Starting phenix.real_space_refine on Tue Apr 29 15:46:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwn_35774/04_2025/8iwn_35774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwn_35774/04_2025/8iwn_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/cci-nas-00/data/ceres_data/8iwn_35774/04_2025/8iwn_35774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwn_35774/04_2025/8iwn_35774.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwn_35774/04_2025/8iwn_35774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwn_35774/04_2025/8iwn_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-5669/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: 6.08, per 1000 atoms: 0.69 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: 2.73 Conformation dependent library (CDL) restraints added in 1.2 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: 1.19 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: 2.75 Time building geometry restraints manager: 2.79 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: 1.040 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.490 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:79.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.890 ------------------------------------------------------------------------------- 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 8946 Z= 0.566 Angle : 1.217 13.657 12138 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 Details of bonding type rmsd hydrogen bonds : bond 0.35167 ( 358) hydrogen bonds : angle 9.75187 ( 1044) SS BOND : bond 0.00130 ( 2) SS BOND : angle 1.17167 ( 4) covalent geometry : bond 0.01322 ( 8944) covalent geometry : angle 1.21671 (12134) *********************** 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 : 1.041 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: 1.8773 time to fit residues: 234.4746 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 : 0.961 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103501 restraints weight = 9791.605| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.66 r_work: 0.2912 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 8946 Z= 0.129 Angle : 0.587 6.342 12138 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 Details of bonding type rmsd hydrogen bonds : bond 0.05375 ( 358) hydrogen bonds : angle 4.50788 ( 1044) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.70003 ( 4) covalent geometry : bond 0.00284 ( 8944) covalent geometry : angle 0.58663 (12134) *********************** 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 : 0.910 Fit side-chains REVERT: A 277 THR cc_start: 0.9022 (m) cc_final: 0.8667 (p) REVERT: A 403 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6243 (p90) REVERT: A 491 MET cc_start: 0.8467 (tpp) cc_final: 0.8109 (tpt) REVERT: A 599 GLU cc_start: 0.7443 (tt0) cc_final: 0.5800 (pm20) REVERT: C 202 THR cc_start: 0.8479 (p) cc_final: 0.8186 (t) REVERT: C 277 THR cc_start: 0.9012 (m) cc_final: 0.8680 (p) REVERT: C 403 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6300 (p90) REVERT: C 491 MET cc_start: 0.8412 (tpp) cc_final: 0.8041 (tpt) REVERT: C 599 GLU cc_start: 0.7488 (tt0) cc_final: 0.5872 (pm20) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 1.5891 time to fit residues: 180.7922 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 : 1.053 ------------------------------------------------------------------------------- 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 13 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097725 restraints weight = 9923.704| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.67 r_work: 0.2858 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 8946 Z= 0.265 Angle : 0.708 7.999 12138 Z= 0.361 Chirality : 0.050 0.180 1442 Planarity : 0.006 0.075 1478 Dihedral : 8.070 64.012 1278 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.21 % Allowed : 9.16 % Favored : 88.63 % 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: -2.93 (0.23), residues: 1098 helix: -1.89 (0.18), residues: 658 sheet: 0.06 (0.56), residues: 82 loop : -2.19 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 447 HIS 0.011 0.002 HIS A 427 PHE 0.022 0.002 PHE C 96 TYR 0.019 0.002 TYR C 526 ARG 0.007 0.001 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.06897 ( 358) hydrogen bonds : angle 4.39211 ( 1044) SS BOND : bond 0.00144 ( 2) SS BOND : angle 1.09438 ( 4) covalent geometry : bond 0.00663 ( 8944) covalent geometry : angle 0.70766 (12134) *********************** 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: 21 poor density : 84 time to evaluate : 2.506 Fit side-chains REVERT: A 403 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.6659 (p90) REVERT: A 491 MET cc_start: 0.8472 (tpp) cc_final: 0.8172 (tpt) REVERT: A 599 GLU cc_start: 0.7618 (tt0) cc_final: 0.5807 (pm20) REVERT: C 202 THR cc_start: 0.8681 (p) cc_final: 0.8469 (t) REVERT: C 403 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.6706 (p90) REVERT: C 491 MET cc_start: 0.8453 (tpp) cc_final: 0.8161 (tpt) REVERT: C 599 GLU cc_start: 0.7657 (tt0) cc_final: 0.5893 (pm20) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 1.5720 time to fit residues: 166.6867 Evaluate side-chains 95 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 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 136 LYS Chi-restraints excluded: chain C residue 174 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.132523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.100963 restraints weight = 9720.040| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.65 r_work: 0.2890 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8946 Z= 0.140 Angle : 0.559 5.970 12138 Z= 0.291 Chirality : 0.044 0.152 1442 Planarity : 0.005 0.074 1478 Dihedral : 7.319 61.347 1278 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.53 % Allowed : 9.37 % Favored : 88.11 % 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 (0.25), residues: 1098 helix: -1.24 (0.20), residues: 654 sheet: -0.44 (0.46), residues: 110 loop : -2.00 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.007 0.001 HIS A 427 PHE 0.013 0.001 PHE C 96 TYR 0.012 0.001 TYR A 526 ARG 0.005 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04817 ( 358) hydrogen bonds : angle 4.03037 ( 1044) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.74329 ( 4) covalent geometry : bond 0.00334 ( 8944) covalent geometry : angle 0.55865 (12134) *********************** 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 107 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.996 Fit side-chains REVERT: A 136 LYS cc_start: 0.8884 (tptm) cc_final: 0.8533 (tptp) REVERT: A 489 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 491 MET cc_start: 0.8476 (tpp) cc_final: 0.8157 (tpt) REVERT: A 599 GLU cc_start: 0.7599 (tt0) cc_final: 0.5774 (pm20) REVERT: C 136 LYS cc_start: 0.8893 (tptm) cc_final: 0.8525 (tptp) REVERT: C 202 THR cc_start: 0.8655 (p) cc_final: 0.8448 (t) REVERT: C 403 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7339 (p90) REVERT: C 491 MET cc_start: 0.8466 (tpp) cc_final: 0.8140 (tpt) REVERT: C 599 GLU cc_start: 0.7576 (tt0) cc_final: 0.5760 (pm20) outliers start: 24 outliers final: 14 residues processed: 101 average time/residue: 1.3203 time to fit residues: 142.1892 Evaluate side-chains 92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 187 SER 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 C residue 90 MET Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 187 SER 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 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.136765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.110014 restraints weight = 9588.504| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.44 r_work: 0.2955 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8946 Z= 0.113 Angle : 0.525 7.736 12138 Z= 0.273 Chirality : 0.042 0.149 1442 Planarity : 0.004 0.074 1478 Dihedral : 6.980 62.800 1278 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.21 % Allowed : 10.00 % Favored : 87.79 % 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: -1.68 (0.25), residues: 1098 helix: -0.78 (0.20), residues: 648 sheet: -0.18 (0.47), residues: 110 loop : -1.81 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.008 0.001 HIS A 403 PHE 0.011 0.001 PHE C 499 TYR 0.010 0.001 TYR C 586 ARG 0.003 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 358) hydrogen bonds : angle 3.88828 ( 1044) SS BOND : bond 0.00052 ( 2) SS BOND : angle 0.66689 ( 4) covalent geometry : bond 0.00257 ( 8944) covalent geometry : angle 0.52464 (12134) *********************** 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 106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.042 Fit side-chains REVERT: A 136 LYS cc_start: 0.8868 (tptm) cc_final: 0.8503 (tptp) REVERT: A 403 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.7185 (p90) REVERT: A 491 MET cc_start: 0.8410 (tpp) cc_final: 0.8092 (tpt) REVERT: A 599 GLU cc_start: 0.7623 (tt0) cc_final: 0.5853 (pm20) REVERT: C 136 LYS cc_start: 0.8838 (tptm) cc_final: 0.8481 (tptp) REVERT: C 403 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.7084 (p90) REVERT: C 491 MET cc_start: 0.8395 (tpp) cc_final: 0.8074 (tpt) REVERT: C 599 GLU cc_start: 0.7592 (tt0) cc_final: 0.5813 (pm20) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 1.5020 time to fit residues: 157.4107 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 : 0.940 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain A residue 397 LEU 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 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 90 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.131341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.099900 restraints weight = 9603.428| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.64 r_work: 0.2878 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8946 Z= 0.191 Angle : 0.605 9.025 12138 Z= 0.310 Chirality : 0.046 0.162 1442 Planarity : 0.005 0.074 1478 Dihedral : 7.369 60.096 1278 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.95 % Allowed : 10.11 % Favored : 86.95 % 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: -1.67 (0.25), residues: 1098 helix: -0.88 (0.20), residues: 658 sheet: 0.57 (0.57), residues: 82 loop : -1.69 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.008 0.002 HIS A 427 PHE 0.014 0.002 PHE C 96 TYR 0.013 0.002 TYR C 586 ARG 0.004 0.000 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 358) hydrogen bonds : angle 4.01633 ( 1044) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.83430 ( 4) covalent geometry : bond 0.00472 ( 8944) covalent geometry : angle 0.60475 (12134) *********************** 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: 28 poor density : 81 time to evaluate : 1.062 Fit side-chains REVERT: A 136 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8573 (tptp) REVERT: A 491 MET cc_start: 0.8447 (tpp) cc_final: 0.8127 (tpt) REVERT: A 492 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: A 599 GLU cc_start: 0.7578 (tt0) cc_final: 0.5763 (pm20) REVERT: A 626 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7559 (pm20) REVERT: A 650 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.6096 (mtt90) REVERT: C 136 LYS cc_start: 0.8877 (tptm) cc_final: 0.8599 (tptp) REVERT: C 403 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7240 (p90) REVERT: C 489 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8130 (tp) REVERT: C 491 MET cc_start: 0.8439 (tpp) cc_final: 0.8125 (tpt) REVERT: C 599 GLU cc_start: 0.7553 (tt0) cc_final: 0.5739 (pm20) REVERT: C 626 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7556 (pm20) REVERT: C 650 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.6092 (mtt90) outliers start: 28 outliers final: 15 residues processed: 101 average time/residue: 1.4088 time to fit residues: 150.9045 Evaluate side-chains 104 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 GLU 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 650 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.134458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103081 restraints weight = 9745.149| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.63 r_work: 0.2917 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8946 Z= 0.108 Angle : 0.513 7.427 12138 Z= 0.266 Chirality : 0.042 0.151 1442 Planarity : 0.004 0.074 1478 Dihedral : 6.929 63.308 1278 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.63 % Allowed : 10.53 % Favored : 86.84 % 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: -1.17 (0.26), residues: 1098 helix: -0.41 (0.21), residues: 652 sheet: 0.11 (0.47), residues: 110 loop : -1.57 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 447 HIS 0.008 0.001 HIS C 403 PHE 0.011 0.001 PHE C 499 TYR 0.009 0.001 TYR C 586 ARG 0.003 0.000 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 358) hydrogen bonds : angle 3.83878 ( 1044) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.58794 ( 4) covalent geometry : bond 0.00243 ( 8944) covalent geometry : angle 0.51273 (12134) *********************** 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 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.964 Fit side-chains REVERT: A 136 LYS cc_start: 0.8822 (tptm) cc_final: 0.8480 (tptp) REVERT: A 491 MET cc_start: 0.8400 (tpp) cc_final: 0.8034 (tpt) REVERT: A 599 GLU cc_start: 0.7551 (tt0) cc_final: 0.5724 (pm20) REVERT: A 626 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7512 (pm20) REVERT: A 627 GLU cc_start: 0.8202 (mp0) cc_final: 0.7248 (mp0) REVERT: C 136 LYS cc_start: 0.8832 (tptm) cc_final: 0.8509 (tptp) REVERT: C 491 MET cc_start: 0.8383 (tpp) cc_final: 0.8006 (tpt) REVERT: C 599 GLU cc_start: 0.7519 (tt0) cc_final: 0.5680 (pm20) REVERT: C 626 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7522 (pm20) REVERT: C 627 GLU cc_start: 0.8207 (mp0) cc_final: 0.7258 (mp0) outliers start: 25 outliers final: 16 residues processed: 102 average time/residue: 1.2980 time to fit residues: 141.4703 Evaluate side-chains 102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 403 HIS Chi-restraints excluded: chain A residue 456 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.100666 restraints weight = 9777.772| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.60 r_work: 0.2855 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8946 Z= 0.176 Angle : 0.588 8.839 12138 Z= 0.301 Chirality : 0.046 0.165 1442 Planarity : 0.005 0.075 1478 Dihedral : 7.302 60.508 1278 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.95 % Allowed : 10.00 % 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: -1.25 (0.25), residues: 1098 helix: -0.53 (0.21), residues: 656 sheet: 0.73 (0.57), residues: 82 loop : -1.56 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.008 0.001 HIS C 427 PHE 0.013 0.002 PHE C 499 TYR 0.012 0.001 TYR C 586 ARG 0.003 0.000 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 358) hydrogen bonds : angle 3.96736 ( 1044) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.78986 ( 4) covalent geometry : bond 0.00433 ( 8944) covalent geometry : angle 0.58818 (12134) *********************** 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 114 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.030 Fit side-chains REVERT: A 136 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8489 (tptp) REVERT: A 489 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7681 (mp) REVERT: A 491 MET cc_start: 0.8395 (tpp) cc_final: 0.8087 (tpt) REVERT: A 492 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 599 GLU cc_start: 0.7564 (tt0) cc_final: 0.5734 (pm20) REVERT: A 626 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7513 (pm20) REVERT: A 627 GLU cc_start: 0.8206 (mp0) cc_final: 0.7303 (mp0) REVERT: A 650 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.6067 (mtt90) REVERT: C 136 LYS cc_start: 0.8845 (tptm) cc_final: 0.8527 (tptp) REVERT: C 491 MET cc_start: 0.8399 (tpp) cc_final: 0.8049 (tpt) REVERT: C 492 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: C 599 GLU cc_start: 0.7598 (tt0) cc_final: 0.5784 (pm20) REVERT: C 626 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7512 (pm20) REVERT: C 627 GLU cc_start: 0.8210 (mp0) cc_final: 0.7308 (mp0) outliers start: 28 outliers final: 17 residues processed: 104 average time/residue: 1.3340 time to fit residues: 147.6176 Evaluate side-chains 108 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 397 LEU 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 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 401 ARG Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 492 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.131978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.099978 restraints weight = 9772.083| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.67 r_work: 0.2855 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8946 Z= 0.143 Angle : 0.554 8.194 12138 Z= 0.285 Chirality : 0.044 0.156 1442 Planarity : 0.004 0.075 1478 Dihedral : 7.141 61.566 1278 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.21 % Allowed : 11.37 % Favored : 86.42 % 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: -1.04 (0.26), residues: 1098 helix: -0.32 (0.21), residues: 652 sheet: 0.78 (0.57), residues: 82 loop : -1.52 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.007 0.001 HIS A 427 PHE 0.012 0.001 PHE C 499 TYR 0.011 0.001 TYR A 586 ARG 0.003 0.000 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 358) hydrogen bonds : angle 3.92035 ( 1044) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.68245 ( 4) covalent geometry : bond 0.00346 ( 8944) covalent geometry : angle 0.55445 (12134) *********************** 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 109 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 136 LYS cc_start: 0.8844 (tptm) cc_final: 0.8474 (tptp) REVERT: A 137 GLN cc_start: 0.7751 (mp10) cc_final: 0.7413 (mm-40) REVERT: A 489 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7716 (mp) REVERT: A 491 MET cc_start: 0.8419 (tpp) cc_final: 0.8123 (tpt) REVERT: A 492 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: A 599 GLU cc_start: 0.7563 (tt0) cc_final: 0.5744 (pm20) REVERT: A 626 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7484 (pm20) REVERT: A 627 GLU cc_start: 0.8202 (mp0) cc_final: 0.7304 (mp0) REVERT: C 136 LYS cc_start: 0.8856 (tptm) cc_final: 0.8548 (tptp) REVERT: C 491 MET cc_start: 0.8437 (tpp) cc_final: 0.8101 (tpt) REVERT: C 492 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: C 599 GLU cc_start: 0.7532 (tt0) cc_final: 0.5713 (pm20) REVERT: C 627 GLU cc_start: 0.8207 (mp0) cc_final: 0.7566 (mp0) REVERT: C 650 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.6075 (mtt90) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 1.4125 time to fit residues: 149.6911 Evaluate side-chains 109 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 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 401 ARG Chi-restraints excluded: chain C residue 403 HIS Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 492 GLU 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 81 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 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 = 0.3387 r_free = 0.3387 target = 0.131171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100409 restraints weight = 9706.263| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.56 r_work: 0.2875 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8946 Z= 0.169 Angle : 0.585 8.736 12138 Z= 0.299 Chirality : 0.046 0.164 1442 Planarity : 0.005 0.075 1478 Dihedral : 7.299 60.965 1278 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.63 % Allowed : 11.05 % Favored : 86.32 % 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: -1.11 (0.26), residues: 1098 helix: -0.40 (0.21), residues: 656 sheet: 0.81 (0.57), residues: 82 loop : -1.53 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 447 HIS 0.008 0.001 HIS C 427 PHE 0.013 0.002 PHE C 499 TYR 0.012 0.001 TYR C 586 ARG 0.003 0.000 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 358) hydrogen bonds : angle 3.97514 ( 1044) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.79287 ( 4) covalent geometry : bond 0.00415 ( 8944) covalent geometry : angle 0.58453 (12134) ********************** 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 110 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.041 Fit side-chains REVERT: A 136 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8472 (tptp) REVERT: A 137 GLN cc_start: 0.7722 (mp10) cc_final: 0.7392 (mm-40) REVERT: A 489 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7707 (mp) REVERT: A 491 MET cc_start: 0.8444 (tpp) cc_final: 0.8121 (tpt) REVERT: A 492 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: A 599 GLU cc_start: 0.7647 (tt0) cc_final: 0.5879 (pm20) REVERT: A 627 GLU cc_start: 0.8207 (mp0) cc_final: 0.7614 (mp0) REVERT: A 650 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.6083 (mtt90) REVERT: C 136 LYS cc_start: 0.8870 (tptm) cc_final: 0.8568 (tptp) REVERT: C 491 MET cc_start: 0.8392 (tpp) cc_final: 0.8092 (tpt) REVERT: C 492 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 599 GLU cc_start: 0.7602 (tt0) cc_final: 0.5853 (pm20) REVERT: C 627 GLU cc_start: 0.8213 (mp0) cc_final: 0.7616 (mp0) REVERT: C 650 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.6059 (mtt90) outliers start: 25 outliers final: 17 residues processed: 102 average time/residue: 1.3543 time to fit residues: 146.8737 Evaluate side-chains 108 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 397 LEU 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 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 492 GLU 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 22 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098993 restraints weight = 9715.953| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.66 r_work: 0.2831 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8946 Z= 0.188 Angle : 0.607 8.888 12138 Z= 0.310 Chirality : 0.047 0.167 1442 Planarity : 0.005 0.075 1478 Dihedral : 7.365 60.118 1278 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.84 % Allowed : 11.05 % Favored : 86.11 % 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: -1.13 (0.26), residues: 1098 helix: -0.41 (0.21), residues: 656 sheet: 0.81 (0.57), residues: 82 loop : -1.55 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 447 HIS 0.008 0.001 HIS A 427 PHE 0.013 0.002 PHE A 499 TYR 0.012 0.002 TYR A 586 ARG 0.003 0.000 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 358) hydrogen bonds : angle 4.01073 ( 1044) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.79161 ( 4) covalent geometry : bond 0.00468 ( 8944) covalent geometry : angle 0.60674 (12134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5990.35 seconds wall clock time: 104 minutes 55.54 seconds (6295.54 seconds total)