Starting phenix.real_space_refine on Fri Sep 27 13:47:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/09_2024/7jpo_22417_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/09_2024/7jpo_22417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/09_2024/7jpo_22417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/09_2024/7jpo_22417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/09_2024/7jpo_22417_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpo_22417/09_2024/7jpo_22417_neut.cif" } resolution = 3.2 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 9 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 10306 2.51 5 N 2724 2.21 5 O 2962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16087 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2795 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 12, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1726 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 1 Chain: "C" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4863 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 24, 'TRANS': 569} Chain breaks: 7 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 1 Chain: "E" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3301 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 19, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" 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: "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} Time building chain proxies: 9.50, per 1000 atoms: 0.59 Number of scatterers: 16087 At special positions: 0 Unit cell: (90.95, 133.75, 160.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 82 16.00 P 9 15.00 Mg 3 11.99 O 2962 8.00 N 2724 7.00 C 10306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 2.0 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 62.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.659A pdb=" N PHE A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 Processing helix chain 'A' and resid 577 through 588 removed outlier: 4.230A pdb=" N VAL A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 605 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.874A pdb=" N LEU A 624 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 626 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 removed outlier: 4.183A pdb=" N TYR A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 removed outlier: 4.195A pdb=" N GLU A 660 " --> pdb=" O ASP A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.505A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 Processing helix chain 'A' and resid 718 through 736 removed outlier: 3.984A pdb=" N CYS A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 760 removed outlier: 3.563A pdb=" N SER A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 795 through 810 removed outlier: 3.952A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 removed outlier: 3.934A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 859 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.937A pdb=" N ASN B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.679A pdb=" N GLN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.705A pdb=" N HIS B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 368 through 383 Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.942A pdb=" N TRP B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 66 removed outlier: 3.598A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 87 removed outlier: 3.509A pdb=" N PHE C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.834A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.742A pdb=" N ASP C 140 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 141 " --> pdb=" O ALA C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 141' Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.579A pdb=" N SER C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.870A pdb=" N LEU C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.668A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.549A pdb=" N HIS C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 320 through 339 removed outlier: 3.614A pdb=" N PHE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.763A pdb=" N LEU C 344 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.612A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 removed outlier: 3.625A pdb=" N CYS C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.609A pdb=" N GLN C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.524A pdb=" N LEU C 394 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 451 through 461 removed outlier: 3.942A pdb=" N SER C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 removed outlier: 3.521A pdb=" N TYR C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.851A pdb=" N ALA C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 566 Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 575 through 579 Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.646A pdb=" N LEU C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 605 Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.711A pdb=" N LYS C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 660 Processing helix chain 'C' and resid 675 through 690 removed outlier: 3.854A pdb=" N LEU C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 72 through 87 removed outlier: 3.965A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.523A pdb=" N ASN D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.813A pdb=" N GLY D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.717A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.540A pdb=" N LEU D 201 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.652A pdb=" N LEU D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.809A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.784A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.937A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.608A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.684A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.590A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 42 through 54 removed outlier: 3.547A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.515A pdb=" N LEU E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 111 removed outlier: 3.970A pdb=" N THR E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 130 Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.795A pdb=" N TYR E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.594A pdb=" N PHE E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 237 through 243 removed outlier: 3.605A pdb=" N VAL E 241 " --> pdb=" O CYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 268 Proline residue: E 259 - end of helix removed outlier: 3.500A pdb=" N MET E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.713A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 3.502A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 removed outlier: 3.913A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 565 through 569 Processing sheet with id=AA2, first strand: chain 'A' and resid 793 through 794 Processing sheet with id=AA3, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.701A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.533A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 250 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA C 103 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 252 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 100 " --> pdb=" O CYS C 272 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLU C 274 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 102 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N PHE C 276 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 104 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 95 through 100 removed outlier: 6.711A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.171A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE E 33 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER E 158 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE E 35 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 393 through 395 809 hydrogen bonds defined for protein. 2376 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: 4.49 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4137 1.33 - 1.46: 3174 1.46 - 1.58: 8968 1.58 - 1.70: 15 1.70 - 1.82: 125 Bond restraints: 16419 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.97e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 ... (remaining 16414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 21979 4.11 - 8.21: 229 8.21 - 12.32: 16 12.32 - 16.43: 3 16.43 - 20.54: 3 Bond angle restraints: 22230 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 119.33 20.54 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 122.38 14.45 1.00e+00 1.00e+00 2.09e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 123.11 13.72 1.00e+00 1.00e+00 1.88e+02 ... (remaining 22225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8831 17.98 - 35.96: 920 35.96 - 53.94: 173 53.94 - 71.92: 48 71.92 - 89.90: 29 Dihedral angle restraints: 10001 sinusoidal: 4163 harmonic: 5838 Sorted by residual: dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ARG D 359 " pdb=" C ARG D 359 " pdb=" N LYS D 360 " pdb=" CA LYS D 360 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA VAL D 364 " pdb=" C VAL D 364 " pdb=" N TYR D 365 " pdb=" CA TYR D 365 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 9998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2109 0.073 - 0.146: 369 0.146 - 0.219: 47 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE C 435 " pdb=" CA ILE C 435 " pdb=" CG1 ILE C 435 " pdb=" CG2 ILE C 435 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE C 643 " pdb=" CA ILE C 643 " pdb=" CG1 ILE C 643 " pdb=" CG2 ILE C 643 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 2535 not shown) Planarity restraints: 2798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 639 " -0.046 2.00e-02 2.50e+03 4.75e-02 5.65e+01 pdb=" CG TRP A 639 " 0.127 2.00e-02 2.50e+03 pdb=" CD1 TRP A 639 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP A 639 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 639 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 639 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 639 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 639 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 639 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 238 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO E 239 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO E 239 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 239 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 448 " 0.015 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP C 448 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 448 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 448 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 448 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 448 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 448 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 448 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 448 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 448 " -0.000 2.00e-02 2.50e+03 ... (remaining 2795 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.69: 190 2.69 - 3.30: 17147 3.30 - 3.91: 29885 3.91 - 4.53: 40412 4.53 - 5.14: 63760 Nonbonded interactions: 151394 Sorted by model distance: nonbonded pdb=" OG1 THR E 44 " pdb="MG MG E 502 " model vdw 2.073 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.090 2.170 nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR A 541 " pdb="MG MG A 902 " model vdw 2.123 2.170 nonbonded pdb=" O3B ATP D 901 " pdb="MG MG D 902 " model vdw 2.124 2.170 ... (remaining 151389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 35.870 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.007 0.081 16419 Z= 0.413 Angle : 1.085 20.536 22230 Z= 0.643 Chirality : 0.059 0.365 2538 Planarity : 0.007 0.079 2798 Dihedral : 15.981 89.895 6179 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.16), residues: 1928 helix: -1.10 (0.13), residues: 1105 sheet: -0.33 (0.35), residues: 187 loop : -1.74 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.005 TRP A 639 HIS 0.019 0.002 HIS C 81 PHE 0.046 0.004 PHE D 132 TYR 0.039 0.003 TYR C 609 ARG 0.028 0.002 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 786 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6896 (mpt-90) REVERT: B 418 ILE cc_start: 0.7203 (tt) cc_final: 0.6987 (mt) REVERT: C 705 ARG cc_start: 0.5936 (mmp80) cc_final: 0.5280 (mmp-170) REVERT: D 247 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6568 (tm-30) REVERT: E 133 MET cc_start: 0.8204 (mtp) cc_final: 0.7691 (mtt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3106 time to fit residues: 111.2902 Evaluate side-chains 180 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 0.0060 chunk 176 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS A 688 GLN C 335 HIS C 458 GLN D 46 HIS D 57 HIS D 362 HIS E 100 ASN E 195 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16419 Z= 0.171 Angle : 0.546 6.090 22230 Z= 0.289 Chirality : 0.040 0.163 2538 Planarity : 0.004 0.055 2798 Dihedral : 8.707 82.339 2208 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.67 % Allowed : 6.16 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 1928 helix: 0.36 (0.15), residues: 1123 sheet: -0.13 (0.36), residues: 188 loop : -1.43 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 639 HIS 0.007 0.001 HIS B 336 PHE 0.020 0.001 PHE D 230 TYR 0.016 0.001 TYR A 683 ARG 0.006 0.001 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 201 time to evaluate : 1.912 Fit side-chains REVERT: A 493 LEU cc_start: 0.7782 (mp) cc_final: 0.7553 (mp) REVERT: A 571 MET cc_start: 0.8451 (tpp) cc_final: 0.8176 (mmt) REVERT: A 688 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: A 733 CYS cc_start: 0.7271 (t) cc_final: 0.6907 (t) REVERT: B 418 ILE cc_start: 0.7475 (tt) cc_final: 0.7112 (mt) REVERT: C 705 ARG cc_start: 0.5921 (mmp80) cc_final: 0.5293 (mmp-170) REVERT: D 113 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6438 (mm-30) REVERT: D 284 MET cc_start: 0.7830 (tpt) cc_final: 0.7016 (tpt) REVERT: E 133 MET cc_start: 0.8215 (mtp) cc_final: 0.7843 (mtt) REVERT: E 252 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7743 (mmmt) outliers start: 12 outliers final: 7 residues processed: 207 average time/residue: 0.3113 time to fit residues: 95.5193 Evaluate side-chains 181 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 17 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN E 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.003 0.052 16419 Z= 0.215 Angle : 0.539 6.515 22230 Z= 0.279 Chirality : 0.040 0.165 2538 Planarity : 0.004 0.045 2798 Dihedral : 8.691 85.335 2208 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.11 % Allowed : 8.32 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1928 helix: 0.92 (0.16), residues: 1127 sheet: 0.01 (0.36), residues: 188 loop : -1.36 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 639 HIS 0.008 0.001 HIS B 336 PHE 0.022 0.002 PHE B 441 TYR 0.015 0.001 TYR B 454 ARG 0.003 0.001 ARG C 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 1.934 Fit side-chains REVERT: A 493 LEU cc_start: 0.7877 (mp) cc_final: 0.7590 (mp) REVERT: A 688 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: A 733 CYS cc_start: 0.7354 (t) cc_final: 0.6890 (t) REVERT: A 752 MET cc_start: 0.7683 (tpp) cc_final: 0.7446 (tpp) REVERT: B 418 ILE cc_start: 0.7435 (tt) cc_final: 0.7090 (mt) REVERT: C 462 MET cc_start: 0.7754 (mmm) cc_final: 0.7218 (mmt) REVERT: C 705 ARG cc_start: 0.5836 (mmp80) cc_final: 0.5181 (mmp-170) REVERT: D 113 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6373 (mm-30) REVERT: D 284 MET cc_start: 0.8074 (tpt) cc_final: 0.7441 (tpt) REVERT: E 252 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7797 (mmmt) outliers start: 20 outliers final: 14 residues processed: 192 average time/residue: 0.2945 time to fit residues: 84.0775 Evaluate side-chains 179 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 688 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 654 ASN A 688 GLN A 825 HIS B 270 GLN B 462 ASN C 485 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 GLN D 381 GLN E 27 HIS E 195 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16419 Z= 0.264 Angle : 0.562 8.833 22230 Z= 0.289 Chirality : 0.041 0.168 2538 Planarity : 0.004 0.040 2798 Dihedral : 8.733 88.066 2208 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.50 % Allowed : 10.82 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 1928 helix: 1.02 (0.15), residues: 1139 sheet: 0.01 (0.36), residues: 188 loop : -1.43 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 639 HIS 0.010 0.001 HIS B 336 PHE 0.022 0.002 PHE B 441 TYR 0.018 0.002 TYR B 454 ARG 0.003 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 2.167 Fit side-chains REVERT: A 493 LEU cc_start: 0.7918 (mp) cc_final: 0.7606 (mp) REVERT: A 571 MET cc_start: 0.8533 (tpp) cc_final: 0.8233 (mmt) REVERT: A 688 GLN cc_start: 0.7312 (tp40) cc_final: 0.6509 (tt0) REVERT: B 273 ARG cc_start: 0.7634 (mpt-90) cc_final: 0.7206 (mpt-90) REVERT: B 418 ILE cc_start: 0.7505 (tt) cc_final: 0.7204 (mt) REVERT: C 705 ARG cc_start: 0.5903 (mmp80) cc_final: 0.5499 (mmp-170) REVERT: D 197 ASP cc_start: 0.8658 (p0) cc_final: 0.8320 (p0) REVERT: D 339 TYR cc_start: 0.6566 (m-10) cc_final: 0.6361 (m-10) outliers start: 27 outliers final: 18 residues processed: 201 average time/residue: 0.3229 time to fit residues: 96.5663 Evaluate side-chains 188 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN E 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16419 Z= 0.235 Angle : 0.552 14.471 22230 Z= 0.282 Chirality : 0.040 0.160 2538 Planarity : 0.004 0.037 2798 Dihedral : 8.523 89.288 2208 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.55 % Allowed : 12.15 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1928 helix: 1.19 (0.16), residues: 1137 sheet: 0.04 (0.37), residues: 188 loop : -1.37 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 639 HIS 0.008 0.001 HIS B 336 PHE 0.022 0.002 PHE E 328 TYR 0.020 0.001 TYR B 454 ARG 0.004 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.843 Fit side-chains REVERT: A 493 LEU cc_start: 0.7971 (mp) cc_final: 0.7644 (mp) REVERT: A 571 MET cc_start: 0.8513 (tpp) cc_final: 0.8208 (mmt) REVERT: A 688 GLN cc_start: 0.7034 (tp40) cc_final: 0.6434 (tt0) REVERT: B 418 ILE cc_start: 0.7526 (tt) cc_final: 0.7210 (mt) REVERT: C 462 MET cc_start: 0.7334 (mmm) cc_final: 0.6830 (mmt) REVERT: D 197 ASP cc_start: 0.8660 (p0) cc_final: 0.8334 (p0) REVERT: D 339 TYR cc_start: 0.6708 (m-10) cc_final: 0.6486 (m-10) outliers start: 28 outliers final: 21 residues processed: 196 average time/residue: 0.2989 time to fit residues: 85.7402 Evaluate side-chains 187 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 15 optimal weight: 0.0470 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN E 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16419 Z= 0.163 Angle : 0.503 13.351 22230 Z= 0.258 Chirality : 0.038 0.152 2538 Planarity : 0.004 0.034 2798 Dihedral : 8.121 89.141 2208 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.77 % Allowed : 12.42 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.19), residues: 1928 helix: 1.48 (0.16), residues: 1125 sheet: 0.11 (0.37), residues: 188 loop : -1.28 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 639 HIS 0.005 0.001 HIS C 636 PHE 0.023 0.001 PHE E 328 TYR 0.014 0.001 TYR B 454 ARG 0.003 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 1.816 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.7990 (mp) cc_final: 0.7625 (mp) REVERT: A 571 MET cc_start: 0.8484 (tpp) cc_final: 0.8244 (mmt) REVERT: A 688 GLN cc_start: 0.7046 (tp40) cc_final: 0.6492 (tt0) REVERT: A 721 ARG cc_start: 0.7010 (mmp80) cc_final: 0.6747 (mmp80) REVERT: B 273 ARG cc_start: 0.7708 (mpt-90) cc_final: 0.7490 (mpt-90) REVERT: B 418 ILE cc_start: 0.7509 (tt) cc_final: 0.7175 (mt) REVERT: D 113 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6233 (mm-30) REVERT: D 197 ASP cc_start: 0.8627 (p0) cc_final: 0.8311 (p0) outliers start: 32 outliers final: 21 residues processed: 208 average time/residue: 0.2907 time to fit residues: 89.1864 Evaluate side-chains 194 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 113 optimal weight: 0.0570 chunk 86 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN E 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16419 Z= 0.246 Angle : 0.555 15.524 22230 Z= 0.282 Chirality : 0.040 0.157 2538 Planarity : 0.004 0.037 2798 Dihedral : 8.292 88.567 2208 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.94 % Allowed : 13.48 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1928 helix: 1.39 (0.16), residues: 1133 sheet: 0.01 (0.37), residues: 188 loop : -1.29 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 639 HIS 0.008 0.001 HIS B 336 PHE 0.022 0.002 PHE E 328 TYR 0.017 0.001 TYR A 683 ARG 0.006 0.000 ARG C 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.8037 (mp) cc_final: 0.7665 (mp) REVERT: B 273 ARG cc_start: 0.7704 (mpt-90) cc_final: 0.7473 (mpt-90) REVERT: B 418 ILE cc_start: 0.7612 (tt) cc_final: 0.7286 (mt) REVERT: D 113 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6323 (mm-30) REVERT: D 197 ASP cc_start: 0.8684 (p0) cc_final: 0.8351 (p0) REVERT: D 381 GLN cc_start: 0.7844 (tp40) cc_final: 0.7625 (tp40) outliers start: 35 outliers final: 27 residues processed: 201 average time/residue: 0.3022 time to fit residues: 89.2936 Evaluate side-chains 197 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 170 optimal weight: 0.0370 chunk 179 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS B 394 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16419 Z= 0.172 Angle : 0.528 16.232 22230 Z= 0.267 Chirality : 0.039 0.151 2538 Planarity : 0.004 0.035 2798 Dihedral : 8.031 89.001 2208 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.72 % Allowed : 13.70 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1928 helix: 1.55 (0.16), residues: 1128 sheet: 0.10 (0.38), residues: 188 loop : -1.25 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 639 HIS 0.005 0.001 HIS C 636 PHE 0.024 0.001 PHE E 328 TYR 0.014 0.001 TYR A 683 ARG 0.006 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.942 Fit side-chains REVERT: A 571 MET cc_start: 0.8517 (tpp) cc_final: 0.8258 (mmt) REVERT: A 620 ASP cc_start: 0.7884 (m-30) cc_final: 0.7569 (m-30) REVERT: B 273 ARG cc_start: 0.7676 (mpt-90) cc_final: 0.7467 (mpt-90) REVERT: B 418 ILE cc_start: 0.7569 (tt) cc_final: 0.7225 (mt) REVERT: D 113 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6324 (mm-30) REVERT: D 197 ASP cc_start: 0.8643 (p0) cc_final: 0.8315 (p0) outliers start: 31 outliers final: 25 residues processed: 198 average time/residue: 0.2967 time to fit residues: 86.4235 Evaluate side-chains 194 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 136 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 164 optimal weight: 0.4980 chunk 173 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16419 Z= 0.152 Angle : 0.524 16.774 22230 Z= 0.265 Chirality : 0.038 0.155 2538 Planarity : 0.003 0.032 2798 Dihedral : 7.814 87.537 2208 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.50 % Allowed : 14.31 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1928 helix: 1.61 (0.16), residues: 1130 sheet: 0.18 (0.38), residues: 188 loop : -1.22 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 639 HIS 0.006 0.001 HIS C 636 PHE 0.027 0.001 PHE E 328 TYR 0.017 0.001 TYR A 565 ARG 0.006 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 2.324 Fit side-chains REVERT: A 571 MET cc_start: 0.8460 (tpp) cc_final: 0.8222 (mmt) REVERT: A 620 ASP cc_start: 0.7862 (m-30) cc_final: 0.7555 (m-30) REVERT: B 273 ARG cc_start: 0.7659 (mpt-90) cc_final: 0.7452 (mpt-90) REVERT: B 418 ILE cc_start: 0.7524 (tt) cc_final: 0.7177 (mt) REVERT: C 705 ARG cc_start: 0.5798 (mmp80) cc_final: 0.5118 (mmp-170) REVERT: D 113 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6316 (mm-30) REVERT: D 197 ASP cc_start: 0.8617 (p0) cc_final: 0.8275 (p0) outliers start: 27 outliers final: 22 residues processed: 196 average time/residue: 0.3007 time to fit residues: 87.4319 Evaluate side-chains 193 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN B 394 ASN ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 381 GLN E 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16419 Z= 0.190 Angle : 0.546 17.151 22230 Z= 0.276 Chirality : 0.039 0.163 2538 Planarity : 0.004 0.035 2798 Dihedral : 7.856 89.247 2208 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.44 % Allowed : 14.81 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1928 helix: 1.60 (0.16), residues: 1129 sheet: 0.15 (0.38), residues: 188 loop : -1.23 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 639 HIS 0.008 0.001 HIS B 393 PHE 0.028 0.001 PHE E 328 TYR 0.017 0.001 TYR D 174 ARG 0.006 0.000 ARG A 691 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.979 Fit side-chains REVERT: A 571 MET cc_start: 0.8482 (tpp) cc_final: 0.8243 (mmt) REVERT: A 620 ASP cc_start: 0.7878 (m-30) cc_final: 0.7570 (m-30) REVERT: B 273 ARG cc_start: 0.7643 (mpt-90) cc_final: 0.7438 (mpt-90) REVERT: B 418 ILE cc_start: 0.7562 (tt) cc_final: 0.7216 (mt) REVERT: C 705 ARG cc_start: 0.5814 (mmp80) cc_final: 0.5128 (mmp-170) REVERT: D 113 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6329 (mm-30) REVERT: D 197 ASP cc_start: 0.8631 (p0) cc_final: 0.8277 (p0) outliers start: 26 outliers final: 21 residues processed: 191 average time/residue: 0.3002 time to fit residues: 84.7608 Evaluate side-chains 191 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 60 PHE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 422 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN D 354 GLN E 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.117770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096846 restraints weight = 26832.022| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.82 r_work: 0.3235 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16419 Z= 0.184 Angle : 0.541 16.433 22230 Z= 0.274 Chirality : 0.039 0.156 2538 Planarity : 0.004 0.035 2798 Dihedral : 7.813 89.516 2208 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.39 % Allowed : 14.75 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1928 helix: 1.61 (0.16), residues: 1129 sheet: 0.16 (0.38), residues: 188 loop : -1.23 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP A 639 HIS 0.006 0.001 HIS B 336 PHE 0.028 0.001 PHE E 328 TYR 0.018 0.001 TYR A 565 ARG 0.006 0.000 ARG A 691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3369.00 seconds wall clock time: 61 minutes 1.34 seconds (3661.34 seconds total)