0.8381 (t60) REVERT: B 30 VAL cc_start: 0.8884 (t) cc_final: 0.8625 (p) REVERT: B 157 ASP cc_start: 0.8467 (t70) cc_final: 0.8159 (t70) REVERT: B 190 MET cc_start: 0.8246 (tmm) cc_final: 0.8010 (tmm) REVERT: B 278 THR cc_start: 0.8462 (m) cc_final: 0.8228 (m) REVERT: B 337 TYR cc_start: 0.9344 (m-80) cc_final: 0.8652 (m-10) REVERT: C 132 MET cc_start: 0.8220 (ppp) cc_final: 0.7814 (ppp) REVERT: C 157 ASP cc_start: 0.8197 (t70) cc_final: 0.7942 (t70) REVERT: C 186 THR cc_start: 0.8198 (m) cc_final: 0.7983 (p) REVERT: C 192 ILE cc_start: 0.8567 (pt) cc_final: 0.8257 (mm) REVERT: C 193 LEU cc_start: 0.8471 (mt) cc_final: 0.8091 (tt) REVERT: C 267 ILE cc_start: 0.9167 (pt) cc_final: 0.8962 (mm) REVERT: C 305 MET cc_start: 0.8243 (mmm) cc_final: 0.7616 (tpp) REVERT: C 352 PHE cc_start: 0.8821 (t80) cc_final: 0.8518 (t80) REVERT: D 119 MET cc_start: 0.8639 (tmm) cc_final: 0.8430 (tmm) REVERT: D 123 MET cc_start: 0.9128 (mmm) cc_final: 0.7260 (mmm) REVERT: D 227 MET cc_start: 0.8718 (mmm) cc_final: 0.8250 (tpp) REVERT: D 325 MET cc_start: 0.7379 (mmm) cc_final: 0.6990 (mmm) REVERT: D 335 ARG cc_start: 0.8628 (ttm170) cc_final: 0.8325 (mtt180) REVERT: D 340 TRP cc_start: 0.8419 (t60) cc_final: 0.7409 (t60) REVERT: D 355 MET cc_start: 0.8132 (mmm) cc_final: 0.7558 (mtt) REVERT: E 169 LEU cc_start: 0.7253 (tt) cc_final: 0.6748 (tp) REVERT: E 253 ILE cc_start: 0.7462 (tp) cc_final: 0.7016 (tp) REVERT: E 254 ASP cc_start: 0.7388 (m-30) cc_final: 0.6384 (t0) REVERT: E 281 MET cc_start: 0.5439 (tmm) cc_final: 0.4749 (tmm) REVERT: F 253 ILE cc_start: 0.7632 (mm) cc_final: 0.7261 (mm) REVERT: J 112 TRP cc_start: 0.8409 (m100) cc_final: 0.7851 (m100) REVERT: J 113 MET cc_start: 0.7894 (mtp) cc_final: 0.7559 (mmm) REVERT: J 257 LYS cc_start: 0.6400 (mmtm) cc_final: 0.5832 (mmtt) REVERT: J 274 ILE cc_start: 0.8699 (tt) cc_final: 0.7284 (tt) REVERT: J 277 LEU cc_start: 0.8742 (mt) cc_final: 0.8294 (mp) REVERT: J 281 ARG cc_start: 0.7684 (mtp85) cc_final: 0.6445 (ptm160) REVERT: J 323 ILE cc_start: 0.8895 (mm) cc_final: 0.8660 (tp) REVERT: J 349 MET cc_start: 0.8305 (mmm) cc_final: 0.6421 (mmt) REVERT: J 361 ASN cc_start: 0.7381 (t0) cc_final: 0.7134 (t0) REVERT: J 380 GLU cc_start: 0.6643 (mm-30) cc_final: 0.5984 (mm-30) REVERT: J 435 MET cc_start: 0.8678 (ttp) cc_final: 0.7692 (ttp) REVERT: J 479 ASN cc_start: 0.8967 (m110) cc_final: 0.8672 (m110) REVERT: J 483 GLU cc_start: 0.9073 (tp30) cc_final: 0.8170 (tp30) REVERT: J 516 ASP cc_start: 0.9087 (m-30) cc_final: 0.8815 (m-30) REVERT: J 517 LEU cc_start: 0.9273 (mt) cc_final: 0.8673 (mt) REVERT: J 601 LEU cc_start: 0.9319 (tp) cc_final: 0.9062 (tp) REVERT: J 629 THR cc_start: 0.8465 (m) cc_final: 0.8152 (p) REVERT: J 659 MET cc_start: 0.7950 (tpt) cc_final: 0.6868 (tpp) REVERT: J 663 ARG cc_start: 0.8397 (mtt180) cc_final: 0.8182 (mmt180) REVERT: K 45 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7537 (mt-10) REVERT: K 194 TYR cc_start: 0.7954 (t80) cc_final: 0.7169 (t80) REVERT: K 303 ILE cc_start: 0.7926 (pt) cc_final: 0.7572 (mp) REVERT: K 337 ASP cc_start: 0.8143 (m-30) cc_final: 0.7776 (m-30) REVERT: K 350 TYR cc_start: 0.8483 (m-10) cc_final: 0.8162 (m-80) REVERT: K 434 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8214 (tptp) REVERT: K 531 MET cc_start: 0.8946 (mmt) cc_final: 0.8275 (mmm) REVERT: K 615 LYS cc_start: 0.9078 (tptp) cc_final: 0.8862 (tppt) REVERT: K 722 TYR cc_start: 0.7199 (m-80) cc_final: 0.6854 (m-80) REVERT: L 50 GLU cc_start: 0.7280 (pt0) cc_final: 0.6852 (pp20) REVERT: L 60 MET cc_start: 0.5713 (ppp) cc_final: 0.5030 (ppp) REVERT: M 89 THR cc_start: 0.6453 (t) cc_final: 0.6154 (t) REVERT: M 144 GLU cc_start: 0.6256 (tp30) cc_final: 0.5630 (tm-30) REVERT: N 137 MET cc_start: 0.4471 (mmt) cc_final: 0.3947 (mmt) REVERT: N 157 MET cc_start: 0.6890 (mmm) cc_final: 0.6225 (tpp) REVERT: O 100 GLN cc_start: 0.7297 (mp-120) cc_final: 0.7085 (mm110) REVERT: P 198 ARG cc_start: 0.7246 (tpt170) cc_final: 0.7013 (ttt90) REVERT: P 212 ARG cc_start: 0.8905 (mmm160) cc_final: 0.8526 (mmm160) outliers start: 2 outliers final: 1 residues processed: 695 average time/residue: 0.2013 time to fit residues: 227.8093 Evaluate side-chains 487 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 486 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 328 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 314 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 92 ASN J 358 HIS K 475 GLN K 789 GLN L 121 HIS O 100 GLN O 122 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096065 restraints weight = 114020.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097183 restraints weight = 73043.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097980 restraints weight = 51952.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098549 restraints weight = 39516.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098948 restraints weight = 31992.047| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34566 Z= 0.164 Angle : 0.621 10.037 46549 Z= 0.321 Chirality : 0.043 0.189 5085 Planarity : 0.004 0.062 6051 Dihedral : 5.520 44.438 4645 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.43 % Rotamer: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4205 helix: 1.04 (0.11), residues: 2159 sheet: -0.60 (0.25), residues: 428 loop : -0.94 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 372 TYR 0.029 0.002 TYR K 142 PHE 0.040 0.002 PHE P 251 TRP 0.024 0.002 TRP J 508 HIS 0.025 0.002 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (34566) covalent geometry : angle 0.62115 / 0.32 (46549) hydrogen bonds : bond 0.04714 / 3.17 ( 1602) hydrogen bonds : angle 4.24950 / 3.00 ( 4437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 652 time to evaluate : 1.326 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 9 VAL cc_start: 0.8535 (t) cc_final: 0.8045 (t) REVERT: A 123 MET cc_start: 0.8204 (mmm) cc_final: 0.7167 (mmm) REVERT: A 132 MET cc_start: 0.9424 (ppp) cc_final: 0.9137 (ppp) REVERT: A 283 MET cc_start: 0.7289 (mmt) cc_final: 0.6826 (mmt) REVERT: A 340 TRP cc_start: 0.8961 (t60) cc_final: 0.8406 (t60) REVERT: B 100 GLU cc_start: 0.7989 (mp0) cc_final: 0.7762 (mp0) REVERT: B 111 ASN cc_start: 0.7890 (t0) cc_final: 0.7297 (t0) REVERT: B 190 MET cc_start: 0.8134 (tmm) cc_final: 0.7909 (tmm) REVERT: C 43 VAL cc_start: 0.9134 (m) cc_final: 0.8696 (p) REVERT: C 82 MET cc_start: 0.8744 (mmm) cc_final: 0.8138 (mmm) REVERT: C 119 MET cc_start: 0.8413 (ttm) cc_final: 0.8044 (ttm) REVERT: C 157 ASP cc_start: 0.8315 (t70) cc_final: 0.8078 (t70) REVERT: C 192 ILE cc_start: 0.8472 (pt) cc_final: 0.8060 (mm) REVERT: C 193 LEU cc_start: 0.8517 (mt) cc_final: 0.8054 (tt) REVERT: C 267 ILE cc_start: 0.9220 (pt) cc_final: 0.8932 (mm) REVERT: C 283 MET cc_start: 0.8393 (mmt) cc_final: 0.8119 (mmt) REVERT: C 305 MET cc_start: 0.8321 (mmm) cc_final: 0.7496 (tpp) REVERT: C 352 PHE cc_start: 0.8796 (t80) cc_final: 0.8531 (t80) REVERT: D 123 MET cc_start: 0.9138 (mmm) cc_final: 0.7661 (mmm) REVERT: D 227 MET cc_start: 0.8522 (mmm) cc_final: 0.8245 (tpp) REVERT: D 325 MET cc_start: 0.7264 (mmm) cc_final: 0.6926 (mmm) REVERT: D 355 MET cc_start: 0.8177 (mmm) cc_final: 0.7758 (mtt) REVERT: E 128 LYS cc_start: 0.5271 (tppt) cc_final: 0.4853 (tppt) REVERT: E 253 ILE cc_start: 0.7358 (tp) cc_final: 0.6926 (tp) REVERT: E 254 ASP cc_start: 0.7431 (m-30) cc_final: 0.6666 (t0) REVERT: E 270 ILE cc_start: 0.7940 (mm) cc_final: 0.7652 (mm) REVERT: E 281 MET cc_start: 0.4902 (tmm) cc_final: 0.4360 (tmm) REVERT: F 253 ILE cc_start: 0.7310 (mm) cc_final: 0.6820 (mm) REVERT: G 8 MET cc_start: 0.7152 (tmm) cc_final: 0.6930 (tmm) REVERT: I 94 MET cc_start: 0.6538 (ppp) cc_final: 0.6257 (ppp) REVERT: J 38 TYR cc_start: 0.6236 (m-80) cc_final: 0.5993 (m-80) REVERT: J 112 TRP cc_start: 0.8371 (m100) cc_final: 0.7874 (m100) REVERT: J 277 LEU cc_start: 0.8129 (mt) cc_final: 0.7900 (mp) REVERT: J 281 ARG cc_start: 0.7740 (mtp85) cc_final: 0.6945 (ptp-170) REVERT: J 310 TYR cc_start: 0.7843 (m-80) cc_final: 0.7569 (m-80) REVERT: J 345 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6292 (mt-10) REVERT: J 349 MET cc_start: 0.8228 (mmm) cc_final: 0.6246 (mmt) REVERT: J 361 ASN cc_start: 0.7411 (t0) cc_final: 0.6545 (t0) REVERT: J 380 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5759 (mm-30) REVERT: J 434 LYS cc_start: 0.8117 (mmpt) cc_final: 0.7912 (mmpt) REVERT: J 435 MET cc_start: 0.8623 (ttp) cc_final: 0.7538 (ttp) REVERT: J 479 ASN cc_start: 0.8919 (m110) cc_final: 0.8669 (m110) REVERT: J 483 GLU cc_start: 0.9050 (tp30) cc_final: 0.8124 (tp30) REVERT: J 516 ASP cc_start: 0.9055 (m-30) cc_final: 0.8784 (m-30) REVERT: J 517 LEU cc_start: 0.9232 (mt) cc_final: 0.8623 (mt) REVERT: K 38 TYR cc_start: 0.7808 (m-80) cc_final: 0.7437 (m-80) REVERT: K 45 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7776 (mm-30) REVERT: K 90 MET cc_start: 0.7965 (mpp) cc_final: 0.7678 (mpp) REVERT: K 112 TRP cc_start: 0.8141 (m100) cc_final: 0.7568 (m100) REVERT: K 113 MET cc_start: 0.8061 (mmm) cc_final: 0.7812 (mmm) REVERT: K 194 TYR cc_start: 0.7952 (t80) cc_final: 0.7219 (t80) REVERT: K 303 ILE cc_start: 0.7828 (pt) cc_final: 0.7618 (mp) REVERT: K 337 ASP cc_start: 0.8004 (m-30) cc_final: 0.7599 (m-30) REVERT: K 379 GLU cc_start: 0.7850 (pm20) cc_final: 0.7528 (pm20) REVERT: K 420 VAL cc_start: 0.8769 (t) cc_final: 0.8546 (t) REVERT: K 434 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8111 (tptp) REVERT: K 481 THR cc_start: 0.9296 (p) cc_final: 0.9062 (p) REVERT: K 533 ILE cc_start: 0.8630 (pt) cc_final: 0.8427 (pt) REVERT: K 615 LYS cc_start: 0.8953 (tptp) cc_final: 0.8730 (tppt) REVERT: K 722 TYR cc_start: 0.7668 (m-80) cc_final: 0.7248 (m-80) REVERT: L 50 GLU cc_start: 0.7337 (pt0) cc_final: 0.7021 (pp20) REVERT: L 60 MET cc_start: 0.5488 (ppp) cc_final: 0.4967 (ppp) REVERT: L 166 THR cc_start: 0.6552 (m) cc_final: 0.6307 (p) REVERT: M 144 GLU cc_start: 0.6203 (tp30) cc_final: 0.5597 (tm-30) REVERT: N 137 MET cc_start: 0.4972 (mmt) cc_final: 0.4112 (mmt) REVERT: O 99 ARG cc_start: 0.6889 (mmm160) cc_final: 0.6570 (mmm160) REVERT: O 100 GLN cc_start: 0.7155 (mp10) cc_final: 0.6878 (mm110) REVERT: O 109 ASP cc_start: 0.6863 (m-30) cc_final: 0.5913 (m-30) REVERT: P 212 ARG cc_start: 0.8876 (mmm160) cc_final: 0.8344 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 654 average time/residue: 0.1884 time to fit residues: 200.6902 Evaluate side-chains 485 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 484 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 87 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 267 optimal weight: 0.7980 chunk 250 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 137 GLN D 49 GLN D 87 HIS D 137 GLN F 216 GLN F 279 ASN G 9 GLN J 104 ASN ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS J 416 ASN J 760 HIS K 65 HIS ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 GLN K 661 ASN K 789 GLN O 131 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.100359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091649 restraints weight = 116248.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092641 restraints weight = 80387.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093086 restraints weight = 58834.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093243 restraints weight = 48493.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093332 restraints weight = 45052.853| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 34566 Z= 0.250 Angle : 0.736 10.887 46549 Z= 0.376 Chirality : 0.046 0.328 5085 Planarity : 0.005 0.045 6051 Dihedral : 5.866 51.646 4645 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.73 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4205 helix: 0.67 (0.11), residues: 2148 sheet: -0.78 (0.26), residues: 423 loop : -1.14 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 335 TYR 0.028 0.002 TYR J 722 PHE 0.040 0.002 PHE P 251 TRP 0.014 0.002 TRP D 79 HIS 0.013 0.002 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (34566) covalent geometry : angle 0.73552 / 0.38 (46549) hydrogen bonds : bond 0.05066 / 3.38 ( 1602) hydrogen bonds : angle 4.55248 / 3.19 ( 4437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 1.381 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: A 123 MET cc_start: 0.8319 (mmm) cc_final: 0.7877 (mmm) REVERT: A 132 MET cc_start: 0.9442 (ppp) cc_final: 0.9088 (ppp) REVERT: A 143 TYR cc_start: 0.8248 (t80) cc_final: 0.7973 (t80) REVERT: A 175 ILE cc_start: 0.8944 (mt) cc_final: 0.8588 (mt) REVERT: A 283 MET cc_start: 0.7596 (mmt) cc_final: 0.7140 (mmt) REVERT: B 111 ASN cc_start: 0.8512 (t0) cc_final: 0.8195 (t0) REVERT: B 190 MET cc_start: 0.8544 (tmm) cc_final: 0.8206 (tmm) REVERT: B 205 GLU cc_start: 0.7972 (pt0) cc_final: 0.7649 (pt0) REVERT: B 278 THR cc_start: 0.8460 (m) cc_final: 0.8234 (m) REVERT: B 325 MET cc_start: 0.8018 (mmm) cc_final: 0.7581 (mmt) REVERT: B 352 PHE cc_start: 0.8706 (t80) cc_final: 0.8452 (t80) REVERT: C 44 MET cc_start: 0.8378 (mtp) cc_final: 0.8045 (mtp) REVERT: C 111 ASN cc_start: 0.8530 (m-40) cc_final: 0.8158 (m110) REVERT: C 119 MET cc_start: 0.8463 (ttm) cc_final: 0.8164 (ttm) REVERT: C 130 PRO cc_start: 0.8653 (Cg_endo) cc_final: 0.8220 (Cg_exo) REVERT: C 137 GLN cc_start: 0.8335 (mt0) cc_final: 0.7767 (mt0) REVERT: C 267 ILE cc_start: 0.9137 (pt) cc_final: 0.8839 (mm) REVERT: C 274 ILE cc_start: 0.8952 (pt) cc_final: 0.8714 (pt) REVERT: C 305 MET cc_start: 0.8276 (mmm) cc_final: 0.7553 (tpp) REVERT: C 360 GLN cc_start: 0.7415 (pm20) cc_final: 0.6966 (pm20) REVERT: D 123 MET cc_start: 0.9087 (mmm) cc_final: 0.7727 (mmm) REVERT: D 227 MET cc_start: 0.8356 (mmm) cc_final: 0.7993 (tpp) REVERT: D 335 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7154 (ttp-110) REVERT: D 355 MET cc_start: 0.8106 (mmm) cc_final: 0.7662 (mtt) REVERT: E 253 ILE cc_start: 0.7570 (tp) cc_final: 0.7179 (tp) REVERT: E 254 ASP cc_start: 0.7584 (m-30) cc_final: 0.6683 (t0) REVERT: F 253 ILE cc_start: 0.7221 (mm) cc_final: 0.6742 (mm) REVERT: H 10 MET cc_start: 0.5809 (tmm) cc_final: 0.5474 (tmm) REVERT: I 94 MET cc_start: 0.6614 (ppp) cc_final: 0.6348 (ppp) REVERT: J 112 TRP cc_start: 0.8415 (m100) cc_final: 0.7836 (m100) REVERT: J 113 MET cc_start: 0.7244 (mtt) cc_final: 0.6269 (mmm) REVERT: J 281 ARG cc_start: 0.7564 (mtp85) cc_final: 0.6825 (ptm160) REVERT: J 310 TYR cc_start: 0.7995 (m-80) cc_final: 0.7777 (m-80) REVERT: J 349 MET cc_start: 0.8373 (mmm) cc_final: 0.7969 (mmm) REVERT: J 361 ASN cc_start: 0.7383 (t0) cc_final: 0.6073 (t0) REVERT: J 380 GLU cc_start: 0.6608 (mm-30) cc_final: 0.5777 (mm-30) REVERT: J 434 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7650 (mmmm) REVERT: J 479 ASN cc_start: 0.8945 (m110) cc_final: 0.8656 (m-40) REVERT: J 483 GLU cc_start: 0.8917 (tp30) cc_final: 0.8651 (tp30) REVERT: J 536 GLU cc_start: 0.8666 (tp30) cc_final: 0.8136 (mm-30) REVERT: J 659 MET cc_start: 0.8376 (tpt) cc_final: 0.6632 (tpp) REVERT: J 663 ARG cc_start: 0.8532 (mtt90) cc_final: 0.7967 (mmt180) REVERT: J 690 MET cc_start: 0.7232 (mmm) cc_final: 0.6938 (tpt) REVERT: K 38 TYR cc_start: 0.7948 (m-80) cc_final: 0.7578 (m-80) REVERT: K 194 TYR cc_start: 0.7992 (t80) cc_final: 0.7114 (t80) REVERT: K 303 ILE cc_start: 0.8104 (pt) cc_final: 0.7714 (mp) REVERT: K 337 ASP cc_start: 0.7965 (m-30) cc_final: 0.7613 (m-30) REVERT: K 531 MET cc_start: 0.8914 (mmt) cc_final: 0.8155 (mmm) REVERT: K 722 TYR cc_start: 0.7839 (m-80) cc_final: 0.7437 (m-80) REVERT: L 50 GLU cc_start: 0.7434 (pt0) cc_final: 0.7001 (pp20) REVERT: L 60 MET cc_start: 0.5542 (ppp) cc_final: 0.5160 (ppp) REVERT: M 144 GLU cc_start: 0.6282 (tp30) cc_final: 0.5908 (tp30) REVERT: N 85 MET cc_start: 0.6031 (mtp) cc_final: 0.5292 (ttm) REVERT: N 137 MET cc_start: 0.5201 (mmt) cc_final: 0.4351 (mmt) REVERT: O 75 ARG cc_start: 0.7663 (mmp80) cc_final: 0.7457 (mmp-170) REVERT: O 100 GLN cc_start: 0.6996 (mp10) cc_final: 0.6732 (mm110) REVERT: O 109 ASP cc_start: 0.7252 (m-30) cc_final: 0.6692 (m-30) REVERT: P 212 ARG cc_start: 0.8987 (mmm160) cc_final: 0.8587 (mmm160) outliers start: 0 outliers final: 0 residues processed: 593 average time/residue: 0.1869 time to fit residues: 182.5604 Evaluate side-chains 445 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 187 optimal weight: 2.9990 chunk 311 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 232 optimal weight: 0.0040 chunk 268 optimal weight: 0.8980 chunk 293 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS F 263 GLN J 595 GLN ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN K 475 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095871 restraints weight = 114427.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096865 restraints weight = 77101.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.097044 restraints weight = 54053.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097484 restraints weight = 49214.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097494 restraints weight = 42161.895| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34566 Z= 0.131 Angle : 0.600 9.177 46549 Z= 0.310 Chirality : 0.042 0.238 5085 Planarity : 0.004 0.077 6051 Dihedral : 5.528 52.262 4645 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4205 helix: 0.96 (0.11), residues: 2145 sheet: -0.76 (0.26), residues: 418 loop : -1.04 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 155 TYR 0.021 0.001 TYR J 134 PHE 0.023 0.002 PHE K 669 TRP 0.012 0.001 TRP J 508 HIS 0.017 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (34566) covalent geometry : angle 0.59986 / 0.31 (46549) hydrogen bonds : bond 0.04545 / 3.04 ( 1602) hydrogen bonds : angle 4.17534 / 2.93 ( 4437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 640 time to evaluate : 1.058 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: A 123 MET cc_start: 0.8262 (mmm) cc_final: 0.7692 (tpp) REVERT: A 132 MET cc_start: 0.9477 (ppp) cc_final: 0.9036 (ppp) REVERT: A 143 TYR cc_start: 0.8138 (t80) cc_final: 0.7679 (t80) REVERT: A 283 MET cc_start: 0.7434 (mmt) cc_final: 0.6969 (mmt) REVERT: B 111 ASN cc_start: 0.8570 (t0) cc_final: 0.8154 (t0) REVERT: B 176 MET cc_start: 0.8270 (mmm) cc_final: 0.7265 (mmt) REVERT: B 190 MET cc_start: 0.8500 (tmm) cc_final: 0.8113 (tmm) REVERT: B 305 MET cc_start: 0.7955 (ttm) cc_final: 0.7655 (ttt) REVERT: B 325 MET cc_start: 0.7977 (mmm) cc_final: 0.7582 (mmt) REVERT: B 346 LEU cc_start: 0.9413 (tp) cc_final: 0.9122 (tt) REVERT: B 352 PHE cc_start: 0.8680 (t80) cc_final: 0.8398 (t80) REVERT: C 44 MET cc_start: 0.8352 (mtp) cc_final: 0.8019 (mtp) REVERT: C 82 MET cc_start: 0.8955 (mmm) cc_final: 0.8579 (mmm) REVERT: C 119 MET cc_start: 0.8321 (ttm) cc_final: 0.8028 (ttm) REVERT: C 130 PRO cc_start: 0.8619 (Cg_endo) cc_final: 0.8180 (Cg_exo) REVERT: C 267 ILE cc_start: 0.9112 (pt) cc_final: 0.8879 (mm) REVERT: C 305 MET cc_start: 0.8178 (mmm) cc_final: 0.7730 (mmm) REVERT: C 330 ILE cc_start: 0.8605 (mp) cc_final: 0.8308 (mm) REVERT: C 360 GLN cc_start: 0.7242 (pm20) cc_final: 0.6908 (pm20) REVERT: D 123 MET cc_start: 0.9064 (mmm) cc_final: 0.8110 (mmm) REVERT: D 227 MET cc_start: 0.8488 (mmm) cc_final: 0.8062 (tpp) REVERT: D 355 MET cc_start: 0.8013 (mmm) cc_final: 0.7640 (mtt) REVERT: E 194 GLU cc_start: 0.7692 (tt0) cc_final: 0.7399 (tt0) REVERT: E 253 ILE cc_start: 0.7420 (tp) cc_final: 0.7071 (tp) REVERT: E 254 ASP cc_start: 0.7722 (m-30) cc_final: 0.6826 (t70) REVERT: E 270 ILE cc_start: 0.7744 (mm) cc_final: 0.7439 (mm) REVERT: F 253 ILE cc_start: 0.7200 (mm) cc_final: 0.6660 (mm) REVERT: I 94 MET cc_start: 0.6467 (ppp) cc_final: 0.6263 (ppp) REVERT: J 112 TRP cc_start: 0.8350 (m100) cc_final: 0.7774 (m100) REVERT: J 113 MET cc_start: 0.7062 (mtt) cc_final: 0.6411 (mmm) REVERT: J 281 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7239 (ptm160) REVERT: J 361 ASN cc_start: 0.7382 (t0) cc_final: 0.6704 (t0) REVERT: J 380 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5916 (mm-30) REVERT: J 434 LYS cc_start: 0.8116 (mmpt) cc_final: 0.7692 (mmmm) REVERT: J 479 ASN cc_start: 0.8872 (m110) cc_final: 0.8580 (m-40) REVERT: J 483 GLU cc_start: 0.8968 (tp30) cc_final: 0.8030 (tp30) REVERT: J 517 LEU cc_start: 0.9226 (mt) cc_final: 0.8715 (mt) REVERT: J 536 GLU cc_start: 0.8694 (tp30) cc_final: 0.8271 (mm-30) REVERT: J 690 MET cc_start: 0.7293 (mmm) cc_final: 0.6866 (tpt) REVERT: K 38 TYR cc_start: 0.7776 (m-80) cc_final: 0.7449 (m-80) REVERT: K 90 MET cc_start: 0.8127 (mpp) cc_final: 0.7818 (mpp) REVERT: K 112 TRP cc_start: 0.8290 (m100) cc_final: 0.7676 (m100) REVERT: K 113 MET cc_start: 0.8269 (mmm) cc_final: 0.7968 (mmm) REVERT: K 194 TYR cc_start: 0.7917 (t80) cc_final: 0.7149 (t80) REVERT: K 303 ILE cc_start: 0.8057 (pt) cc_final: 0.7704 (mp) REVERT: K 337 ASP cc_start: 0.7952 (m-30) cc_final: 0.7531 (m-30) REVERT: K 432 TYR cc_start: 0.8802 (t80) cc_final: 0.8460 (t80) REVERT: K 481 THR cc_start: 0.9405 (p) cc_final: 0.9156 (p) REVERT: K 531 MET cc_start: 0.8894 (mmt) cc_final: 0.8189 (mmm) REVERT: K 567 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7450 (tpp-160) REVERT: K 722 TYR cc_start: 0.7793 (m-80) cc_final: 0.7377 (m-80) REVERT: L 50 GLU cc_start: 0.7306 (pt0) cc_final: 0.6883 (pp20) REVERT: L 60 MET cc_start: 0.5708 (ppp) cc_final: 0.5140 (ppp) REVERT: L 166 THR cc_start: 0.6073 (m) cc_final: 0.5842 (m) REVERT: M 144 GLU cc_start: 0.6291 (tp30) cc_final: 0.5954 (tp30) REVERT: N 137 MET cc_start: 0.5318 (mmt) cc_final: 0.4525 (mmt) REVERT: N 157 MET cc_start: 0.5365 (mmm) cc_final: 0.5110 (mmm) REVERT: O 100 GLN cc_start: 0.7152 (mp10) cc_final: 0.6924 (mm110) REVERT: P 211 GLU cc_start: 0.6058 (mm-30) cc_final: 0.5744 (mp0) REVERT: P 212 ARG cc_start: 0.8976 (mmm160) cc_final: 0.8603 (mmm160) outliers start: 2 outliers final: 1 residues processed: 642 average time/residue: 0.1887 time to fit residues: 197.9382 Evaluate side-chains 471 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 204 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 327 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 298 optimal weight: 3.9990 chunk 345 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS G 9 GLN I 90 HIS J 595 GLN ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 GLN K 562 ASN O 102 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.095846 restraints weight = 113303.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096559 restraints weight = 78999.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097051 restraints weight = 61204.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097304 restraints weight = 51590.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097436 restraints weight = 44844.688| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34566 Z= 0.134 Angle : 0.601 8.928 46549 Z= 0.308 Chirality : 0.042 0.292 5085 Planarity : 0.004 0.064 6051 Dihedral : 5.399 52.394 4645 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.76 % Favored : 95.17 % Rotamer: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4205 helix: 1.03 (0.11), residues: 2150 sheet: -0.68 (0.27), residues: 406 loop : -1.01 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 99 TYR 0.037 0.002 TYR K 422 PHE 0.034 0.002 PHE K 669 TRP 0.010 0.001 TRP D 79 HIS 0.011 0.001 HIS I 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (34566) covalent geometry : angle 0.60108 / 0.31 (46549) hydrogen bonds : bond 0.04432 / 2.96 ( 1602) hydrogen bonds : angle 4.13239 / 2.90 ( 4437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 611 time to evaluate : 1.333 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: A 123 MET cc_start: 0.8257 (mmm) cc_final: 0.7691 (tpp) REVERT: A 132 MET cc_start: 0.9394 (ppp) cc_final: 0.9026 (ppp) REVERT: A 143 TYR cc_start: 0.8199 (t80) cc_final: 0.7683 (t80) REVERT: A 283 MET cc_start: 0.7329 (mmt) cc_final: 0.6912 (mmt) REVERT: A 305 MET cc_start: 0.7866 (mmt) cc_final: 0.7661 (mmt) REVERT: B 157 ASP cc_start: 0.8534 (t70) cc_final: 0.7622 (t0) REVERT: B 176 MET cc_start: 0.8292 (mmm) cc_final: 0.7295 (mmt) REVERT: B 190 MET cc_start: 0.8517 (tmm) cc_final: 0.8026 (tmm) REVERT: B 305 MET cc_start: 0.7784 (ttm) cc_final: 0.7512 (ttt) REVERT: B 325 MET cc_start: 0.7910 (mmm) cc_final: 0.7525 (mmt) REVERT: B 346 LEU cc_start: 0.9408 (tp) cc_final: 0.9129 (tt) REVERT: B 352 PHE cc_start: 0.8728 (t80) cc_final: 0.8406 (t80) REVERT: C 44 MET cc_start: 0.8326 (mtp) cc_final: 0.8012 (mtp) REVERT: C 119 MET cc_start: 0.8351 (ttm) cc_final: 0.8059 (ttm) REVERT: C 130 PRO cc_start: 0.8634 (Cg_endo) cc_final: 0.8173 (Cg_exo) REVERT: C 267 ILE cc_start: 0.9130 (pt) cc_final: 0.8885 (mm) REVERT: C 283 MET cc_start: 0.8438 (mmt) cc_final: 0.8039 (mmt) REVERT: C 305 MET cc_start: 0.8218 (mmm) cc_final: 0.7215 (tpt) REVERT: C 330 ILE cc_start: 0.8569 (mp) cc_final: 0.8272 (mm) REVERT: C 360 GLN cc_start: 0.7206 (pm20) cc_final: 0.6854 (pm20) REVERT: D 123 MET cc_start: 0.9151 (mmm) cc_final: 0.7953 (mmm) REVERT: D 185 LEU cc_start: 0.7891 (tp) cc_final: 0.7686 (tp) REVERT: D 227 MET cc_start: 0.8426 (mmm) cc_final: 0.8052 (tpp) REVERT: D 355 MET cc_start: 0.8064 (mmm) cc_final: 0.7823 (mtt) REVERT: E 253 ILE cc_start: 0.7461 (tp) cc_final: 0.7140 (tp) REVERT: E 254 ASP cc_start: 0.7746 (m-30) cc_final: 0.6830 (t70) REVERT: E 270 ILE cc_start: 0.7565 (mm) cc_final: 0.7303 (mm) REVERT: E 281 MET cc_start: 0.4879 (tmm) cc_final: 0.4411 (tmt) REVERT: F 253 ILE cc_start: 0.7153 (mm) cc_final: 0.6614 (mm) REVERT: J 112 TRP cc_start: 0.8296 (m100) cc_final: 0.7802 (m100) REVERT: J 281 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7260 (ptm160) REVERT: J 349 MET cc_start: 0.8296 (mmm) cc_final: 0.8072 (tpp) REVERT: J 380 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6179 (mm-30) REVERT: J 427 LEU cc_start: 0.9056 (mt) cc_final: 0.8518 (tt) REVERT: J 434 LYS cc_start: 0.8459 (mmpt) cc_final: 0.8008 (mmmm) REVERT: J 435 MET cc_start: 0.8479 (ttm) cc_final: 0.8215 (ttm) REVERT: J 479 ASN cc_start: 0.8899 (m110) cc_final: 0.8612 (m-40) REVERT: J 483 GLU cc_start: 0.8889 (tp30) cc_final: 0.8022 (tp30) REVERT: J 517 LEU cc_start: 0.9198 (mt) cc_final: 0.8700 (mt) REVERT: J 536 GLU cc_start: 0.8673 (tp30) cc_final: 0.8245 (mm-30) REVERT: J 567 ARG cc_start: 0.7508 (mmp80) cc_final: 0.7228 (mmp80) REVERT: J 690 MET cc_start: 0.7043 (mmm) cc_final: 0.6346 (tpt) REVERT: J 799 MET cc_start: 0.6421 (mtp) cc_final: 0.6118 (ttt) REVERT: K 38 TYR cc_start: 0.7798 (m-80) cc_final: 0.7468 (m-80) REVERT: K 112 TRP cc_start: 0.8278 (m100) cc_final: 0.7672 (m100) REVERT: K 113 MET cc_start: 0.8246 (mmm) cc_final: 0.7930 (mmm) REVERT: K 194 TYR cc_start: 0.7934 (t80) cc_final: 0.7144 (t80) REVERT: K 198 ILE cc_start: 0.8970 (pt) cc_final: 0.8746 (pt) REVERT: K 297 LEU cc_start: 0.8203 (mt) cc_final: 0.7587 (mt) REVERT: K 303 ILE cc_start: 0.7941 (pt) cc_final: 0.7664 (mp) REVERT: K 337 ASP cc_start: 0.7910 (m-30) cc_final: 0.7482 (m-30) REVERT: K 344 GLU cc_start: 0.7572 (mp0) cc_final: 0.7240 (mp0) REVERT: K 432 TYR cc_start: 0.8874 (t80) cc_final: 0.8574 (t80) REVERT: K 481 THR cc_start: 0.9443 (p) cc_final: 0.9189 (p) REVERT: K 531 MET cc_start: 0.9053 (mmt) cc_final: 0.8410 (mmm) REVERT: K 567 ARG cc_start: 0.7761 (tpp-160) cc_final: 0.7424 (tpp-160) REVERT: K 722 TYR cc_start: 0.7763 (m-80) cc_final: 0.7413 (m-80) REVERT: L 50 GLU cc_start: 0.7299 (pt0) cc_final: 0.6912 (pp20) REVERT: L 60 MET cc_start: 0.5741 (ppp) cc_final: 0.5307 (ppp) REVERT: L 166 THR cc_start: 0.6386 (m) cc_final: 0.5883 (m) REVERT: M 144 GLU cc_start: 0.6326 (tp30) cc_final: 0.5931 (tp30) REVERT: N 55 GLU cc_start: 0.7182 (tt0) cc_final: 0.6534 (mm-30) REVERT: N 137 MET cc_start: 0.5378 (mmt) cc_final: 0.4430 (mmt) REVERT: N 157 MET cc_start: 0.5694 (mmm) cc_final: 0.5381 (mmm) REVERT: O 99 ARG cc_start: 0.7071 (mmm160) cc_final: 0.6866 (mmm160) REVERT: P 212 ARG cc_start: 0.8977 (mmm160) cc_final: 0.8604 (mmm160) outliers start: 1 outliers final: 0 residues processed: 612 average time/residue: 0.1841 time to fit residues: 184.4427 Evaluate side-chains 460 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 301 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 165 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 412 optimal weight: 0.9990 chunk 231 optimal weight: 1.9990 chunk 361 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS J 153 HIS ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 GLN O 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.094256 restraints weight = 115330.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094882 restraints weight = 84856.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.095582 restraints weight = 63317.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095921 restraints weight = 47873.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095970 restraints weight = 42806.659| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34566 Z= 0.173 Angle : 0.638 10.629 46549 Z= 0.328 Chirality : 0.044 0.281 5085 Planarity : 0.004 0.049 6051 Dihedral : 5.470 56.004 4645 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 0.03 % Allowed : 1.56 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.13), residues: 4205 helix: 0.97 (0.11), residues: 2132 sheet: -0.63 (0.26), residues: 448 loop : -1.06 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 23 TYR 0.018 0.002 TYR C 337 PHE 0.031 0.002 PHE J 312 TRP 0.052 0.002 TRP K 508 HIS 0.008 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (34566) covalent geometry : angle 0.63752 / 0.33 (46549) hydrogen bonds : bond 0.04598 / 3.07 ( 1602) hydrogen bonds : angle 4.24812 / 2.99 ( 4437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 587 time to evaluate : 1.135 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: A 123 MET cc_start: 0.8224 (mmm) cc_final: 0.7612 (tpp) REVERT: A 132 MET cc_start: 0.9380 (ppp) cc_final: 0.9038 (ppp) REVERT: A 246 GLN cc_start: 0.4972 (pt0) cc_final: 0.4757 (pt0) REVERT: A 283 MET cc_start: 0.7419 (mmt) cc_final: 0.6884 (mmt) REVERT: B 190 MET cc_start: 0.8601 (tmm) cc_final: 0.8205 (tmm) REVERT: B 305 MET cc_start: 0.7849 (ttm) cc_final: 0.7597 (ttt) REVERT: B 325 MET cc_start: 0.7846 (mmm) cc_final: 0.7473 (mmt) REVERT: B 352 PHE cc_start: 0.8778 (t80) cc_final: 0.8567 (t80) REVERT: C 44 MET cc_start: 0.8485 (mtp) cc_final: 0.8221 (mtp) REVERT: C 119 MET cc_start: 0.8377 (ttm) cc_final: 0.8030 (ttm) REVERT: C 130 PRO cc_start: 0.8706 (Cg_endo) cc_final: 0.8327 (Cg_exo) REVERT: C 267 ILE cc_start: 0.9165 (pt) cc_final: 0.8842 (mm) REVERT: C 305 MET cc_start: 0.8173 (mmm) cc_final: 0.7250 (tpt) REVERT: C 330 ILE cc_start: 0.8559 (mp) cc_final: 0.8236 (mm) REVERT: C 360 GLN cc_start: 0.7426 (pm20) cc_final: 0.6967 (pm20) REVERT: D 123 MET cc_start: 0.9001 (mmm) cc_final: 0.7910 (mmm) REVERT: D 227 MET cc_start: 0.8481 (mmm) cc_final: 0.8177 (tpp) REVERT: D 355 MET cc_start: 0.8020 (mmm) cc_final: 0.7699 (mtt) REVERT: E 254 ASP cc_start: 0.7701 (m-30) cc_final: 0.6814 (t0) REVERT: E 281 MET cc_start: 0.4734 (tmm) cc_final: 0.4486 (tmt) REVERT: F 253 ILE cc_start: 0.7142 (mm) cc_final: 0.6662 (mm) REVERT: I 94 MET cc_start: 0.6463 (ppp) cc_final: 0.6256 (ppp) REVERT: J 112 TRP cc_start: 0.8277 (m100) cc_final: 0.7728 (m100) REVERT: J 281 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7064 (ptm160) REVERT: J 349 MET cc_start: 0.8296 (mmm) cc_final: 0.8009 (tpp) REVERT: J 361 ASN cc_start: 0.6921 (t0) cc_final: 0.5796 (t0) REVERT: J 380 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6181 (mm-30) REVERT: J 427 LEU cc_start: 0.9057 (mt) cc_final: 0.8559 (tt) REVERT: J 434 LYS cc_start: 0.8430 (mmpt) cc_final: 0.8020 (mmmm) REVERT: J 479 ASN cc_start: 0.8816 (m110) cc_final: 0.8567 (m-40) REVERT: J 483 GLU cc_start: 0.8921 (tp30) cc_final: 0.8031 (tp30) REVERT: J 517 LEU cc_start: 0.9174 (mt) cc_final: 0.8647 (mt) REVERT: J 536 GLU cc_start: 0.8679 (tp30) cc_final: 0.8263 (mm-30) REVERT: J 567 ARG cc_start: 0.7465 (mmp80) cc_final: 0.7220 (mmp80) REVERT: J 690 MET cc_start: 0.7182 (mmm) cc_final: 0.6432 (tpt) REVERT: J 799 MET cc_start: 0.6415 (mtp) cc_final: 0.6107 (ttt) REVERT: K 38 TYR cc_start: 0.7781 (m-80) cc_final: 0.7445 (m-80) REVERT: K 90 MET cc_start: 0.8231 (mpp) cc_final: 0.7890 (mpp) REVERT: K 112 TRP cc_start: 0.8281 (m100) cc_final: 0.7596 (m100) REVERT: K 113 MET cc_start: 0.8291 (mmm) cc_final: 0.8035 (mmm) REVERT: K 194 TYR cc_start: 0.8040 (t80) cc_final: 0.7179 (t80) REVERT: K 198 ILE cc_start: 0.8966 (pt) cc_final: 0.8742 (pt) REVERT: K 303 ILE cc_start: 0.7992 (pt) cc_final: 0.7773 (mp) REVERT: K 337 ASP cc_start: 0.7880 (m-30) cc_final: 0.7483 (m-30) REVERT: K 344 GLU cc_start: 0.7715 (mp0) cc_final: 0.7382 (mp0) REVERT: K 421 MET cc_start: 0.7871 (mmm) cc_final: 0.7255 (mmp) REVERT: K 432 TYR cc_start: 0.8890 (t80) cc_final: 0.8656 (t80) REVERT: K 435 MET cc_start: 0.8334 (ptm) cc_final: 0.8106 (ptp) REVERT: K 481 THR cc_start: 0.9448 (p) cc_final: 0.9227 (p) REVERT: K 531 MET cc_start: 0.9216 (mmt) cc_final: 0.8508 (mmm) REVERT: K 563 PHE cc_start: 0.7737 (t80) cc_final: 0.7499 (t80) REVERT: K 567 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7428 (tpp-160) REVERT: K 585 THR cc_start: 0.8660 (m) cc_final: 0.7512 (m) REVERT: K 722 TYR cc_start: 0.7882 (m-80) cc_final: 0.7494 (m-80) REVERT: L 50 GLU cc_start: 0.7488 (pt0) cc_final: 0.7034 (pp20) REVERT: L 60 MET cc_start: 0.5800 (ppp) cc_final: 0.5333 (ppp) REVERT: M 97 LEU cc_start: 0.5088 (tp) cc_final: 0.4839 (mt) REVERT: M 144 GLU cc_start: 0.6281 (tp30) cc_final: 0.5794 (tp30) REVERT: N 55 GLU cc_start: 0.7157 (tt0) cc_final: 0.6498 (mm-30) REVERT: N 85 MET cc_start: 0.6065 (mtp) cc_final: 0.5157 (ttm) REVERT: N 137 MET cc_start: 0.5356 (mmt) cc_final: 0.4544 (mmt) REVERT: N 157 MET cc_start: 0.6429 (mmm) cc_final: 0.6115 (mmp) REVERT: O 99 ARG cc_start: 0.6906 (mmm160) cc_final: 0.6128 (tpm170) REVERT: P 212 ARG cc_start: 0.9020 (mmm160) cc_final: 0.8583 (mmm160) outliers start: 1 outliers final: 0 residues processed: 588 average time/residue: 0.1910 time to fit residues: 184.0297 Evaluate side-chains 441 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 0.9980 chunk 341 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 137 optimal weight: 0.0770 chunk 127 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 334 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 403 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS J 358 HIS ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 GLN ** K 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095860 restraints weight = 113520.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096547 restraints weight = 83412.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096876 restraints weight = 64844.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097342 restraints weight = 53253.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.097690 restraints weight = 42812.840| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34566 Z= 0.132 Angle : 0.604 8.330 46549 Z= 0.309 Chirality : 0.042 0.242 5085 Planarity : 0.004 0.042 6051 Dihedral : 5.318 55.407 4645 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.90 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 4205 helix: 1.08 (0.11), residues: 2127 sheet: -0.63 (0.27), residues: 402 loop : -1.02 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 23 TYR 0.032 0.001 TYR K 422 PHE 0.029 0.002 PHE J 312 TRP 0.026 0.001 TRP K 508 HIS 0.007 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (34566) covalent geometry : angle 0.60379 / 0.31 (46549) hydrogen bonds : bond 0.04402 / 2.95 ( 1602) hydrogen bonds : angle 4.09911 / 2.88 ( 4437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 0.900 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 123 MET cc_start: 0.8236 (mmm) cc_final: 0.7647 (tpp) REVERT: A 132 MET cc_start: 0.9357 (ppp) cc_final: 0.8978 (ppp) REVERT: A 283 MET cc_start: 0.7279 (mmt) cc_final: 0.6863 (mmt) REVERT: A 355 MET cc_start: 0.8227 (tpp) cc_final: 0.7979 (mmt) REVERT: B 176 MET cc_start: 0.8263 (mmm) cc_final: 0.7259 (mmt) REVERT: B 190 MET cc_start: 0.8583 (tmm) cc_final: 0.8208 (tmm) REVERT: B 325 MET cc_start: 0.7770 (mmm) cc_final: 0.7431 (mmt) REVERT: B 346 LEU cc_start: 0.9374 (tp) cc_final: 0.9106 (tt) REVERT: B 352 PHE cc_start: 0.8756 (t80) cc_final: 0.8479 (t80) REVERT: C 8 LEU cc_start: 0.8611 (mt) cc_final: 0.8345 (tt) REVERT: C 44 MET cc_start: 0.8426 (mtp) cc_final: 0.8211 (mtp) REVERT: C 119 MET cc_start: 0.8282 (ttm) cc_final: 0.7965 (ttm) REVERT: C 130 PRO cc_start: 0.8718 (Cg_endo) cc_final: 0.8292 (Cg_exo) REVERT: C 267 ILE cc_start: 0.9159 (pt) cc_final: 0.8823 (mm) REVERT: C 305 MET cc_start: 0.8087 (mmm) cc_final: 0.7194 (tpt) REVERT: C 360 GLN cc_start: 0.7416 (pm20) cc_final: 0.6945 (pm20) REVERT: C 372 ARG cc_start: 0.7891 (ptp-110) cc_final: 0.7521 (ptp-170) REVERT: D 123 MET cc_start: 0.8982 (mmm) cc_final: 0.7701 (mmm) REVERT: D 227 MET cc_start: 0.8371 (mmm) cc_final: 0.8038 (tpp) REVERT: D 355 MET cc_start: 0.7949 (mmm) cc_final: 0.7683 (mtt) REVERT: E 253 ILE cc_start: 0.7505 (tp) cc_final: 0.7156 (tp) REVERT: E 254 ASP cc_start: 0.7804 (m-30) cc_final: 0.7126 (t0) REVERT: E 270 ILE cc_start: 0.7003 (mm) cc_final: 0.6774 (mm) REVERT: E 281 MET cc_start: 0.4771 (tmm) cc_final: 0.4408 (tmm) REVERT: F 253 ILE cc_start: 0.7107 (mm) cc_final: 0.6556 (mm) REVERT: J 112 TRP cc_start: 0.8216 (m100) cc_final: 0.7719 (m100) REVERT: J 281 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7087 (ptm160) REVERT: J 349 MET cc_start: 0.8423 (mmm) cc_final: 0.7312 (mmt) REVERT: J 361 ASN cc_start: 0.7163 (t0) cc_final: 0.5913 (t0) REVERT: J 380 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6127 (mm-30) REVERT: J 427 LEU cc_start: 0.9031 (mt) cc_final: 0.8546 (tt) REVERT: J 434 LYS cc_start: 0.8429 (mmpt) cc_final: 0.7983 (mmmm) REVERT: J 479 ASN cc_start: 0.8779 (m110) cc_final: 0.8505 (m-40) REVERT: J 483 GLU cc_start: 0.8945 (tp30) cc_final: 0.8585 (tp30) REVERT: J 567 ARG cc_start: 0.7465 (mmp80) cc_final: 0.7222 (mmp80) REVERT: J 690 MET cc_start: 0.7178 (mmm) cc_final: 0.6439 (tpt) REVERT: J 799 MET cc_start: 0.6393 (mtp) cc_final: 0.6079 (ttt) REVERT: K 38 TYR cc_start: 0.7728 (m-80) cc_final: 0.7413 (m-80) REVERT: K 90 MET cc_start: 0.7848 (mpp) cc_final: 0.7490 (mpp) REVERT: K 194 TYR cc_start: 0.7963 (t80) cc_final: 0.7106 (t80) REVERT: K 198 ILE cc_start: 0.8947 (pt) cc_final: 0.8712 (pt) REVERT: K 297 LEU cc_start: 0.7765 (mt) cc_final: 0.7561 (mt) REVERT: K 337 ASP cc_start: 0.7824 (m-30) cc_final: 0.7419 (m-30) REVERT: K 344 GLU cc_start: 0.7710 (mp0) cc_final: 0.7309 (mp0) REVERT: K 481 THR cc_start: 0.9461 (p) cc_final: 0.9171 (p) REVERT: K 483 GLU cc_start: 0.8669 (tt0) cc_final: 0.8395 (tt0) REVERT: K 567 ARG cc_start: 0.7733 (tpp-160) cc_final: 0.7407 (tpp-160) REVERT: K 585 THR cc_start: 0.8621 (m) cc_final: 0.7528 (m) REVERT: K 722 TYR cc_start: 0.7857 (m-80) cc_final: 0.7483 (m-80) REVERT: L 50 GLU cc_start: 0.7343 (pt0) cc_final: 0.6913 (pp20) REVERT: L 60 MET cc_start: 0.5795 (ppp) cc_final: 0.5334 (ppp) REVERT: M 97 LEU cc_start: 0.5022 (tp) cc_final: 0.4780 (mt) REVERT: M 144 GLU cc_start: 0.6326 (tp30) cc_final: 0.5889 (tp30) REVERT: N 55 GLU cc_start: 0.7016 (tt0) cc_final: 0.6532 (mm-30) REVERT: N 137 MET cc_start: 0.5300 (mmt) cc_final: 0.4523 (mmt) REVERT: O 99 ARG cc_start: 0.6944 (mmm160) cc_final: 0.6674 (mmm160) REVERT: P 212 ARG cc_start: 0.8986 (mmm160) cc_final: 0.8568 (mmm160) outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.1815 time to fit residues: 177.1603 Evaluate side-chains 455 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 340 optimal weight: 0.6980 chunk 365 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 371 optimal weight: 2.9990 chunk 212 optimal weight: 0.2980 chunk 315 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 416 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 309 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 GLN K 661 ASN K 789 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096685 restraints weight = 112673.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097582 restraints weight = 81803.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097906 restraints weight = 58053.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098421 restraints weight = 48982.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098332 restraints weight = 41976.804| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34566 Z= 0.135 Angle : 0.611 10.265 46549 Z= 0.311 Chirality : 0.043 0.240 5085 Planarity : 0.004 0.047 6051 Dihedral : 5.276 56.922 4645 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 4205 helix: 1.06 (0.11), residues: 2155 sheet: -0.51 (0.26), residues: 446 loop : -1.04 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 123 TYR 0.031 0.002 TYR F 261 PHE 0.049 0.002 PHE P 251 TRP 0.023 0.001 TRP K 508 HIS 0.009 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (34566) covalent geometry : angle 0.61114 / 0.31 (46549) hydrogen bonds : bond 0.04373 / 2.93 ( 1602) hydrogen bonds : angle 4.12030 / 2.91 ( 4437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 1.094 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: A 123 MET cc_start: 0.8285 (mmm) cc_final: 0.7665 (tpp) REVERT: A 132 MET cc_start: 0.9328 (ppp) cc_final: 0.8959 (ppp) REVERT: A 283 MET cc_start: 0.7087 (mmt) cc_final: 0.6597 (mmt) REVERT: A 355 MET cc_start: 0.8258 (tpp) cc_final: 0.7964 (mmt) REVERT: B 190 MET cc_start: 0.8585 (tmm) cc_final: 0.8215 (tmm) REVERT: B 325 MET cc_start: 0.7726 (mmm) cc_final: 0.7459 (mmt) REVERT: B 346 LEU cc_start: 0.9374 (tp) cc_final: 0.9049 (tt) REVERT: C 8 LEU cc_start: 0.8636 (mt) cc_final: 0.8318 (tt) REVERT: C 44 MET cc_start: 0.8721 (mtp) cc_final: 0.8332 (mtp) REVERT: C 119 MET cc_start: 0.8278 (ttm) cc_final: 0.7949 (ttm) REVERT: C 130 PRO cc_start: 0.8741 (Cg_endo) cc_final: 0.8336 (Cg_exo) REVERT: C 267 ILE cc_start: 0.9149 (pt) cc_final: 0.8817 (mm) REVERT: C 274 ILE cc_start: 0.8919 (pt) cc_final: 0.8718 (pt) REVERT: C 305 MET cc_start: 0.8154 (mmm) cc_final: 0.7258 (tpt) REVERT: C 360 GLN cc_start: 0.7441 (pm20) cc_final: 0.6951 (pm20) REVERT: C 372 ARG cc_start: 0.7786 (ptp-110) cc_final: 0.7462 (ptp-170) REVERT: D 123 MET cc_start: 0.9097 (mmm) cc_final: 0.7740 (mmm) REVERT: D 227 MET cc_start: 0.8343 (mmm) cc_final: 0.8075 (tpp) REVERT: D 283 MET cc_start: 0.4733 (mmm) cc_final: 0.4487 (mmt) REVERT: D 335 ARG cc_start: 0.7796 (ttm110) cc_final: 0.7432 (mtm110) REVERT: D 355 MET cc_start: 0.7855 (mmm) cc_final: 0.7629 (mtt) REVERT: E 254 ASP cc_start: 0.7765 (m-30) cc_final: 0.7133 (t0) REVERT: E 281 MET cc_start: 0.4793 (tmm) cc_final: 0.4398 (tmm) REVERT: F 253 ILE cc_start: 0.7080 (mm) cc_final: 0.6589 (mm) REVERT: I 119 SER cc_start: 0.7940 (m) cc_final: 0.7358 (t) REVERT: J 112 TRP cc_start: 0.8205 (m100) cc_final: 0.7723 (m100) REVERT: J 361 ASN cc_start: 0.7097 (t0) cc_final: 0.5912 (t0) REVERT: J 380 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6117 (mm-30) REVERT: J 427 LEU cc_start: 0.8993 (mt) cc_final: 0.8556 (tt) REVERT: J 434 LYS cc_start: 0.8409 (mmpt) cc_final: 0.7950 (mmmm) REVERT: J 479 ASN cc_start: 0.8774 (m110) cc_final: 0.8510 (m-40) REVERT: J 664 SER cc_start: 0.9398 (p) cc_final: 0.9124 (t) REVERT: J 690 MET cc_start: 0.7198 (mmm) cc_final: 0.6498 (tpt) REVERT: J 799 MET cc_start: 0.6352 (mtp) cc_final: 0.6050 (ttt) REVERT: K 38 TYR cc_start: 0.7746 (m-80) cc_final: 0.7408 (m-80) REVERT: K 90 MET cc_start: 0.7826 (mpp) cc_final: 0.7498 (mpp) REVERT: K 194 TYR cc_start: 0.7938 (t80) cc_final: 0.7143 (t80) REVERT: K 198 ILE cc_start: 0.8951 (pt) cc_final: 0.8710 (pt) REVERT: K 337 ASP cc_start: 0.7734 (m-30) cc_final: 0.7312 (m-30) REVERT: K 421 MET cc_start: 0.8220 (mmp) cc_final: 0.7769 (mmp) REVERT: K 481 THR cc_start: 0.9401 (p) cc_final: 0.9103 (p) REVERT: K 531 MET cc_start: 0.9010 (mmp) cc_final: 0.8127 (mmm) REVERT: K 567 ARG cc_start: 0.7697 (tpp-160) cc_final: 0.7421 (tpp-160) REVERT: K 585 THR cc_start: 0.8733 (m) cc_final: 0.7652 (m) REVERT: K 722 TYR cc_start: 0.7844 (m-80) cc_final: 0.7490 (m-80) REVERT: L 50 GLU cc_start: 0.7336 (pt0) cc_final: 0.6912 (pp20) REVERT: L 60 MET cc_start: 0.5780 (ppp) cc_final: 0.5340 (ppp) REVERT: L 118 MET cc_start: 0.1354 (mmp) cc_final: 0.0897 (mmp) REVERT: M 97 LEU cc_start: 0.5032 (tp) cc_final: 0.4788 (mt) REVERT: M 110 MET cc_start: 0.7143 (tpp) cc_final: 0.6935 (tpp) REVERT: M 144 GLU cc_start: 0.6419 (tp30) cc_final: 0.5985 (tp30) REVERT: N 55 GLU cc_start: 0.7239 (tt0) cc_final: 0.6718 (mm-30) REVERT: N 137 MET cc_start: 0.5251 (mmt) cc_final: 0.4511 (mmt) REVERT: N 157 MET cc_start: 0.5686 (mmp) cc_final: 0.4808 (mmp) REVERT: O 99 ARG cc_start: 0.6861 (mmm160) cc_final: 0.5989 (tpm170) REVERT: P 212 ARG cc_start: 0.8965 (mmm160) cc_final: 0.8517 (mmm160) REVERT: P 261 LEU cc_start: 0.7958 (mm) cc_final: 0.7749 (mm) outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.1836 time to fit residues: 178.4765 Evaluate side-chains 460 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 106 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 251 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 288 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 327 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095434 restraints weight = 114730.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096249 restraints weight = 82088.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096561 restraints weight = 59926.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096981 restraints weight = 50650.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096962 restraints weight = 42336.156| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 34566 Z= 0.166 Angle : 0.650 11.265 46549 Z= 0.329 Chirality : 0.043 0.226 5085 Planarity : 0.004 0.074 6051 Dihedral : 5.366 58.749 4645 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.04 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4205 helix: 1.00 (0.11), residues: 2140 sheet: -0.61 (0.25), residues: 449 loop : -1.05 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 23 TYR 0.029 0.002 TYR J 134 PHE 0.049 0.002 PHE B 352 TRP 0.020 0.002 TRP K 508 HIS 0.011 0.001 HIS K 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (34566) covalent geometry : angle 0.64954 / 0.33 (46549) hydrogen bonds : bond 0.04483 / 3.00 ( 1602) hydrogen bonds : angle 4.22361 / 2.98 ( 4437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.239 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 123 MET cc_start: 0.8178 (mmm) cc_final: 0.7568 (tpp) REVERT: A 132 MET cc_start: 0.9325 (ppp) cc_final: 0.8989 (ppp) REVERT: A 283 MET cc_start: 0.7002 (mmt) cc_final: 0.6520 (mmt) REVERT: B 190 MET cc_start: 0.8627 (tmm) cc_final: 0.8241 (tmm) REVERT: B 305 MET cc_start: 0.9062 (mtp) cc_final: 0.8817 (mtp) REVERT: B 325 MET cc_start: 0.7706 (mmm) cc_final: 0.7347 (mmt) REVERT: C 44 MET cc_start: 0.8709 (mtp) cc_final: 0.8276 (mtp) REVERT: C 119 MET cc_start: 0.8303 (ttm) cc_final: 0.7995 (ttm) REVERT: C 130 PRO cc_start: 0.8772 (Cg_endo) cc_final: 0.8390 (Cg_exo) REVERT: C 132 MET cc_start: 0.8248 (ppp) cc_final: 0.8011 (ppp) REVERT: C 267 ILE cc_start: 0.9160 (pt) cc_final: 0.8825 (mm) REVERT: C 274 ILE cc_start: 0.8991 (pt) cc_final: 0.8790 (pt) REVERT: C 305 MET cc_start: 0.8203 (mmm) cc_final: 0.7223 (tpt) REVERT: C 360 GLN cc_start: 0.7547 (pm20) cc_final: 0.7038 (pm20) REVERT: C 372 ARG cc_start: 0.7727 (ptp-110) cc_final: 0.7387 (ptp-170) REVERT: D 123 MET cc_start: 0.9065 (mmm) cc_final: 0.8015 (mmm) REVERT: D 227 MET cc_start: 0.8403 (mmm) cc_final: 0.8113 (tpp) REVERT: D 355 MET cc_start: 0.7901 (mmm) cc_final: 0.7655 (mtt) REVERT: E 254 ASP cc_start: 0.7702 (m-30) cc_final: 0.6998 (t0) REVERT: E 281 MET cc_start: 0.4620 (tmm) cc_final: 0.4320 (tmm) REVERT: F 253 ILE cc_start: 0.7117 (mm) cc_final: 0.6595 (mm) REVERT: I 119 SER cc_start: 0.7978 (m) cc_final: 0.7367 (t) REVERT: J 112 TRP cc_start: 0.8289 (m100) cc_final: 0.7856 (m100) REVERT: J 281 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7055 (ptp-110) REVERT: J 349 MET cc_start: 0.8160 (tpp) cc_final: 0.7950 (mmt) REVERT: J 361 ASN cc_start: 0.7132 (t0) cc_final: 0.5949 (t0) REVERT: J 380 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6277 (mm-30) REVERT: J 427 LEU cc_start: 0.9028 (mt) cc_final: 0.8566 (tt) REVERT: J 434 LYS cc_start: 0.8393 (mmpt) cc_final: 0.7927 (mmmm) REVERT: J 479 ASN cc_start: 0.8825 (m110) cc_final: 0.8522 (m-40) REVERT: J 536 GLU cc_start: 0.8619 (tp30) cc_final: 0.7767 (mm-30) REVERT: J 664 SER cc_start: 0.9404 (p) cc_final: 0.9139 (t) REVERT: J 690 MET cc_start: 0.7223 (mmm) cc_final: 0.6487 (tpt) REVERT: J 799 MET cc_start: 0.6378 (mtp) cc_final: 0.6072 (ttt) REVERT: K 38 TYR cc_start: 0.7749 (m-80) cc_final: 0.7402 (m-80) REVERT: K 90 MET cc_start: 0.7926 (mpp) cc_final: 0.7541 (mpp) REVERT: K 194 TYR cc_start: 0.8005 (t80) cc_final: 0.7088 (t80) REVERT: K 198 ILE cc_start: 0.8953 (pt) cc_final: 0.8728 (pt) REVERT: K 337 ASP cc_start: 0.7642 (m-30) cc_final: 0.7217 (m-30) REVERT: K 344 GLU cc_start: 0.7387 (mp0) cc_final: 0.7163 (mp0) REVERT: K 363 LYS cc_start: 0.8055 (mppt) cc_final: 0.7806 (mppt) REVERT: K 421 MET cc_start: 0.8236 (mmp) cc_final: 0.7440 (mmp) REVERT: K 481 THR cc_start: 0.9406 (p) cc_final: 0.9154 (p) REVERT: K 531 MET cc_start: 0.9000 (mmp) cc_final: 0.8026 (mmm) REVERT: K 567 ARG cc_start: 0.7734 (tpp-160) cc_final: 0.7396 (tpp-160) REVERT: K 585 THR cc_start: 0.8750 (m) cc_final: 0.7612 (m) REVERT: K 722 TYR cc_start: 0.7878 (m-80) cc_final: 0.7410 (m-80) REVERT: K 724 ILE cc_start: 0.7823 (pt) cc_final: 0.7179 (tp) REVERT: L 50 GLU cc_start: 0.7475 (pt0) cc_final: 0.7018 (pp20) REVERT: L 60 MET cc_start: 0.5823 (ppp) cc_final: 0.5360 (ppp) REVERT: L 118 MET cc_start: 0.1365 (mmp) cc_final: 0.1058 (mmp) REVERT: M 144 GLU cc_start: 0.6369 (tp30) cc_final: 0.5879 (tp30) REVERT: M 160 THR cc_start: 0.7168 (p) cc_final: 0.6874 (p) REVERT: N 103 MET cc_start: 0.6137 (mmm) cc_final: 0.5858 (mmt) REVERT: N 137 MET cc_start: 0.5285 (mmt) cc_final: 0.4503 (mmt) REVERT: O 99 ARG cc_start: 0.6948 (mmm160) cc_final: 0.6119 (tpm170) REVERT: P 212 ARG cc_start: 0.9008 (mmm160) cc_final: 0.8564 (mmm160) REVERT: P 261 LEU cc_start: 0.8095 (mm) cc_final: 0.7833 (mm) outliers start: 0 outliers final: 0 residues processed: 568 average time/residue: 0.1901 time to fit residues: 177.0615 Evaluate side-chains 451 residues out of total 3657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 102 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 360 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 204 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 363 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** J 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 GLN P 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.104862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096075 restraints weight = 113411.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096904 restraints weight = 81230.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097272 restraints weight = 58667.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097742 restraints weight = 48467.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097710 restraints weight = 41642.157| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34566 Z= 0.143 Angle : 0.629 11.807 46549 Z= 0.319 Chirality : 0.043 0.219 5085 Planarity : 0.004 0.041 6051 Dihedral : 5.295 56.411 4645 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4205 helix: 1.07 (0.11), residues: 2118 sheet: -0.62 (0.26), residues: 445 loop : -1.04 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 23 TYR 0.041 0.002 TYR K 422 PHE 0.028 0.002 PHE K 669 TRP 0.019 0.001 TRP K 508 HIS 0.006 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (34566) covalent geometry : angle 0.62910 / 0.32 (46549) hydrogen bonds : bond 0.04409 / 2.96 ( 1602) hydrogen bonds : angle 4.18598 / 2.95 ( 4437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5011.65 seconds wall clock time: 87 minutes 54.24 seconds (5274.24 seconds total)