Starting phenix.real_space_refine on Mon Feb 19 17:19:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/02_2024/7xkq_33264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/02_2024/7xkq_33264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/02_2024/7xkq_33264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/02_2024/7xkq_33264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/02_2024/7xkq_33264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/02_2024/7xkq_33264_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 6 5.21 5 S 80 5.16 5 C 15921 2.51 5 N 4405 2.21 5 O 4867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 290": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25299 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3660 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 997 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.05, per 1000 atoms: 0.52 Number of scatterers: 25299 At special positions: 0 Unit cell: (126.72, 124.08, 156.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 20 15.00 Mg 6 11.99 O 4867 8.00 N 4405 7.00 C 15921 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 - 3.50 Amino acid : False - 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: 9.71 Conformation dependent library (CDL) restraints added in 4.5 seconds 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 25 sheets defined 41.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.569A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.991A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 288 through 300 removed outlier: 4.590A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 295 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 296 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.685A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 397 removed outlier: 4.140A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 403 through 406 No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 408 through 420 Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.592A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.657A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 467 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.509A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 188 removed outlier: 3.712A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ASP B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.759A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 290 through 300 removed outlier: 4.424A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.587A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 382 through 396 removed outlier: 3.994A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.176A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.501A pdb=" N VAL B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 461 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.638A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.672A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.503A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.466A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG C 300 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 382 through 398 removed outlier: 4.636A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.881A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.831A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 removed outlier: 3.586A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.806A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 4.448A pdb=" N ALA D 266 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 removed outlier: 4.603A pdb=" N ALA D 282 " --> pdb=" O PRO D 279 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 283 " --> pdb=" O THR D 280 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN D 287 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU D 290 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.568A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 387 removed outlier: 3.596A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.524A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.083A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 removed outlier: 3.576A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 450 through 453' Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 179 Processing helix chain 'E' and resid 192 through 204 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 222 through 241 removed outlier: 3.672A pdb=" N VAL E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.605A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 324 removed outlier: 3.533A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 361 through 387 removed outlier: 3.590A pdb=" N GLN E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.578A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 430 through 442 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.547A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 179 removed outlier: 4.449A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.634A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.874A pdb=" N ALA F 266 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.525A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 324 removed outlier: 3.635A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 391 removed outlier: 3.544A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N MET F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP F 390 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU F 391 " --> pdb=" O LEU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.897A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 removed outlier: 3.562A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR F 421 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 460 through 469 Processing helix chain 'G' and resid 4 through 57 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 91 through 106 removed outlier: 4.243A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 120 through 128 removed outlier: 3.703A pdb=" N SER G 124 " --> pdb=" O ARG G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 161 removed outlier: 4.985A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 90 through 105 removed outlier: 3.995A pdb=" N ARG H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN H 105 " --> pdb=" O GLU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 128 removed outlier: 4.726A pdb=" N LEU H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.498A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.120A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 340 through 344 Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.622A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.412A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.574A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.614A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.730A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.352A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.194A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 6.734A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.348A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.909A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.784A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.691A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.750A pdb=" N VAL F 76 " --> pdb=" O GLY F 4 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 6 through 10 removed outlier: 6.639A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= V, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.906A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASP F 252 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA F 186 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.478A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU G 189 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.570A pdb=" N GLY H 66 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU H 41 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 30 through 33 removed outlier: 3.885A pdb=" N ALA H 27 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 32 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL H 25 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS H 26 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA H 49 " --> pdb=" O LYS H 26 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2676 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: 8.31 Time building geometry restraints manager: 10.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7659 1.33 - 1.45: 3166 1.45 - 1.57: 14702 1.57 - 1.69: 33 1.69 - 1.81: 160 Bond restraints: 25720 Sorted by residual: bond pdb=" N GLU A 54 " pdb=" CA GLU A 54 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.47e+00 bond pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.22e-02 6.72e+03 6.39e+00 bond pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.35e-02 5.49e+03 4.51e+00 bond pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 1.528 1.496 0.032 1.59e-02 3.96e+03 4.04e+00 ... (remaining 25715 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.85: 1011 107.85 - 115.85: 16206 115.85 - 123.85: 17171 123.85 - 131.85: 472 131.85 - 139.84: 20 Bond angle restraints: 34880 Sorted by residual: angle pdb=" C GLU A 54 " pdb=" CA GLU A 54 " pdb=" CB GLU A 54 " ideal model delta sigma weight residual 109.71 103.44 6.27 1.83e+00 2.99e-01 1.18e+01 angle pdb=" CA PHE A 55 " pdb=" CB PHE A 55 " pdb=" CG PHE A 55 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" C PHE A 55 " pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 120.29 124.89 -4.60 1.42e+00 4.96e-01 1.05e+01 angle pdb=" N GLY A 58 " pdb=" CA GLY A 58 " pdb=" C GLY A 58 " ideal model delta sigma weight residual 115.00 110.52 4.48 1.44e+00 4.82e-01 9.67e+00 angle pdb=" N VAL E 207 " pdb=" CA VAL E 207 " pdb=" C VAL E 207 " ideal model delta sigma weight residual 112.96 109.88 3.08 1.00e+00 1.00e+00 9.51e+00 ... (remaining 34875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14367 17.91 - 35.81: 1076 35.81 - 53.72: 226 53.72 - 71.63: 69 71.63 - 89.54: 29 Dihedral angle restraints: 15767 sinusoidal: 6467 harmonic: 9300 Sorted by residual: dihedral pdb=" CA GLN D 217 " pdb=" C GLN D 217 " pdb=" N MET D 218 " pdb=" CA MET D 218 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA VAL H 15 " pdb=" C VAL H 15 " pdb=" N TYR H 16 " pdb=" CA TYR H 16 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ARG E 454 " pdb=" C ARG E 454 " pdb=" N LEU E 455 " pdb=" CA LEU E 455 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 15764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3014 0.046 - 0.092: 738 0.092 - 0.138: 260 0.138 - 0.184: 4 0.184 - 0.231: 2 Chirality restraints: 4018 Sorted by residual: chirality pdb=" CA PHE A 55 " pdb=" N PHE A 55 " pdb=" C PHE A 55 " pdb=" CB PHE A 55 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU A 54 " pdb=" N GLU A 54 " pdb=" C GLU A 54 " pdb=" CB GLU A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 57 " pdb=" N ASN A 57 " pdb=" C ASN A 57 " pdb=" CB ASN A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 4015 not shown) Planarity restraints: 4541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 53 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C VAL A 53 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL A 53 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 54 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 428 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO F 429 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 429 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 429 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO E 316 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.026 5.00e-02 4.00e+02 ... (remaining 4538 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 175 2.55 - 3.14: 20255 3.14 - 3.73: 38428 3.73 - 4.31: 53744 4.31 - 4.90: 92051 Nonbonded interactions: 204653 Sorted by model distance: nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 1.967 2.170 nonbonded pdb=" O3G ATP F 501 " pdb="MG MG F 502 " model vdw 1.968 2.170 nonbonded pdb=" O3B ATP C 600 " pdb="MG MG C 601 " model vdw 1.979 2.170 nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 1.983 2.170 nonbonded pdb=" O3B ATP E 501 " pdb="MG MG E 502 " model vdw 2.002 2.170 ... (remaining 204648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and (resid 24 through 54 or (resid 55 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 56 through 501)) selection = (chain 'C' and (resid 24 through 54 or (resid 55 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 56 through 501)) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 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: 11.800 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 64.670 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25720 Z= 0.219 Angle : 0.505 6.275 34880 Z= 0.276 Chirality : 0.044 0.231 4018 Planarity : 0.004 0.056 4541 Dihedral : 14.152 89.537 9811 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3243 helix: 1.66 (0.15), residues: 1249 sheet: 0.87 (0.22), residues: 540 loop : 0.13 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.013 0.001 PHE B 494 TYR 0.016 0.001 TYR B 248 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.882 Fit side-chains REVERT: C 60 MET cc_start: 0.8503 (mmt) cc_final: 0.8278 (mmt) REVERT: D 253 ASN cc_start: 0.7710 (m-40) cc_final: 0.7227 (m-40) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3601 time to fit residues: 76.3832 Evaluate side-chains 101 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 293 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 172 GLN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN H 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25720 Z= 0.330 Angle : 0.553 7.315 34880 Z= 0.290 Chirality : 0.045 0.175 4018 Planarity : 0.004 0.044 4541 Dihedral : 8.005 85.888 3756 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 0.37 % Allowed : 5.39 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3243 helix: 1.64 (0.15), residues: 1253 sheet: 0.69 (0.22), residues: 565 loop : 0.10 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.023 0.001 PHE B 395 TYR 0.019 0.001 TYR B 248 ARG 0.006 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 2.936 Fit side-chains REVERT: B 60 MET cc_start: 0.8762 (mmm) cc_final: 0.8347 (mmm) REVERT: B 137 MET cc_start: 0.9166 (mmm) cc_final: 0.8715 (mmt) REVERT: C 137 MET cc_start: 0.8665 (mmm) cc_final: 0.8420 (mmm) REVERT: D 253 ASN cc_start: 0.8099 (m-40) cc_final: 0.7478 (m-40) outliers start: 10 outliers final: 6 residues processed: 107 average time/residue: 0.3368 time to fit residues: 61.8695 Evaluate side-chains 106 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 293 optimal weight: 20.0000 chunk 317 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 25720 Z= 0.464 Angle : 0.613 6.002 34880 Z= 0.320 Chirality : 0.047 0.163 4018 Planarity : 0.004 0.047 4541 Dihedral : 8.252 87.504 3756 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 1.08 % Allowed : 8.23 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3243 helix: 1.40 (0.15), residues: 1244 sheet: 0.51 (0.22), residues: 547 loop : -0.09 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 200 PHE 0.016 0.002 PHE F 257 TYR 0.017 0.002 TYR B 248 ARG 0.005 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 2.758 Fit side-chains REVERT: B 60 MET cc_start: 0.9011 (mmm) cc_final: 0.8552 (mmm) REVERT: H 71 ARG cc_start: 0.6553 (ttp80) cc_final: 0.6301 (ttp80) outliers start: 29 outliers final: 13 residues processed: 126 average time/residue: 0.3234 time to fit residues: 70.4655 Evaluate side-chains 110 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 197 optimal weight: 0.5980 chunk 294 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN G 181 GLN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25720 Z= 0.188 Angle : 0.477 6.538 34880 Z= 0.249 Chirality : 0.043 0.144 4018 Planarity : 0.004 0.043 4541 Dihedral : 7.678 84.721 3756 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 0.64 % Allowed : 9.61 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3243 helix: 1.67 (0.15), residues: 1257 sheet: 0.61 (0.22), residues: 544 loop : 0.05 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.010 0.001 PHE D 125 TYR 0.016 0.001 TYR B 248 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 3.071 Fit side-chains REVERT: B 60 MET cc_start: 0.8872 (mmm) cc_final: 0.8493 (mmm) REVERT: B 62 MET cc_start: 0.7916 (ttm) cc_final: 0.7185 (ttp) REVERT: C 129 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9295 (mt) REVERT: H 71 ARG cc_start: 0.6530 (ttp80) cc_final: 0.6256 (ttp80) outliers start: 17 outliers final: 8 residues processed: 116 average time/residue: 0.3700 time to fit residues: 73.2588 Evaluate side-chains 106 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain H residue 87 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 128 optimal weight: 0.0030 chunk 266 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 280 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 426 GLN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25720 Z= 0.296 Angle : 0.510 7.470 34880 Z= 0.265 Chirality : 0.044 0.146 4018 Planarity : 0.004 0.044 4541 Dihedral : 7.672 83.113 3756 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 1.12 % Allowed : 10.03 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3243 helix: 1.66 (0.15), residues: 1256 sheet: 0.56 (0.22), residues: 549 loop : 0.03 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 200 PHE 0.012 0.001 PHE F 257 TYR 0.015 0.001 TYR B 248 ARG 0.002 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 2.863 Fit side-chains REVERT: B 60 MET cc_start: 0.8864 (mmm) cc_final: 0.8397 (mmm) outliers start: 30 outliers final: 24 residues processed: 122 average time/residue: 0.3254 time to fit residues: 67.7716 Evaluate side-chains 121 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 407 GLN ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25720 Z= 0.248 Angle : 0.489 10.530 34880 Z= 0.253 Chirality : 0.043 0.142 4018 Planarity : 0.004 0.043 4541 Dihedral : 7.519 86.850 3756 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.23 % Allowed : 10.85 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3243 helix: 1.72 (0.15), residues: 1248 sheet: 0.58 (0.22), residues: 545 loop : 0.09 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 200 PHE 0.010 0.001 PHE A 494 TYR 0.016 0.001 TYR B 248 ARG 0.006 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 3.139 Fit side-chains REVERT: B 60 MET cc_start: 0.8915 (mmm) cc_final: 0.8435 (mmm) REVERT: H 71 ARG cc_start: 0.6219 (ttp80) cc_final: 0.6012 (ttp80) outliers start: 33 outliers final: 27 residues processed: 124 average time/residue: 0.3224 time to fit residues: 69.3673 Evaluate side-chains 125 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 176 optimal weight: 0.0670 chunk 263 optimal weight: 0.3980 chunk 174 optimal weight: 2.9990 chunk 311 optimal weight: 20.0000 chunk 194 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25720 Z= 0.260 Angle : 0.494 10.146 34880 Z= 0.255 Chirality : 0.044 0.144 4018 Planarity : 0.004 0.043 4541 Dihedral : 7.454 89.466 3756 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 1.53 % Allowed : 10.89 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3243 helix: 1.72 (0.15), residues: 1248 sheet: 0.58 (0.22), residues: 539 loop : 0.06 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 200 PHE 0.017 0.001 PHE C 398 TYR 0.016 0.001 TYR B 248 ARG 0.003 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 96 time to evaluate : 3.140 Fit side-chains REVERT: B 60 MET cc_start: 0.8910 (mmm) cc_final: 0.8437 (mmm) REVERT: B 137 MET cc_start: 0.9035 (mmm) cc_final: 0.8629 (mmt) REVERT: D 213 MET cc_start: 0.9018 (mtt) cc_final: 0.8747 (mtt) REVERT: H 71 ARG cc_start: 0.6162 (ttp80) cc_final: 0.5926 (ttp80) outliers start: 41 outliers final: 30 residues processed: 130 average time/residue: 0.3328 time to fit residues: 74.7843 Evaluate side-chains 126 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 1.9990 chunk 124 optimal weight: 0.0040 chunk 185 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 25720 Z= 0.152 Angle : 0.456 9.432 34880 Z= 0.236 Chirality : 0.042 0.143 4018 Planarity : 0.003 0.042 4541 Dihedral : 7.077 87.470 3756 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.19 % Favored : 97.78 % Rotamer: Outliers : 1.01 % Allowed : 11.60 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.15), residues: 3243 helix: 1.87 (0.15), residues: 1242 sheet: 0.79 (0.23), residues: 527 loop : 0.10 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 173 PHE 0.010 0.001 PHE G 165 TYR 0.016 0.001 TYR B 248 ARG 0.003 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 2.747 Fit side-chains REVERT: A 404 LYS cc_start: 0.8538 (ptmm) cc_final: 0.8211 (ptpp) REVERT: B 60 MET cc_start: 0.8828 (mmm) cc_final: 0.8352 (mmm) REVERT: B 137 MET cc_start: 0.8987 (mmm) cc_final: 0.8502 (mmt) REVERT: B 404 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8287 (mmtp) REVERT: C 129 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9306 (mt) REVERT: H 71 ARG cc_start: 0.6137 (ttp80) cc_final: 0.5886 (ttp80) outliers start: 27 outliers final: 17 residues processed: 123 average time/residue: 0.3363 time to fit residues: 71.0287 Evaluate side-chains 115 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 244 MET Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 9.9990 chunk 298 optimal weight: 20.0000 chunk 272 optimal weight: 1.9990 chunk 290 optimal weight: 0.0470 chunk 174 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25720 Z= 0.184 Angle : 0.467 9.828 34880 Z= 0.241 Chirality : 0.043 0.144 4018 Planarity : 0.003 0.042 4541 Dihedral : 6.883 83.323 3756 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 0.86 % Allowed : 11.97 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.15), residues: 3243 helix: 1.91 (0.15), residues: 1240 sheet: 0.83 (0.23), residues: 531 loop : 0.10 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 363 PHE 0.018 0.001 PHE C 398 TYR 0.015 0.001 TYR B 248 ARG 0.003 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 2.900 Fit side-chains REVERT: A 404 LYS cc_start: 0.8522 (ptmm) cc_final: 0.8199 (ptpp) REVERT: B 60 MET cc_start: 0.8853 (mmm) cc_final: 0.8305 (mmm) REVERT: B 404 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8257 (mmtp) REVERT: G 6 ASP cc_start: 0.7688 (m-30) cc_final: 0.6995 (m-30) REVERT: G 165 PHE cc_start: 0.7575 (p90) cc_final: 0.7073 (p90) outliers start: 23 outliers final: 20 residues processed: 118 average time/residue: 0.3475 time to fit residues: 70.6689 Evaluate side-chains 118 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 244 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25720 Z= 0.266 Angle : 0.499 9.791 34880 Z= 0.258 Chirality : 0.044 0.145 4018 Planarity : 0.004 0.043 4541 Dihedral : 6.987 82.913 3756 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 1.05 % Allowed : 11.90 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.15), residues: 3243 helix: 1.83 (0.15), residues: 1245 sheet: 0.76 (0.23), residues: 525 loop : 0.08 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 200 PHE 0.020 0.001 PHE C 398 TYR 0.016 0.001 TYR B 248 ARG 0.006 0.000 ARG H 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 3.123 Fit side-chains REVERT: A 404 LYS cc_start: 0.8573 (ptmm) cc_final: 0.8231 (ptpp) REVERT: B 60 MET cc_start: 0.8864 (mmm) cc_final: 0.8218 (mmm) REVERT: B 404 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8328 (mmtp) REVERT: E 48 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9324 (mt) REVERT: G 6 ASP cc_start: 0.7725 (m-30) cc_final: 0.6984 (m-30) outliers start: 28 outliers final: 24 residues processed: 121 average time/residue: 0.3212 time to fit residues: 67.1607 Evaluate side-chains 121 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 463 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 37 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 263 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.056388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.042773 restraints weight = 87845.906| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.82 r_work: 0.2577 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25720 Z= 0.168 Angle : 0.464 10.043 34880 Z= 0.240 Chirality : 0.042 0.145 4018 Planarity : 0.003 0.042 4541 Dihedral : 6.817 84.255 3756 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 1.01 % Allowed : 11.93 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.15), residues: 3243 helix: 1.93 (0.15), residues: 1239 sheet: 0.83 (0.22), residues: 537 loop : 0.11 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 173 PHE 0.009 0.001 PHE A 494 TYR 0.016 0.001 TYR B 248 ARG 0.006 0.000 ARG H 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3832.08 seconds wall clock time: 71 minutes 51.27 seconds (4311.27 seconds total)