Starting phenix.real_space_refine on Thu Feb 13 06:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwn_35774/02_2025/8iwn_35774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwn_35774/02_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_35774/02_2025/8iwn_35774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwn_35774/02_2025/8iwn_35774.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwn_35774/02_2025/8iwn_35774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwn_35774/02_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-5592/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: 5.61, per 1000 atoms: 0.64 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 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: 0.88 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: 2.43 Time building geometry restraints manager: 2.52 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: 1.010 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.430 Find NCS groups from input model: 0.470 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:14.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- 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 : 0.976 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: 1.8761 time to fit residues: 233.6452 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 : 1.010 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103515 restraints weight = 9791.617| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.66 r_work: 0.2907 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.840 Fit side-chains REVERT: A 277 THR cc_start: 0.9020 (m) cc_final: 0.8663 (p) REVERT: A 403 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6246 (p90) REVERT: A 491 MET cc_start: 0.8466 (tpp) cc_final: 0.8107 (tpt) REVERT: A 599 GLU cc_start: 0.7422 (tt0) cc_final: 0.5778 (pm20) REVERT: C 202 THR cc_start: 0.8480 (p) cc_final: 0.8187 (t) REVERT: C 277 THR cc_start: 0.9011 (m) cc_final: 0.8676 (p) REVERT: C 403 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.6301 (p90) REVERT: C 491 MET cc_start: 0.8411 (tpp) cc_final: 0.8040 (tpt) REVERT: C 599 GLU cc_start: 0.7466 (tt0) cc_final: 0.5850 (pm20) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 1.6421 time to fit residues: 186.7584 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 : 0.941 ------------------------------------------------------------------------------- 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: 5.9990 chunk 67 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.129926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.098383 restraints weight = 9905.372| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.66 r_work: 0.2834 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8944 Z= 0.381 Angle : 0.678 7.613 12134 Z= 0.347 Chirality : 0.049 0.174 1442 Planarity : 0.006 0.074 1478 Dihedral : 7.926 61.187 1278 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.00 % Allowed : 9.47 % Favored : 88.53 % 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: -2.86 (0.23), residues: 1098 helix: -1.84 (0.18), residues: 658 sheet: 0.09 (0.57), residues: 82 loop : -2.17 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 447 HIS 0.010 0.001 HIS C 427 PHE 0.021 0.002 PHE A 96 TYR 0.017 0.002 TYR A 526 ARG 0.007 0.001 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 102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.913 Fit side-chains REVERT: A 403 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6609 (p90) REVERT: A 491 MET cc_start: 0.8469 (tpp) cc_final: 0.8178 (tpt) REVERT: A 599 GLU cc_start: 0.7614 (tt0) cc_final: 0.5821 (pm20) REVERT: C 202 THR cc_start: 0.8671 (p) cc_final: 0.8462 (t) REVERT: C 403 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6666 (p90) REVERT: C 491 MET cc_start: 0.8454 (tpp) cc_final: 0.8110 (tpt) REVERT: C 599 GLU cc_start: 0.7611 (tt0) cc_final: 0.5800 (pm20) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 1.4717 time to fit residues: 151.6132 Evaluate side-chains 92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 0.0370 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101905 restraints weight = 9702.476| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.62 r_work: 0.2879 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8944 Z= 0.215 Angle : 0.554 5.982 12134 Z= 0.289 Chirality : 0.044 0.152 1442 Planarity : 0.005 0.073 1478 Dihedral : 7.277 61.457 1278 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.63 % Allowed : 9.16 % Favored : 88.21 % 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: -2.12 (0.25), residues: 1098 helix: -1.21 (0.20), residues: 654 sheet: 0.29 (0.56), residues: 82 loop : -1.90 (0.32), residues: 362 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 0.013 0.001 PHE C 96 TYR 0.012 0.001 TYR A 526 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 108 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.953 Fit side-chains REVERT: A 136 LYS cc_start: 0.8857 (tptm) cc_final: 0.8494 (tptp) REVERT: A 491 MET cc_start: 0.8395 (tpp) cc_final: 0.8043 (tpt) REVERT: A 599 GLU cc_start: 0.7563 (tt0) cc_final: 0.5710 (pm20) REVERT: C 136 LYS cc_start: 0.8857 (tptm) cc_final: 0.8507 (tptp) REVERT: C 403 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7281 (p90) REVERT: C 491 MET cc_start: 0.8430 (tpp) cc_final: 0.8088 (tpt) REVERT: C 599 GLU cc_start: 0.7557 (tt0) cc_final: 0.5704 (pm20) outliers start: 25 outliers final: 14 residues processed: 103 average time/residue: 1.2834 time to fit residues: 140.9443 Evaluate side-chains 90 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 411 ILE 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 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: 0.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 79 optimal weight: 0.0030 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.134094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.102363 restraints weight = 9651.427| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.67 r_work: 0.2902 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8944 Z= 0.162 Angle : 0.519 7.636 12134 Z= 0.271 Chirality : 0.042 0.150 1442 Planarity : 0.004 0.073 1478 Dihedral : 6.960 62.804 1278 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.53 % Allowed : 9.89 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1098 helix: -0.75 (0.20), residues: 648 sheet: -0.19 (0.47), residues: 110 loop : -1.78 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.009 0.001 HIS A 403 PHE 0.011 0.001 PHE C 96 TYR 0.010 0.001 TYR A 586 ARG 0.004 0.000 ARG A 180 *********************** 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 107 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.025 Fit side-chains REVERT: A 136 LYS cc_start: 0.8846 (tptm) cc_final: 0.8447 (tptp) REVERT: A 403 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.7118 (p90) REVERT: A 491 MET cc_start: 0.8459 (tpp) cc_final: 0.8131 (tpt) REVERT: A 492 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 599 GLU cc_start: 0.7572 (tt0) cc_final: 0.5760 (pm20) REVERT: C 136 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8454 (tptp) REVERT: C 403 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.7120 (p90) REVERT: C 491 MET cc_start: 0.8431 (tpp) cc_final: 0.8109 (tpt) REVERT: C 599 GLU cc_start: 0.7560 (tt0) cc_final: 0.5732 (pm20) outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 1.3484 time to fit residues: 139.5624 Evaluate side-chains 102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 403 HIS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 492 GLU 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 305 SER 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: 0.4980 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.135841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.105366 restraints weight = 9570.048| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.56 r_work: 0.2935 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8944 Z= 0.149 Angle : 0.501 7.329 12134 Z= 0.261 Chirality : 0.042 0.147 1442 Planarity : 0.004 0.072 1478 Dihedral : 6.780 63.435 1278 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.63 % Allowed : 10.00 % 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: -1.21 (0.26), residues: 1098 helix: -0.42 (0.21), residues: 650 sheet: 0.05 (0.46), residues: 110 loop : -1.61 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.005 0.001 HIS A 403 PHE 0.010 0.001 PHE C 499 TYR 0.009 0.001 TYR A 586 ARG 0.003 0.000 ARG C 396 *********************** 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 117 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.952 Fit side-chains REVERT: A 136 LYS cc_start: 0.8743 (tptm) cc_final: 0.8404 (tptp) REVERT: A 489 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 491 MET cc_start: 0.8405 (tpp) cc_final: 0.8058 (tpt) REVERT: A 599 GLU cc_start: 0.7547 (tt0) cc_final: 0.5750 (pm20) REVERT: A 626 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7523 (pm20) REVERT: A 627 GLU cc_start: 0.8247 (mp0) cc_final: 0.7350 (mp0) REVERT: C 136 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8395 (tptp) REVERT: C 489 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7972 (tp) REVERT: C 491 MET cc_start: 0.8376 (tpp) cc_final: 0.8000 (tpt) REVERT: C 599 GLU cc_start: 0.7519 (tt0) cc_final: 0.5686 (pm20) REVERT: C 626 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7520 (pm20) REVERT: C 627 GLU cc_start: 0.8241 (mp0) cc_final: 0.7341 (mp0) outliers start: 25 outliers final: 18 residues processed: 106 average time/residue: 1.2247 time to fit residues: 138.7211 Evaluate side-chains 110 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 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 489 LEU 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 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.137496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.107178 restraints weight = 9726.312| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.54 r_work: 0.2963 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8944 Z= 0.135 Angle : 0.487 7.127 12134 Z= 0.254 Chirality : 0.041 0.146 1442 Planarity : 0.004 0.071 1478 Dihedral : 6.625 64.285 1278 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.84 % Allowed : 9.89 % 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: -0.85 (0.26), residues: 1098 helix: -0.13 (0.21), residues: 648 sheet: 0.26 (0.46), residues: 110 loop : -1.49 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 447 HIS 0.006 0.001 HIS C 403 PHE 0.010 0.001 PHE C 499 TYR 0.008 0.001 TYR C 586 ARG 0.002 0.000 ARG A 431 *********************** 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 117 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.938 Fit side-chains REVERT: A 136 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8416 (tptp) REVERT: A 137 GLN cc_start: 0.7713 (mp10) cc_final: 0.7388 (mm-40) REVERT: A 489 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 491 MET cc_start: 0.8424 (tpp) cc_final: 0.8102 (tpt) REVERT: A 599 GLU cc_start: 0.7566 (tt0) cc_final: 0.5806 (pm20) REVERT: A 626 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7575 (pm20) REVERT: A 627 GLU cc_start: 0.8272 (mp0) cc_final: 0.7408 (mp0) REVERT: C 136 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8416 (tptp) REVERT: C 489 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8032 (tp) REVERT: C 491 MET cc_start: 0.8405 (tpp) cc_final: 0.8045 (tpt) REVERT: C 599 GLU cc_start: 0.7531 (tt0) cc_final: 0.5746 (pm20) REVERT: C 626 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7574 (pm20) REVERT: C 627 GLU cc_start: 0.8264 (mp0) cc_final: 0.7396 (mp0) outliers start: 27 outliers final: 17 residues processed: 103 average time/residue: 1.2633 time to fit residues: 138.8275 Evaluate side-chains 110 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL 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 411 ILE 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 49 VAL 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 489 LEU Chi-restraints excluded: chain C residue 569 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: 2.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 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 = 0.3376 r_free = 0.3376 target = 0.130240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.098398 restraints weight = 9868.973| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.66 r_work: 0.2830 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8944 Z= 0.361 Angle : 0.634 9.276 12134 Z= 0.322 Chirality : 0.048 0.168 1442 Planarity : 0.005 0.071 1478 Dihedral : 7.456 57.739 1278 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.05 % Allowed : 9.89 % 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: -1.28 (0.25), residues: 1098 helix: -0.55 (0.20), residues: 656 sheet: 0.66 (0.56), residues: 82 loop : -1.55 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 447 HIS 0.009 0.002 HIS C 427 PHE 0.015 0.002 PHE C 96 TYR 0.013 0.002 TYR A 526 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 111 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.770 Fit side-chains REVERT: A 136 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8566 (tptp) REVERT: A 220 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: A 489 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 491 MET cc_start: 0.8478 (tpp) cc_final: 0.8193 (tpt) REVERT: A 599 GLU cc_start: 0.7645 (tt0) cc_final: 0.5865 (pm20) REVERT: A 626 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7582 (pm20) REVERT: A 650 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.6078 (mtt90) REVERT: C 136 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8535 (tptp) REVERT: C 220 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: C 489 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8032 (tp) REVERT: C 491 MET cc_start: 0.8443 (tpp) cc_final: 0.8108 (tpt) REVERT: C 599 GLU cc_start: 0.7618 (tt0) cc_final: 0.5857 (pm20) REVERT: C 626 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7578 (pm20) REVERT: C 650 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.6083 (mtt90) outliers start: 29 outliers final: 14 residues processed: 103 average time/residue: 1.4085 time to fit residues: 153.9192 Evaluate side-chains 106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL 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 220 GLU 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 650 ARG Chi-restraints excluded: chain C residue 49 VAL 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 220 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.135832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.103824 restraints weight = 9753.931| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.68 r_work: 0.2921 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8944 Z= 0.128 Angle : 0.487 6.918 12134 Z= 0.254 Chirality : 0.041 0.158 1442 Planarity : 0.004 0.072 1478 Dihedral : 6.719 65.533 1278 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.21 % Allowed : 11.26 % 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: -0.76 (0.26), residues: 1098 helix: -0.05 (0.21), residues: 650 sheet: 0.27 (0.46), residues: 110 loop : -1.46 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 447 HIS 0.004 0.001 HIS A 427 PHE 0.010 0.001 PHE C 499 TYR 0.008 0.001 TYR A 586 ARG 0.002 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 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.004 Fit side-chains REVERT: A 136 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8490 (tptp) REVERT: A 489 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 491 MET cc_start: 0.8384 (tpp) cc_final: 0.8075 (tpt) REVERT: A 599 GLU cc_start: 0.7547 (tt0) cc_final: 0.5747 (pm20) REVERT: A 626 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7497 (pm20) REVERT: A 627 GLU cc_start: 0.8234 (mp0) cc_final: 0.7345 (mp0) REVERT: A 650 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.5908 (mtt90) REVERT: C 136 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8458 (tptp) REVERT: C 489 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7988 (tp) REVERT: C 491 MET cc_start: 0.8415 (tpp) cc_final: 0.8051 (tpt) REVERT: C 599 GLU cc_start: 0.7514 (tt0) cc_final: 0.5684 (pm20) REVERT: C 626 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7494 (pm20) REVERT: C 627 GLU cc_start: 0.8225 (mp0) cc_final: 0.7336 (mp0) REVERT: C 650 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.5916 (mtt90) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 1.3704 time to fit residues: 152.9403 Evaluate side-chains 111 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL 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 650 ARG Chi-restraints excluded: chain C residue 49 VAL 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 489 LEU 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: 8.9990 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.133216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101116 restraints weight = 9663.888| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.66 r_work: 0.2919 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2532 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= 0.215 Angle : 0.544 8.050 12134 Z= 0.280 Chirality : 0.044 0.152 1442 Planarity : 0.004 0.072 1478 Dihedral : 6.920 62.205 1278 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.32 % Allowed : 10.95 % 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: -0.78 (0.26), residues: 1098 helix: -0.07 (0.21), residues: 656 sheet: 0.22 (0.46), residues: 110 loop : -1.47 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 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 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 106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.934 Fit side-chains REVERT: A 136 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8556 (tptp) REVERT: A 489 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 491 MET cc_start: 0.8420 (tpp) cc_final: 0.8115 (tpt) REVERT: A 599 GLU cc_start: 0.7600 (tt0) cc_final: 0.5779 (pm20) REVERT: A 626 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7482 (pm20) REVERT: A 627 GLU cc_start: 0.8257 (mp0) cc_final: 0.7382 (mp0) REVERT: A 650 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.6108 (mtt90) REVERT: C 136 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8441 (tptp) REVERT: C 489 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8081 (tp) REVERT: C 491 MET cc_start: 0.8402 (tpp) cc_final: 0.8080 (tpt) REVERT: C 599 GLU cc_start: 0.7555 (tt0) cc_final: 0.5737 (pm20) REVERT: C 626 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7485 (pm20) REVERT: C 627 GLU cc_start: 0.8253 (mp0) cc_final: 0.7380 (mp0) REVERT: C 650 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.6117 (mtt90) outliers start: 22 outliers final: 13 residues processed: 98 average time/residue: 1.4843 time to fit residues: 154.4454 Evaluate side-chains 103 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL 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 650 ARG Chi-restraints excluded: chain C residue 49 VAL 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 489 LEU 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: 3.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.098637 restraints weight = 9725.841| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.64 r_work: 0.2827 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8944 Z= 0.395 Angle : 0.661 9.117 12134 Z= 0.334 Chirality : 0.050 0.182 1442 Planarity : 0.005 0.072 1478 Dihedral : 7.486 58.276 1278 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: -1.12 (0.26), residues: 1098 helix: -0.41 (0.21), residues: 654 sheet: 0.74 (0.57), residues: 82 loop : -1.50 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 426 HIS 0.011 0.002 HIS A 427 PHE 0.017 0.002 PHE C 96 TYR 0.013 0.002 TYR C 526 ARG 0.004 0.001 ARG C 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5406.12 seconds wall clock time: 96 minutes 1.29 seconds (5761.29 seconds total)