Starting phenix.real_space_refine on Fri Nov 15 10:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwn_35774/11_2024/8iwn_35774.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwn_35774/11_2024/8iwn_35774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwn_35774/11_2024/8iwn_35774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwn_35774/11_2024/8iwn_35774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwn_35774/11_2024/8iwn_35774.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwn_35774/11_2024/8iwn_35774.cif" } resolution = 3.0 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= 0.004 sd= 0.147 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 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5682 2.51 5 N 1470 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8764 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4350 Classifications: {'peptide': 559} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 540} Chain breaks: 4 Chain: "C" Number of atoms: 4350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4350 Classifications: {'peptide': 559} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 540} Chain breaks: 4 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.39, per 1000 atoms: 0.62 Number of scatterers: 8764 At special positions: 0 Unit cell: (100.1, 75.9, 127.6, 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 58 16.00 P 6 15.00 Mg 2 11.99 O 1546 8.00 N 1470 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 622 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 58.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.733A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.507A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.579A pdb=" N GLU A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.777A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.521A pdb=" N GLY A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.753A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.964A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.731A pdb=" N LEU A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.541A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.641A pdb=" N LEU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.888A pdb=" N LYS A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.505A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.915A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.697A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.545A pdb=" N GLY A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.505A pdb=" N MET A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 507 removed outlier: 3.551A pdb=" N VAL A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix removed outlier: 3.611A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.577A pdb=" N THR A 519 " --> pdb=" O PRO A 515 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 4.223A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.736A pdb=" N MET A 576 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.230A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 623 through 627 removed outlier: 3.590A pdb=" N GLU A 627 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.635A pdb=" N LEU A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 3.524A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.732A pdb=" N LEU C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 169 removed outlier: 3.506A pdb=" N PHE C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.580A pdb=" N GLU C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.778A pdb=" N ARG C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 256 removed outlier: 3.521A pdb=" N GLY C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.754A pdb=" N PHE C 275 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.965A pdb=" N SER C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.731A pdb=" N LEU C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.541A pdb=" N THR C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 349 removed outlier: 3.642A pdb=" N LEU C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 357 removed outlier: 3.887A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 408 through 425 removed outlier: 3.505A pdb=" N VAL C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 455 removed outlier: 3.916A pdb=" N GLY C 438 " --> pdb=" O HIS C 434 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Proline residue: C 451 - end of helix removed outlier: 3.697A pdb=" N ASN C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 473 removed outlier: 3.545A pdb=" N GLY C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.506A pdb=" N MET C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 488 " --> pdb=" O HIS C 484 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 489 " --> pdb=" O VAL C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 507 removed outlier: 3.551A pdb=" N VAL C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix removed outlier: 3.611A pdb=" N THR C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TRP C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 541 removed outlier: 3.577A pdb=" N THR C 519 " --> pdb=" O PRO C 515 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 561 removed outlier: 4.223A pdb=" N THR C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE C 550 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.736A pdb=" N MET C 576 " --> pdb=" O MET C 573 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 577 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 removed outlier: 4.230A pdb=" N TYR C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 588 " --> pdb=" O TYR C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 604 Processing helix chain 'C' and resid 623 through 627 removed outlier: 3.592A pdb=" N GLU C 627 " --> pdb=" O PHE C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.635A pdb=" N LEU C 642 " --> pdb=" O SER C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 658 removed outlier: 3.524A pdb=" N TYR C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 653 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 91 removed outlier: 6.452A pdb=" N TYR A 47 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 85 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 45 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 87 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 43 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY A 89 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS A 41 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.341A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASP A 231 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL A 145 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 277 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 81 through 91 removed outlier: 6.451A pdb=" N TYR C 47 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 85 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 45 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 87 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL C 43 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY C 89 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS C 41 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE C 42 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU C 128 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP C 44 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS C 126 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 142 through 145 removed outlier: 6.341A pdb=" N GLY C 143 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP C 231 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL C 145 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 277 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 278 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 289 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 280 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1044 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: 2.41 Time building geometry restraints manager: 2.47 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: 2613 1.33 - 1.45: 1520 1.45 - 1.57: 4709 1.57 - 1.69: 10 1.69 - 1.81: 92 Bond restraints: 8944 Sorted by residual: bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.29e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.26e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.47e+01 bond pdb=" C5 ATP C 701 " pdb=" C6 ATP C 701 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.39e+01 bond pdb=" C4 ATP C 701 " pdb=" N9 ATP C 701 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.55e+01 ... (remaining 8939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 11641 2.73 - 5.46: 413 5.46 - 8.19: 56 8.19 - 10.93: 18 10.93 - 13.66: 6 Bond angle restraints: 12134 Sorted by residual: angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 126.21 13.66 1.00e+00 1.00e+00 1.87e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 126.25 13.62 1.00e+00 1.00e+00 1.85e+02 angle pdb=" PA ATP C 701 " pdb=" O3A ATP C 701 " pdb=" PB ATP C 701 " ideal model delta sigma weight residual 136.83 128.20 8.63 1.00e+00 1.00e+00 7.45e+01 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 128.22 8.61 1.00e+00 1.00e+00 7.41e+01 angle pdb=" C5 ATP C 701 " pdb=" C4 ATP C 701 " pdb=" N3 ATP C 701 " ideal model delta sigma weight residual 126.80 119.11 7.69 1.00e+00 1.00e+00 5.92e+01 ... (remaining 12129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 4981 15.76 - 31.52: 255 31.52 - 47.28: 56 47.28 - 63.04: 4 63.04 - 78.80: 8 Dihedral angle restraints: 5304 sinusoidal: 2104 harmonic: 3200 Sorted by residual: dihedral pdb=" CA SER A 405 " pdb=" C SER A 405 " pdb=" N PHE A 406 " pdb=" CA PHE A 406 " ideal model delta harmonic sigma weight residual 180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA SER C 405 " pdb=" C SER C 405 " pdb=" N PHE C 406 " pdb=" CA PHE C 406 " ideal model delta harmonic sigma weight residual -180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ASP C 176 " pdb=" C ASP C 176 " pdb=" N VAL C 177 " pdb=" CA VAL C 177 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 952 0.063 - 0.127: 414 0.127 - 0.190: 55 0.190 - 0.253: 15 0.253 - 0.316: 6 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CB VAL C 456 " pdb=" CA VAL C 456 " pdb=" CG1 VAL C 456 " pdb=" CG2 VAL C 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB VAL A 456 " pdb=" CA VAL A 456 " pdb=" CG1 VAL A 456 " pdb=" CG2 VAL A 456 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB ILE A 91 " pdb=" CA ILE A 91 " pdb=" CG1 ILE A 91 " pdb=" CG2 ILE A 91 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1439 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 96 " 0.019 2.00e-02 2.50e+03 1.98e-02 6.83e+00 pdb=" CG PHE C 96 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 96 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 96 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 96 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 96 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 96 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 96 " -0.019 2.00e-02 2.50e+03 1.96e-02 6.74e+00 pdb=" CG PHE A 96 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 96 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 96 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 96 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 96 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 96 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 569 " 0.043 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO A 570 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 570 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 570 " 0.035 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3190 2.90 - 3.40: 7618 3.40 - 3.90: 13108 3.90 - 4.40: 16119 4.40 - 4.90: 27439 Nonbonded interactions: 67474 Sorted by model distance: nonbonded pdb=" N ASP C 238 " pdb=" OD1 ASP C 238 " model vdw 2.398 3.120 nonbonded pdb=" N ASP A 238 " pdb=" OD1 ASP A 238 " model vdw 2.398 3.120 nonbonded pdb=" O ASN C 336 " pdb=" OG1 THR C 340 " model vdw 2.401 3.040 nonbonded pdb=" O ASN A 336 " pdb=" OG1 THR A 340 " model vdw 2.401 3.040 nonbonded pdb=" O THR C 192 " pdb=" OG1 THR C 192 " model vdw 2.419 3.040 ... (remaining 67469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 662 or resid 701)) selection = chain 'C' } 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: 0.590 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.520 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.114 8944 Z= 0.846 Angle : 1.217 13.657 12134 Z= 0.681 Chirality : 0.069 0.316 1442 Planarity : 0.008 0.064 1478 Dihedral : 10.546 78.801 3242 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -5.96 (0.17), residues: 1098 helix: -4.65 (0.08), residues: 626 sheet: -0.59 (0.56), residues: 82 loop : -3.07 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP A 426 HIS 0.016 0.004 HIS C 427 PHE 0.045 0.004 PHE C 96 TYR 0.023 0.003 TYR C 526 ARG 0.010 0.002 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.047 Fit side-chains REVERT: A 50 LYS cc_start: 0.8042 (ttmp) cc_final: 0.7808 (tttp) REVERT: A 491 MET cc_start: 0.7966 (tpp) cc_final: 0.7619 (tpt) REVERT: A 545 LYS cc_start: 0.9252 (tttm) cc_final: 0.9044 (tttt) REVERT: A 599 GLU cc_start: 0.7530 (tt0) cc_final: 0.6110 (pm20) REVERT: C 50 LYS cc_start: 0.7998 (ttmp) cc_final: 0.7751 (tttp) REVERT: C 202 THR cc_start: 0.8611 (p) cc_final: 0.8356 (t) REVERT: C 491 MET cc_start: 0.7983 (tpp) cc_final: 0.7639 (tpt) REVERT: C 545 LYS cc_start: 0.9243 (tttm) cc_final: 0.9040 (tttt) REVERT: C 599 GLU cc_start: 0.7559 (tt0) cc_final: 0.6193 (pm20) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.8330 time to fit residues: 229.0692 Evaluate side-chains 84 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8944 Z= 0.183 Angle : 0.587 6.342 12134 Z= 0.310 Chirality : 0.043 0.159 1442 Planarity : 0.006 0.063 1478 Dihedral : 7.799 64.777 1278 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.37 % Allowed : 6.21 % Favored : 92.42 % 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: -3.89 (0.21), residues: 1098 helix: -2.75 (0.16), residues: 650 sheet: -0.74 (0.49), residues: 110 loop : -2.39 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 447 HIS 0.007 0.001 HIS C 427 PHE 0.018 0.001 PHE A 96 TYR 0.013 0.001 TYR A 586 ARG 0.006 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.024 Fit side-chains REVERT: A 277 THR cc_start: 0.8895 (m) cc_final: 0.8593 (p) REVERT: A 403 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6108 (p90) REVERT: A 491 MET cc_start: 0.7892 (tpp) cc_final: 0.7588 (tpt) REVERT: A 599 GLU cc_start: 0.7537 (tt0) cc_final: 0.6192 (pm20) REVERT: C 202 THR cc_start: 0.8673 (p) cc_final: 0.8442 (t) REVERT: C 277 THR cc_start: 0.8879 (m) cc_final: 0.8597 (p) REVERT: C 403 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6162 (p90) REVERT: C 491 MET cc_start: 0.7856 (tpp) cc_final: 0.7545 (tpt) REVERT: C 599 GLU cc_start: 0.7569 (tt0) cc_final: 0.6267 (pm20) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 1.6262 time to fit residues: 184.8838 Evaluate side-chains 97 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8944 Z= 0.189 Angle : 0.551 6.140 12134 Z= 0.287 Chirality : 0.043 0.150 1442 Planarity : 0.005 0.071 1478 Dihedral : 7.098 62.580 1278 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.68 % Allowed : 9.37 % Favored : 88.95 % 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: -2.58 (0.24), residues: 1098 helix: -1.55 (0.19), residues: 648 sheet: -0.53 (0.48), residues: 110 loop : -2.08 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 447 HIS 0.006 0.001 HIS C 427 PHE 0.014 0.001 PHE A 96 TYR 0.014 0.001 TYR C 586 ARG 0.008 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.024 Fit side-chains REVERT: A 403 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.6668 (p-80) REVERT: A 491 MET cc_start: 0.7839 (tpp) cc_final: 0.7529 (tpt) REVERT: A 599 GLU cc_start: 0.7687 (tt0) cc_final: 0.6147 (pm20) REVERT: A 626 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7773 (pm20) REVERT: C 403 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6521 (p90) REVERT: C 491 MET cc_start: 0.7839 (tpp) cc_final: 0.7545 (tpt) REVERT: C 599 GLU cc_start: 0.7682 (tt0) cc_final: 0.6185 (pm20) REVERT: C 626 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7753 (pm20) outliers start: 16 outliers final: 9 residues processed: 101 average time/residue: 1.4387 time to fit residues: 154.1248 Evaluate side-chains 92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS C 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8944 Z= 0.211 Angle : 0.546 5.972 12134 Z= 0.285 Chirality : 0.044 0.146 1442 Planarity : 0.005 0.071 1478 Dihedral : 7.088 62.235 1278 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.21 % Allowed : 10.11 % Favored : 87.68 % 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: -2.09 (0.25), residues: 1098 helix: -1.10 (0.20), residues: 650 sheet: -0.36 (0.47), residues: 110 loop : -1.99 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.007 0.001 HIS A 427 PHE 0.014 0.001 PHE C 96 TYR 0.012 0.001 TYR A 586 ARG 0.005 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 1.000 Fit side-chains REVERT: A 136 LYS cc_start: 0.8653 (tptm) cc_final: 0.8359 (tptp) REVERT: A 403 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.7161 (p90) REVERT: A 491 MET cc_start: 0.7863 (tpp) cc_final: 0.7547 (tpt) REVERT: A 599 GLU cc_start: 0.7687 (tt0) cc_final: 0.6150 (pm20) REVERT: A 626 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7703 (pm20) REVERT: A 627 GLU cc_start: 0.8314 (mp0) cc_final: 0.7661 (mp0) REVERT: C 136 LYS cc_start: 0.8642 (tptm) cc_final: 0.8349 (tptp) REVERT: C 491 MET cc_start: 0.7877 (tpp) cc_final: 0.7573 (tpt) REVERT: C 599 GLU cc_start: 0.7669 (tt0) cc_final: 0.6131 (pm20) REVERT: C 627 GLU cc_start: 0.8306 (mp0) cc_final: 0.7805 (mp0) outliers start: 21 outliers final: 12 residues processed: 96 average time/residue: 1.4199 time to fit residues: 144.5905 Evaluate side-chains 93 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 8944 Z= 0.497 Angle : 0.735 8.737 12134 Z= 0.374 Chirality : 0.053 0.197 1442 Planarity : 0.006 0.076 1478 Dihedral : 7.904 57.302 1278 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.05 % Allowed : 9.58 % Favored : 87.37 % 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: -2.24 (0.24), residues: 1098 helix: -1.30 (0.19), residues: 662 sheet: 0.39 (0.56), residues: 82 loop : -2.01 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 447 HIS 0.012 0.002 HIS A 427 PHE 0.020 0.002 PHE A 96 TYR 0.017 0.002 TYR A 526 ARG 0.005 0.001 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.994 Fit side-chains REVERT: A 136 LYS cc_start: 0.8715 (tptm) cc_final: 0.8409 (tptp) REVERT: A 491 MET cc_start: 0.7968 (tpp) cc_final: 0.7670 (tpt) REVERT: A 599 GLU cc_start: 0.7752 (tt0) cc_final: 0.6225 (pm20) REVERT: C 136 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8403 (tptp) REVERT: C 403 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7094 (p90) REVERT: C 491 MET cc_start: 0.7969 (tpp) cc_final: 0.7688 (tpt) REVERT: C 599 GLU cc_start: 0.7747 (tt0) cc_final: 0.6234 (pm20) outliers start: 29 outliers final: 16 residues processed: 102 average time/residue: 1.3944 time to fit residues: 151.1637 Evaluate side-chains 100 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8944 Z= 0.174 Angle : 0.528 5.397 12134 Z= 0.277 Chirality : 0.043 0.152 1442 Planarity : 0.004 0.073 1478 Dihedral : 7.131 62.828 1278 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.63 % Allowed : 10.32 % Favored : 87.05 % 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: -1.63 (0.25), residues: 1098 helix: -0.76 (0.20), residues: 652 sheet: -0.04 (0.47), residues: 110 loop : -1.81 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.006 0.001 HIS C 427 PHE 0.011 0.001 PHE A 96 TYR 0.010 0.001 TYR A 526 ARG 0.004 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.988 Fit side-chains REVERT: A 136 LYS cc_start: 0.8621 (tptm) cc_final: 0.8365 (tptp) REVERT: A 403 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.7020 (p90) REVERT: A 491 MET cc_start: 0.7890 (tpp) cc_final: 0.7565 (tpt) REVERT: A 599 GLU cc_start: 0.7676 (tt0) cc_final: 0.6140 (pm20) REVERT: A 650 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.5911 (mtt90) REVERT: C 136 LYS cc_start: 0.8626 (tptm) cc_final: 0.8373 (tptp) REVERT: C 403 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6831 (p90) REVERT: C 491 MET cc_start: 0.7910 (tpp) cc_final: 0.7587 (tpt) REVERT: C 599 GLU cc_start: 0.7661 (tt0) cc_final: 0.6147 (pm20) REVERT: C 626 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7753 (pm20) outliers start: 25 outliers final: 12 residues processed: 101 average time/residue: 1.4413 time to fit residues: 154.7642 Evaluate side-chains 99 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 569 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS C 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8944 Z= 0.240 Angle : 0.562 6.106 12134 Z= 0.291 Chirality : 0.045 0.154 1442 Planarity : 0.005 0.074 1478 Dihedral : 7.202 61.506 1278 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.42 % Allowed : 10.32 % Favored : 87.26 % 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: -1.43 (0.25), residues: 1098 helix: -0.59 (0.21), residues: 654 sheet: 0.07 (0.46), residues: 110 loop : -1.78 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 447 HIS 0.007 0.001 HIS A 427 PHE 0.013 0.001 PHE C 499 TYR 0.011 0.001 TYR C 586 ARG 0.003 0.000 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8604 (tptm) cc_final: 0.8327 (tptp) REVERT: A 403 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6549 (p-80) REVERT: A 489 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 491 MET cc_start: 0.7921 (tpp) cc_final: 0.7583 (tpt) REVERT: A 599 GLU cc_start: 0.7670 (tt0) cc_final: 0.6144 (pm20) REVERT: A 627 GLU cc_start: 0.8212 (mp0) cc_final: 0.7710 (mp0) REVERT: A 650 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.5917 (mtt90) REVERT: C 136 LYS cc_start: 0.8629 (tptm) cc_final: 0.8348 (tptp) REVERT: C 403 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.7207 (p90) REVERT: C 491 MET cc_start: 0.7938 (tpp) cc_final: 0.7609 (tpt) REVERT: C 599 GLU cc_start: 0.7662 (tt0) cc_final: 0.6152 (pm20) REVERT: C 626 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7750 (pm20) REVERT: C 627 GLU cc_start: 0.8213 (mp0) cc_final: 0.7579 (mp0) REVERT: C 650 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.5911 (mtt90) outliers start: 23 outliers final: 15 residues processed: 102 average time/residue: 1.4462 time to fit residues: 156.5697 Evaluate side-chains 107 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.0000 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8944 Z= 0.187 Angle : 0.532 7.971 12134 Z= 0.276 Chirality : 0.043 0.149 1442 Planarity : 0.004 0.074 1478 Dihedral : 7.037 62.280 1278 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.63 % Allowed : 10.63 % Favored : 86.74 % 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: -1.18 (0.26), residues: 1098 helix: -0.38 (0.21), residues: 654 sheet: 0.16 (0.46), residues: 110 loop : -1.68 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 447 HIS 0.006 0.001 HIS C 427 PHE 0.012 0.001 PHE C 499 TYR 0.010 0.001 TYR C 586 ARG 0.003 0.000 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.086 Fit side-chains REVERT: A 136 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8274 (tptp) REVERT: A 137 GLN cc_start: 0.7608 (mp10) cc_final: 0.7288 (mm-40) REVERT: A 403 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6611 (p90) REVERT: A 489 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 491 MET cc_start: 0.7900 (tpp) cc_final: 0.7573 (tpt) REVERT: A 599 GLU cc_start: 0.7636 (tt0) cc_final: 0.6105 (pm20) REVERT: A 626 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7722 (pm20) REVERT: A 627 GLU cc_start: 0.8195 (mp0) cc_final: 0.7519 (mp0) REVERT: A 650 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.5928 (mtt90) REVERT: C 136 LYS cc_start: 0.8555 (tptm) cc_final: 0.8300 (tptp) REVERT: C 137 GLN cc_start: 0.7602 (mp10) cc_final: 0.7297 (mm-40) REVERT: C 489 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7689 (mp) REVERT: C 491 MET cc_start: 0.7909 (tpp) cc_final: 0.7604 (tpt) REVERT: C 599 GLU cc_start: 0.7649 (tt0) cc_final: 0.6153 (pm20) REVERT: C 626 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7721 (pm20) REVERT: C 627 GLU cc_start: 0.8197 (mp0) cc_final: 0.7507 (mp0) REVERT: C 650 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.5921 (mtt90) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 1.4009 time to fit residues: 157.5106 Evaluate side-chains 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8944 Z= 0.214 Angle : 0.549 8.404 12134 Z= 0.283 Chirality : 0.044 0.149 1442 Planarity : 0.004 0.074 1478 Dihedral : 7.057 62.104 1278 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.74 % Allowed : 10.21 % Favored : 87.05 % 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: -1.01 (0.26), residues: 1098 helix: -0.28 (0.21), residues: 654 sheet: 0.83 (0.56), residues: 82 loop : -1.57 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.006 0.001 HIS C 427 PHE 0.012 0.001 PHE C 499 TYR 0.011 0.001 TYR C 586 ARG 0.003 0.000 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.977 Fit side-chains REVERT: A 136 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8312 (tptp) REVERT: A 137 GLN cc_start: 0.7663 (mp10) cc_final: 0.7362 (mm-40) REVERT: A 403 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7206 (p90) REVERT: A 489 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 491 MET cc_start: 0.7936 (tpp) cc_final: 0.7631 (tpt) REVERT: A 492 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 599 GLU cc_start: 0.7630 (tt0) cc_final: 0.6102 (pm20) REVERT: A 626 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7719 (pm20) REVERT: A 627 GLU cc_start: 0.8189 (mp0) cc_final: 0.7507 (mp0) REVERT: A 650 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.5916 (mtt90) REVERT: C 136 LYS cc_start: 0.8562 (tptm) cc_final: 0.8308 (tptp) REVERT: C 137 GLN cc_start: 0.7652 (mp10) cc_final: 0.7368 (mm-40) REVERT: C 403 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.7127 (p90) REVERT: C 489 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7694 (mp) REVERT: C 491 MET cc_start: 0.7924 (tpp) cc_final: 0.7583 (tpt) REVERT: C 599 GLU cc_start: 0.7633 (tt0) cc_final: 0.6113 (pm20) REVERT: C 626 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7709 (pm20) REVERT: C 627 GLU cc_start: 0.8195 (mp0) cc_final: 0.7509 (mp0) REVERT: C 650 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.5908 (mtt90) outliers start: 26 outliers final: 15 residues processed: 108 average time/residue: 1.3925 time to fit residues: 159.6538 Evaluate side-chains 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8944 Z= 0.192 Angle : 0.534 7.535 12134 Z= 0.276 Chirality : 0.043 0.149 1442 Planarity : 0.004 0.073 1478 Dihedral : 6.981 62.452 1278 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.42 % Allowed : 10.95 % Favored : 86.63 % 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: -0.93 (0.26), residues: 1098 helix: -0.17 (0.21), residues: 654 sheet: 0.28 (0.46), residues: 110 loop : -1.63 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.006 0.001 HIS C 427 PHE 0.012 0.001 PHE C 499 TYR 0.010 0.001 TYR A 586 ARG 0.003 0.000 ARG C 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.975 Fit side-chains REVERT: A 136 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8344 (tptp) REVERT: A 137 GLN cc_start: 0.7664 (mp10) cc_final: 0.7387 (mm-40) REVERT: A 403 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6470 (p90) REVERT: A 489 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 491 MET cc_start: 0.7912 (tpp) cc_final: 0.7618 (tpt) REVERT: A 492 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 599 GLU cc_start: 0.7623 (tt0) cc_final: 0.6101 (pm20) REVERT: A 626 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7738 (pm20) REVERT: A 627 GLU cc_start: 0.8181 (mp0) cc_final: 0.7444 (mp0) REVERT: A 650 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.5935 (mtt90) REVERT: C 136 LYS cc_start: 0.8591 (tptm) cc_final: 0.8304 (tptp) REVERT: C 137 GLN cc_start: 0.7655 (mp10) cc_final: 0.7389 (mm-40) REVERT: C 403 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.7213 (p90) REVERT: C 489 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7706 (mp) REVERT: C 491 MET cc_start: 0.7932 (tpp) cc_final: 0.7593 (tpt) REVERT: C 599 GLU cc_start: 0.7628 (tt0) cc_final: 0.6115 (pm20) REVERT: C 626 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7706 (pm20) REVERT: C 627 GLU cc_start: 0.8186 (mp0) cc_final: 0.7502 (mp0) REVERT: C 650 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.5923 (mtt90) outliers start: 23 outliers final: 15 residues processed: 105 average time/residue: 1.4370 time to fit residues: 159.8901 Evaluate side-chains 114 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 650 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS C 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.134159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103167 restraints weight = 9551.120| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.59 r_work: 0.2925 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8944 Z= 0.164 Angle : 0.515 7.132 12134 Z= 0.267 Chirality : 0.042 0.149 1442 Planarity : 0.004 0.073 1478 Dihedral : 6.845 62.982 1278 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.53 % Allowed : 10.95 % Favored : 86.53 % 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: -0.75 (0.26), residues: 1098 helix: -0.02 (0.21), residues: 652 sheet: 0.32 (0.46), residues: 110 loop : -1.53 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.005 0.001 HIS C 427 PHE 0.011 0.001 PHE C 499 TYR 0.009 0.001 TYR C 586 ARG 0.004 0.000 ARG C 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.39 seconds wall clock time: 55 minutes 34.97 seconds (3334.97 seconds total)