Starting phenix.real_space_refine on Mon Feb 19 09:46:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh3_34750/02_2024/8hh3_34750_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh3_34750/02_2024/8hh3_34750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh3_34750/02_2024/8hh3_34750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh3_34750/02_2024/8hh3_34750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh3_34750/02_2024/8hh3_34750_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh3_34750/02_2024/8hh3_34750_updated.pdb" } resolution = 4.3 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 19 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 237": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24281 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, '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: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 23, '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: "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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'ATP': 1, 'PO4': 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} Time building chain proxies: 12.30, per 1000 atoms: 0.51 Number of scatterers: 24281 At special positions: 0 Unit cell: (125.84, 127.6, 157.52, 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 77 16.00 P 19 15.00 Mg 5 11.99 O 4674 8.00 N 4219 7.00 C 15287 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: 9.07 Conformation dependent library (CDL) restraints added in 4.4 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 22 sheets defined 41.9% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' 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 188 removed outlier: 3.660A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 250 Proline residue: A 239 - end of helix removed outlier: 3.617A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.112A 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 290 through 300 removed outlier: 3.925A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 373 through 395 removed outlier: 3.894A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.982A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP A 465 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.762A 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 186 removed outlier: 3.743A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (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: 3.623A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (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: 3.686A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 373 through 395 removed outlier: 3.712A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 420 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.804A pdb=" N HIS B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.637A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) 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: 4.646A 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 220 removed outlier: 3.539A pdb=" N TYR C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 220' Processing helix chain 'C' and resid 232 through 251 Proline residue: C 239 - end of helix removed outlier: 3.562A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (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 299 removed outlier: 4.488A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 293 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 removed outlier: 3.510A pdb=" N SER C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 396 removed outlier: 3.767A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 430 through 442 removed outlier: 3.945A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.484A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 477 Processing helix chain 'C' and resid 484 through 495 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' 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 241 removed outlier: 3.747A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 4.048A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 291 removed outlier: 4.290A pdb=" N ARG D 291 " --> 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: 3.805A pdb=" N THR D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE D 322 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 5.134A 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: 3.710A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 409 removed outlier: 3.646A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.764A 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 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.596A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) 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 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 5.287A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.117A 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 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.188A 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 323 removed outlier: 3.580A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 361 through 384 removed outlier: 4.046A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.676A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 421 removed outlier: 4.734A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 removed outlier: 3.666A 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: 4.613A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 203 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 228 through 241 removed outlier: 3.809A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 3.815A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.543A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.580A 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: 3.504A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 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 387 removed outlier: 4.322A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.766A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.675A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.598A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 56 removed outlier: 4.040A pdb=" N PHE G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 64 through 67 No H-bonds generated for 'chain 'G' and resid 64 through 67' Processing helix chain 'G' and resid 89 through 106 removed outlier: 4.477A pdb=" N ASN G 92 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN G 94 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 104 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 105 " --> pdb=" O THR G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 161 removed outlier: 5.102A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 282 removed outlier: 3.936A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.543A pdb=" N GLY G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.685A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.603A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 341 through 344 removed outlier: 7.001A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.511A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.073A 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: 6.648A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.617A 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: 8.671A pdb=" N ILE B 222 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.690A 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: 6.230A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS B 255 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 194 " --> pdb=" O HIS B 255 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 257 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 196 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL B 259 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 198 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.360A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.549A 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: 3.854A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.703A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.818A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.737A 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 330 removed outlier: 7.990A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.711A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.872A 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: 8.655A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.513A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.855A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 113 through 118 removed outlier: 6.037A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2595 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: 8.18 Time building geometry restraints manager: 9.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4187 1.32 - 1.44: 5900 1.44 - 1.56: 14417 1.56 - 1.68: 30 1.68 - 1.80: 154 Bond restraints: 24688 Sorted by residual: bond pdb=" C VAL B 378 " pdb=" O VAL B 378 " ideal model delta sigma weight residual 1.237 1.413 -0.176 1.23e-02 6.61e+03 2.05e+02 bond pdb=" C ALA B 374 " pdb=" O ALA B 374 " ideal model delta sigma weight residual 1.236 1.368 -0.132 1.22e-02 6.72e+03 1.16e+02 bond pdb=" C LYS B 377 " pdb=" O LYS B 377 " ideal model delta sigma weight residual 1.236 1.318 -0.082 1.15e-02 7.56e+03 5.06e+01 bond pdb=" CA ILE F 340 " pdb=" C ILE F 340 " ideal model delta sigma weight residual 1.524 1.448 0.076 1.16e-02 7.43e+03 4.25e+01 bond pdb=" C GLY B 380 " pdb=" O GLY B 380 " ideal model delta sigma weight residual 1.234 1.303 -0.070 1.21e-02 6.83e+03 3.34e+01 ... (remaining 24683 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.66: 953 107.66 - 115.70: 15381 115.70 - 123.74: 16642 123.74 - 131.78: 490 131.78 - 139.82: 19 Bond angle restraints: 33485 Sorted by residual: angle pdb=" C TYR F 341 " pdb=" N PRO F 342 " pdb=" CA PRO F 342 " ideal model delta sigma weight residual 119.84 105.96 13.88 1.25e+00 6.40e-01 1.23e+02 angle pdb=" CA LYS B 377 " pdb=" C LYS B 377 " pdb=" N VAL B 378 " ideal model delta sigma weight residual 116.92 127.12 -10.20 1.16e+00 7.43e-01 7.73e+01 angle pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta sigma weight residual 119.32 109.44 9.88 1.14e+00 7.69e-01 7.52e+01 angle pdb=" O LYS B 377 " pdb=" C LYS B 377 " pdb=" N VAL B 378 " ideal model delta sigma weight residual 122.03 113.08 8.95 1.04e+00 9.25e-01 7.41e+01 angle pdb=" O LYS B 373 " pdb=" C LYS B 373 " pdb=" N ALA B 374 " ideal model delta sigma weight residual 122.22 114.00 8.22 1.17e+00 7.31e-01 4.94e+01 ... (remaining 33480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.76: 14642 30.76 - 61.52: 386 61.52 - 92.28: 63 92.28 - 123.03: 0 123.03 - 153.79: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" O2A ADP D 503 " pdb=" O3A ADP D 503 " pdb=" PA ADP D 503 " pdb=" PB ADP D 503 " ideal model delta sinusoidal sigma weight residual -60.00 93.79 -153.79 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C THR B 381 " pdb=" N THR B 381 " pdb=" CA THR B 381 " pdb=" CB THR B 381 " ideal model delta harmonic sigma weight residual -122.00 -137.97 15.97 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C5' ADP D 503 " pdb=" O5' ADP D 503 " pdb=" PA ADP D 503 " pdb=" O2A ADP D 503 " ideal model delta sinusoidal sigma weight residual -60.00 74.45 -134.45 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 3843 0.151 - 0.303: 8 0.303 - 0.454: 2 0.454 - 0.605: 2 0.605 - 0.757: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA TYR F 341 " pdb=" N TYR F 341 " pdb=" C TYR F 341 " pdb=" CB TYR F 341 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA TYR E 341 " pdb=" N TYR E 341 " pdb=" C TYR E 341 " pdb=" CB TYR E 341 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA THR B 381 " pdb=" N THR B 381 " pdb=" C THR B 381 " pdb=" CB THR B 381 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 340 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C ILE E 340 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE E 340 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR E 341 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 383 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE E 383 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE E 383 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE E 384 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 385 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP B 385 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP B 385 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 386 " -0.020 2.00e-02 2.50e+03 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 22 2.33 - 2.97: 11743 2.97 - 3.62: 35421 3.62 - 4.26: 56236 4.26 - 4.90: 95736 Nonbonded interactions: 199158 Sorted by model distance: nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 502 " model vdw 1.690 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.003 2.170 ... (remaining 199153 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 501) selection = (chain 'C' and resid 24 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.020 Extract box with map and model: 11.140 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 63.940 Find NCS groups from input model: 1.700 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.004 0.176 24688 Z= 0.271 Angle : 0.643 13.884 33485 Z= 0.392 Chirality : 0.049 0.757 3856 Planarity : 0.004 0.063 4363 Dihedral : 14.209 153.792 9381 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 0.51 % Allowed : 0.39 % Favored : 99.10 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1242 sheet: 0.59 (0.22), residues: 526 loop : 0.04 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.010 0.001 PHE F 257 TYR 0.033 0.001 TYR F 341 ARG 0.003 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 2.715 Fit side-chains REVERT: A 87 GLU cc_start: 0.8252 (tt0) cc_final: 0.7690 (tt0) REVERT: B 60 MET cc_start: 0.8717 (mmt) cc_final: 0.8351 (mmt) REVERT: B 373 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8070 (ttpp) REVERT: B 451 GLU cc_start: 0.7715 (tt0) cc_final: 0.7126 (tp30) REVERT: C 109 ASN cc_start: 0.8404 (t0) cc_final: 0.7986 (t0) REVERT: C 272 GLU cc_start: 0.7742 (tt0) cc_final: 0.7172 (tt0) REVERT: C 457 GLU cc_start: 0.7709 (tt0) cc_final: 0.7450 (tt0) REVERT: D 334 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7896 (ttmt) REVERT: D 376 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6741 (mmm160) REVERT: D 389 MET cc_start: 0.7395 (mmt) cc_final: 0.7019 (mmm) REVERT: E 56 ASP cc_start: 0.7588 (t0) cc_final: 0.7213 (t0) REVERT: F 389 MET cc_start: 0.6932 (ttm) cc_final: 0.6640 (ttp) REVERT: F 390 ASP cc_start: 0.8181 (m-30) cc_final: 0.7962 (m-30) REVERT: G 222 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: G 225 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7252 (mp) outliers start: 13 outliers final: 5 residues processed: 237 average time/residue: 0.3930 time to fit residues: 141.7850 Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS B 467 ASN C 407 GLN D 179 HIS D 365 GLN E 371 GLN E 381 GLN G 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 24688 Z= 0.515 Angle : 0.652 7.837 33485 Z= 0.341 Chirality : 0.051 0.286 3856 Planarity : 0.005 0.065 4363 Dihedral : 8.788 179.559 3580 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 0.23 % Allowed : 4.52 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3115 helix: 1.04 (0.15), residues: 1229 sheet: 0.32 (0.22), residues: 549 loop : -0.23 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 215 PHE 0.020 0.002 PHE D 125 TYR 0.024 0.002 TYR G 100 ARG 0.004 0.000 ARG G 266 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6516 (tm-30) REVERT: A 87 GLU cc_start: 0.8352 (tt0) cc_final: 0.7612 (tt0) REVERT: B 373 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7867 (ttpp) REVERT: B 381 THR cc_start: 0.6258 (m) cc_final: 0.5715 (m) REVERT: B 382 LEU cc_start: 0.7710 (tp) cc_final: 0.7387 (tp) REVERT: B 451 GLU cc_start: 0.7773 (tt0) cc_final: 0.7143 (tp30) REVERT: B 465 ASP cc_start: 0.8190 (t70) cc_final: 0.7964 (t0) REVERT: C 272 GLU cc_start: 0.7822 (tt0) cc_final: 0.7386 (tt0) REVERT: C 457 GLU cc_start: 0.7655 (tt0) cc_final: 0.7390 (tt0) REVERT: E 56 ASP cc_start: 0.7908 (t0) cc_final: 0.7270 (t0) REVERT: E 387 LEU cc_start: 0.5986 (tt) cc_final: 0.5101 (mt) REVERT: G 167 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6597 (mt-10) outliers start: 6 outliers final: 4 residues processed: 171 average time/residue: 0.4140 time to fit residues: 108.9928 Evaluate side-chains 142 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 279 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN D 365 GLN E 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24688 Z= 0.148 Angle : 0.479 5.743 33485 Z= 0.249 Chirality : 0.043 0.137 3856 Planarity : 0.004 0.067 4363 Dihedral : 8.005 179.230 3580 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.70 % Favored : 98.20 % Rotamer: Outliers : 0.08 % Allowed : 2.10 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3115 helix: 1.52 (0.15), residues: 1223 sheet: 0.54 (0.22), residues: 543 loop : -0.09 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 425 PHE 0.020 0.001 PHE F 322 TYR 0.010 0.001 TYR C 389 ARG 0.003 0.000 ARG E 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 3.106 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6770 (tm-30) REVERT: A 87 GLU cc_start: 0.8296 (tt0) cc_final: 0.7689 (tt0) REVERT: B 32 ILE cc_start: 0.8404 (mt) cc_final: 0.8068 (mm) REVERT: B 89 ARG cc_start: 0.6635 (ptp-110) cc_final: 0.6197 (ptp-170) REVERT: B 382 LEU cc_start: 0.7502 (tp) cc_final: 0.7298 (tp) REVERT: B 451 GLU cc_start: 0.7792 (tt0) cc_final: 0.7208 (tp30) REVERT: C 168 ILE cc_start: 0.7741 (pt) cc_final: 0.7420 (tt) REVERT: C 191 MET cc_start: 0.7293 (ttm) cc_final: 0.6907 (ttm) REVERT: C 272 GLU cc_start: 0.7631 (tt0) cc_final: 0.7113 (tt0) REVERT: C 407 GLN cc_start: 0.7863 (mt0) cc_final: 0.6996 (tp40) REVERT: E 56 ASP cc_start: 0.7779 (t0) cc_final: 0.7112 (t0) REVERT: E 395 GLU cc_start: 0.7664 (mp0) cc_final: 0.7422 (mp0) REVERT: F 1 MET cc_start: 0.6557 (ptt) cc_final: 0.5938 (ttp) REVERT: F 389 MET cc_start: 0.7212 (ttm) cc_final: 0.6827 (ttp) REVERT: G 136 ASP cc_start: 0.7259 (p0) cc_final: 0.6804 (p0) REVERT: G 249 ASP cc_start: 0.7382 (m-30) cc_final: 0.7078 (m-30) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.4351 time to fit residues: 127.3634 Evaluate side-chains 141 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 283 optimal weight: 7.9990 chunk 299 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 365 GLN E 381 GLN E 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 24688 Z= 0.466 Angle : 0.623 7.836 33485 Z= 0.325 Chirality : 0.049 0.226 3856 Planarity : 0.005 0.053 4363 Dihedral : 8.287 173.003 3580 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Rotamer: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3115 helix: 1.11 (0.15), residues: 1224 sheet: 0.34 (0.22), residues: 532 loop : -0.32 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 65 PHE 0.016 0.002 PHE D 257 TYR 0.018 0.002 TYR G 100 ARG 0.005 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 3.034 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6864 (tm-30) REVERT: A 87 GLU cc_start: 0.8334 (tt0) cc_final: 0.7611 (tt0) REVERT: B 89 ARG cc_start: 0.6539 (ptp-110) cc_final: 0.6094 (ptp-170) REVERT: B 451 GLU cc_start: 0.7779 (tt0) cc_final: 0.7300 (tp30) REVERT: C 272 GLU cc_start: 0.7868 (tt0) cc_final: 0.7424 (tt0) REVERT: E 56 ASP cc_start: 0.7914 (t0) cc_final: 0.7231 (t0) REVERT: E 334 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7645 (mmtm) REVERT: F 1 MET cc_start: 0.6725 (ptt) cc_final: 0.6071 (ttt) REVERT: G 136 ASP cc_start: 0.7340 (p0) cc_final: 0.6906 (p0) REVERT: G 167 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6658 (mt-10) REVERT: G 249 ASP cc_start: 0.7218 (m-30) cc_final: 0.6940 (m-30) outliers start: 3 outliers final: 1 residues processed: 161 average time/residue: 0.4113 time to fit residues: 102.2596 Evaluate side-chains 135 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN D 365 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24688 Z= 0.333 Angle : 0.555 6.682 33485 Z= 0.290 Chirality : 0.047 0.193 3856 Planarity : 0.004 0.053 4363 Dihedral : 8.086 175.075 3580 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 0.04 % Allowed : 2.14 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3115 helix: 1.18 (0.15), residues: 1223 sheet: 0.38 (0.22), residues: 532 loop : -0.34 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 215 PHE 0.015 0.001 PHE D 257 TYR 0.016 0.001 TYR C 389 ARG 0.005 0.000 ARG E 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6828 (tm-30) REVERT: A 87 GLU cc_start: 0.8333 (tt0) cc_final: 0.7625 (tt0) REVERT: B 89 ARG cc_start: 0.6509 (ptp-110) cc_final: 0.6093 (ptp-170) REVERT: C 272 GLU cc_start: 0.7818 (tt0) cc_final: 0.7377 (tt0) REVERT: C 407 GLN cc_start: 0.7902 (mt0) cc_final: 0.6895 (tp40) REVERT: E 56 ASP cc_start: 0.7897 (t0) cc_final: 0.7225 (t0) REVERT: E 395 GLU cc_start: 0.7617 (mp0) cc_final: 0.7404 (mp0) REVERT: F 1 MET cc_start: 0.6653 (ptt) cc_final: 0.6053 (ttt) REVERT: F 469 MET cc_start: 0.7720 (ptp) cc_final: 0.7495 (ptm) REVERT: G 249 ASP cc_start: 0.7225 (m-30) cc_final: 0.6956 (m-30) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.3963 time to fit residues: 101.2130 Evaluate side-chains 136 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 365 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24688 Z= 0.219 Angle : 0.505 5.764 33485 Z= 0.263 Chirality : 0.044 0.164 3856 Planarity : 0.004 0.052 4363 Dihedral : 7.769 177.404 3580 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3115 helix: 1.40 (0.15), residues: 1220 sheet: 0.48 (0.23), residues: 523 loop : -0.20 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.014 0.001 PHE D 257 TYR 0.013 0.001 TYR C 389 ARG 0.005 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 87 GLU cc_start: 0.8324 (tt0) cc_final: 0.7629 (tt0) REVERT: B 89 ARG cc_start: 0.6562 (ptp-110) cc_final: 0.6165 (ptp-170) REVERT: C 272 GLU cc_start: 0.7793 (tt0) cc_final: 0.7310 (tt0) REVERT: C 407 GLN cc_start: 0.7928 (mt0) cc_final: 0.7100 (tp40) REVERT: E 56 ASP cc_start: 0.7826 (t0) cc_final: 0.7143 (t0) REVERT: E 333 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7498 (ttm110) REVERT: E 395 GLU cc_start: 0.7531 (mp0) cc_final: 0.7329 (mp0) REVERT: F 1 MET cc_start: 0.6645 (ptt) cc_final: 0.5931 (ttp) REVERT: F 469 MET cc_start: 0.7717 (ptp) cc_final: 0.7517 (ptm) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.4270 time to fit residues: 104.8267 Evaluate side-chains 135 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 170 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 365 GLN E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24688 Z= 0.291 Angle : 0.534 6.012 33485 Z= 0.278 Chirality : 0.046 0.186 3856 Planarity : 0.004 0.051 4363 Dihedral : 7.822 176.996 3580 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.50 % Rotamer: Outliers : 0.04 % Allowed : 1.17 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3115 helix: 1.36 (0.15), residues: 1221 sheet: 0.47 (0.23), residues: 523 loop : -0.26 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.015 0.001 PHE C 463 TYR 0.019 0.001 TYR C 389 ARG 0.003 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 87 GLU cc_start: 0.8327 (tt0) cc_final: 0.7633 (tt0) REVERT: C 272 GLU cc_start: 0.7822 (tt0) cc_final: 0.7363 (tt0) REVERT: E 56 ASP cc_start: 0.7855 (t0) cc_final: 0.7187 (t0) REVERT: E 395 GLU cc_start: 0.7512 (mp0) cc_final: 0.7283 (mp0) REVERT: F 1 MET cc_start: 0.6654 (ptt) cc_final: 0.5930 (ttp) REVERT: F 469 MET cc_start: 0.7707 (ptp) cc_final: 0.7502 (ptm) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.4168 time to fit residues: 102.4915 Evaluate side-chains 135 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24688 Z= 0.168 Angle : 0.482 7.450 33485 Z= 0.250 Chirality : 0.044 0.155 3856 Planarity : 0.004 0.051 4363 Dihedral : 7.555 178.669 3580 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 0.04 % Allowed : 0.90 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3115 helix: 1.57 (0.15), residues: 1223 sheet: 0.63 (0.23), residues: 511 loop : -0.13 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 363 PHE 0.011 0.001 PHE F 257 TYR 0.022 0.001 TYR C 389 ARG 0.002 0.000 ARG D 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6756 (tm-30) REVERT: A 87 GLU cc_start: 0.8221 (tt0) cc_final: 0.7559 (tt0) REVERT: C 272 GLU cc_start: 0.7697 (tt0) cc_final: 0.7199 (tt0) REVERT: C 407 GLN cc_start: 0.7850 (mt0) cc_final: 0.6800 (tp40) REVERT: E 56 ASP cc_start: 0.7824 (t0) cc_final: 0.7110 (t0) REVERT: F 1 MET cc_start: 0.6521 (ptt) cc_final: 0.5915 (ttp) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.4413 time to fit residues: 108.9415 Evaluate side-chains 131 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24688 Z= 0.351 Angle : 0.571 9.478 33485 Z= 0.297 Chirality : 0.047 0.187 3856 Planarity : 0.004 0.052 4363 Dihedral : 7.864 177.009 3580 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3115 helix: 1.34 (0.15), residues: 1212 sheet: 0.53 (0.23), residues: 513 loop : -0.26 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 425 PHE 0.016 0.002 PHE C 463 TYR 0.022 0.001 TYR C 389 ARG 0.007 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 2.936 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6755 (tm-30) REVERT: A 87 GLU cc_start: 0.8332 (tt0) cc_final: 0.7635 (tt0) REVERT: B 382 LEU cc_start: 0.7442 (tp) cc_final: 0.7240 (tp) REVERT: B 451 GLU cc_start: 0.8002 (tt0) cc_final: 0.7617 (tp30) REVERT: C 272 GLU cc_start: 0.7844 (tt0) cc_final: 0.7416 (tt0) REVERT: C 407 GLN cc_start: 0.7908 (mt0) cc_final: 0.6892 (tp40) REVERT: E 56 ASP cc_start: 0.7871 (t0) cc_final: 0.7200 (t0) REVERT: F 1 MET cc_start: 0.6623 (ptt) cc_final: 0.5913 (ttp) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.4036 time to fit residues: 98.5879 Evaluate side-chains 131 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.6980 chunk 294 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24688 Z= 0.149 Angle : 0.480 6.341 33485 Z= 0.248 Chirality : 0.043 0.158 3856 Planarity : 0.004 0.052 4363 Dihedral : 7.459 175.250 3580 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 0.27 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: 1.01 (0.15), residues: 3115 helix: 1.62 (0.15), residues: 1212 sheet: 0.69 (0.23), residues: 516 loop : -0.12 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 425 PHE 0.014 0.001 PHE B 444 TYR 0.018 0.001 TYR C 389 ARG 0.005 0.000 ARG B 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.826 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6737 (tm-30) REVERT: A 87 GLU cc_start: 0.8208 (tt0) cc_final: 0.7531 (tt0) REVERT: B 89 ARG cc_start: 0.6573 (ptp-110) cc_final: 0.6285 (ptp-170) REVERT: B 451 GLU cc_start: 0.7944 (tt0) cc_final: 0.7578 (tp30) REVERT: C 272 GLU cc_start: 0.7690 (tt0) cc_final: 0.7185 (tt0) REVERT: C 407 GLN cc_start: 0.7884 (mt0) cc_final: 0.7227 (tp40) REVERT: D 376 ARG cc_start: 0.6980 (mmm160) cc_final: 0.6515 (mmm160) REVERT: E 56 ASP cc_start: 0.7812 (t0) cc_final: 0.7083 (t0) REVERT: F 1 MET cc_start: 0.6552 (ptt) cc_final: 0.5933 (ttp) REVERT: F 389 MET cc_start: 0.7123 (ttm) cc_final: 0.6853 (ttp) REVERT: G 167 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6813 (mt-10) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.4095 time to fit residues: 102.6905 Evaluate side-chains 134 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.063680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.052333 restraints weight = 57099.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.052002 restraints weight = 54453.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.052364 restraints weight = 53124.663| |-----------------------------------------------------------------------------| r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 24688 Z= 0.484 Angle : 0.647 10.268 33485 Z= 0.335 Chirality : 0.050 0.224 3856 Planarity : 0.005 0.055 4363 Dihedral : 8.058 176.930 3580 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: 0.52 (0.15), residues: 3115 helix: 1.16 (0.15), residues: 1215 sheet: 0.47 (0.23), residues: 520 loop : -0.36 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 363 PHE 0.029 0.002 PHE F 322 TYR 0.020 0.002 TYR C 389 ARG 0.007 0.001 ARG E 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.34 seconds wall clock time: 71 minutes 39.14 seconds (4299.14 seconds total)