Starting phenix.real_space_refine on Fri Aug 7 10:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9g_72697/08_2026/9y9g_72697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9g_72697/08_2026/9y9g_72697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y9g_72697/08_2026/9y9g_72697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9g_72697/08_2026/9y9g_72697.map" model { file = "/net/cci-nas-00/data/ceres_data/9y9g_72697/08_2026/9y9g_72697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9g_72697/08_2026/9y9g_72697.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 12 5.49 5 Mg 16 5.21 5 S 112 5.16 5 C 13028 2.51 5 N 3334 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20362 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5081 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 22, 'TRANS': 616} Chain breaks: 2 Chain: "B" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5030 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 615} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5081 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 22, 'TRANS': 616} Chain breaks: 2 Chain: "D" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5030 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 615} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 4.66, per 1000 atoms: 0.23 Number of scatterers: 20362 At special positions: 0 Unit cell: (106.887, 132.957, 230.285, 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 112 16.00 P 12 15.00 Mg 16 11.99 O 3860 8.00 N 3334 7.00 C 13028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 151 " 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: 1.70 Conformation dependent library (CDL) restraints added in 855.9 milliseconds 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4836 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 38 sheets defined 48.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 181 through 208 removed outlier: 3.793A pdb=" N ILE A 189 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 222 through 239 Proline residue: A 234 - end of helix removed outlier: 4.110A pdb=" N LYS A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 265 Processing helix chain 'A' and resid 268 through 284 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 302 through 329 Proline residue: A 315 - end of helix Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.872A pdb=" N ILE A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.568A pdb=" N GLY A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.279A pdb=" N PHE A 429 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.670A pdb=" N CYS A 435 " --> pdb=" O PRO A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.673A pdb=" N GLY A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.876A pdb=" N VAL A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 641 through 646 removed outlier: 4.119A pdb=" N THR A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 728 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.635A pdb=" N HIS B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 181 through 209 removed outlier: 4.083A pdb=" N MET B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 222 through 238 Proline residue: B 234 - end of helix removed outlier: 4.078A pdb=" N LYS B 238 " --> pdb=" O PRO B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 265 Processing helix chain 'B' and resid 268 through 284 removed outlier: 3.513A pdb=" N GLU B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 302 through 313 removed outlier: 3.507A pdb=" N THR B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 329 Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 355 through 368 Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.023A pdb=" N ILE B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.574A pdb=" N GLY B 404 " --> pdb=" O ILE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.790A pdb=" N GLY B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 505 Processing helix chain 'B' and resid 527 through 538 removed outlier: 3.869A pdb=" N ASP B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.591A pdb=" N TYR B 601 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 removed outlier: 4.529A pdb=" N THR B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 641 through 646' Processing helix chain 'B' and resid 713 through 728 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 181 through 208 removed outlier: 3.968A pdb=" N ILE C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 222 through 239 Proline residue: C 234 - end of helix removed outlier: 4.123A pdb=" N LYS C 238 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'C' and resid 268 through 284 Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 302 through 329 Proline residue: C 315 - end of helix Proline residue: C 319 - end of helix Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 355 through 367 Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.860A pdb=" N ILE C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.543A pdb=" N GLY C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 428 Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.656A pdb=" N CYS C 435 " --> pdb=" O PRO C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 457 through 468 removed outlier: 3.682A pdb=" N GLY C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.886A pdb=" N VAL C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 597 through 601 Processing helix chain 'C' and resid 641 through 646 removed outlier: 4.119A pdb=" N THR C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 728 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.635A pdb=" N HIS D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 181 through 209 removed outlier: 4.095A pdb=" N MET D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 238 Proline residue: D 234 - end of helix removed outlier: 4.070A pdb=" N LYS D 238 " --> pdb=" O PRO D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 265 Processing helix chain 'D' and resid 268 through 284 Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 313 through 329 Proline residue: D 319 - end of helix Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 355 through 368 Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.026A pdb=" N ILE D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.573A pdb=" N GLY D 404 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 427 No H-bonds generated for 'chain 'D' and resid 425 through 427' Processing helix chain 'D' and resid 431 through 435 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 457 through 468 removed outlier: 3.825A pdb=" N GLY D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 527 through 538 removed outlier: 3.902A pdb=" N ASP D 531 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 597 through 601 removed outlier: 3.624A pdb=" N TYR D 601 " --> pdb=" O ALA D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 646 removed outlier: 4.539A pdb=" N THR D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 646 " --> pdb=" O MET D 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 641 through 646' Processing helix chain 'D' and resid 713 through 728 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 7.078A pdb=" N THR A 73 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS A 54 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN A 75 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.253A pdb=" N SER A 129 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A 122 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 131 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 120 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 133 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.550A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 68 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.550A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A 68 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 378 through 379 removed outlier: 5.538A pdb=" N VAL A 490 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS A 477 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS A 450 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN A 476 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 452 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL A 478 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.268A pdb=" N THR A 436 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 585 through 588 removed outlier: 6.724A pdb=" N GLN A 707 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 607 through 608 removed outlier: 4.082A pdb=" N LYS A 607 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 633 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 54 removed outlier: 7.278A pdb=" N VAL B 47 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N TYR B 81 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N MET B 49 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR B 79 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 51 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ARG B 77 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER B 129 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B 123 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 119 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 135 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 117 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.554A pdb=" N ILE B 66 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 173 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 68 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.554A pdb=" N ILE B 66 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 173 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 68 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.169A pdb=" N TYR B 488 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 479 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL B 490 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 477 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 492 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS B 450 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLN B 476 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 452 " --> pdb=" O GLN B 476 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 478 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 386 through 387 removed outlier: 6.108A pdb=" N ILE B 386 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 408 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE B 421 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 410 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.870A pdb=" N THR B 436 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.560A pdb=" N GLN B 707 " --> pdb=" O LEU B 616 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 607 through 608 removed outlier: 3.929A pdb=" N LYS B 607 " --> pdb=" O SER B 696 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 629 through 633 Processing sheet with id=AC2, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.496A pdb=" N ILE C 46 " --> pdb=" O TYR C 81 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR C 81 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ARG C 77 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU C 51 " --> pdb=" O ARG C 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 45 through 48 removed outlier: 5.496A pdb=" N ILE C 46 " --> pdb=" O TYR C 81 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR C 81 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 129 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN C 122 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL C 131 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU C 120 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C 133 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.564A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL C 68 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.564A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL C 68 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 378 through 379 removed outlier: 5.525A pdb=" N VAL C 490 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS C 477 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS C 450 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN C 476 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL C 452 " --> pdb=" O GLN C 476 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL C 478 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC8, first strand: chain 'C' and resid 391 through 392 removed outlier: 4.276A pdb=" N THR C 436 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 585 through 588 removed outlier: 6.703A pdb=" N GLN C 707 " --> pdb=" O LEU C 616 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 607 through 608 removed outlier: 4.087A pdb=" N LYS C 607 " --> pdb=" O SER C 696 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 629 through 633 Processing sheet with id=AD3, first strand: chain 'D' and resid 45 through 54 removed outlier: 7.270A pdb=" N VAL D 47 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N TYR D 81 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N MET D 49 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR D 79 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU D 51 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ARG D 77 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER D 129 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL D 123 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN D 119 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU D 135 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL D 117 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.554A pdb=" N ILE D 66 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL D 173 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL D 68 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.554A pdb=" N ILE D 66 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL D 173 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL D 68 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 378 through 379 removed outlier: 6.168A pdb=" N TYR D 488 " --> pdb=" O ASN D 479 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN D 479 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N VAL D 490 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS D 477 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 492 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N HIS D 450 " --> pdb=" O ILE D 474 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN D 476 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL D 452 " --> pdb=" O GLN D 476 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL D 478 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 386 through 387 removed outlier: 6.110A pdb=" N ILE D 386 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE D 408 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE D 421 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 410 " --> pdb=" O VAL D 419 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 391 through 392 removed outlier: 3.875A pdb=" N THR D 436 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 585 through 588 removed outlier: 6.559A pdb=" N GLN D 707 " --> pdb=" O LEU D 616 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 607 through 608 removed outlier: 3.927A pdb=" N LYS D 607 " --> pdb=" O SER D 696 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 629 through 633 1000 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6535 1.34 - 1.46: 3808 1.46 - 1.58: 10161 1.58 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 20708 Sorted by residual: bond pdb=" N VAL D 253 " pdb=" CA VAL D 253 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.39e+00 bond pdb=" N ASN D 254 " pdb=" CA ASN D 254 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 6.94e+00 bond pdb=" N ASN B 250 " pdb=" CA ASN B 250 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.18e-02 7.18e+03 6.58e+00 bond pdb=" N ASN A 254 " pdb=" CA ASN A 254 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.19e+00 bond pdb=" N HIS C 454 " pdb=" CA HIS C 454 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.27e-02 6.20e+03 6.16e+00 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 27116 1.22 - 2.43: 737 2.43 - 3.65: 144 3.65 - 4.86: 34 4.86 - 6.08: 13 Bond angle restraints: 28044 Sorted by residual: angle pdb=" N LEU B 248 " pdb=" CA LEU B 248 " pdb=" C LEU B 248 " ideal model delta sigma weight residual 111.33 105.36 5.97 1.21e+00 6.83e-01 2.43e+01 angle pdb=" O VAL D 253 " pdb=" C VAL D 253 " pdb=" N ASN D 254 " ideal model delta sigma weight residual 121.91 126.03 -4.12 9.80e-01 1.04e+00 1.77e+01 angle pdb=" CA PHE B 199 " pdb=" CB PHE B 199 " pdb=" CG PHE B 199 " ideal model delta sigma weight residual 113.80 110.16 3.64 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA ASN B 250 " pdb=" C ASN B 250 " pdb=" O ASN B 250 " ideal model delta sigma weight residual 120.90 117.55 3.35 1.03e+00 9.43e-01 1.06e+01 angle pdb=" CA PHE D 199 " pdb=" CB PHE D 199 " pdb=" CG PHE D 199 " ideal model delta sigma weight residual 113.80 110.62 3.18 1.00e+00 1.00e+00 1.01e+01 ... (remaining 28039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 12164 17.83 - 35.66: 404 35.66 - 53.49: 82 53.49 - 71.32: 15 71.32 - 89.15: 3 Dihedral angle restraints: 12668 sinusoidal: 5200 harmonic: 7468 Sorted by residual: dihedral pdb=" CA LEU B 706 " pdb=" C LEU B 706 " pdb=" N GLN B 707 " pdb=" CA GLN B 707 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU D 706 " pdb=" C LEU D 706 " pdb=" N GLN D 707 " pdb=" CA GLN D 707 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR D 611 " pdb=" C TYR D 611 " pdb=" N PHE D 612 " pdb=" CA PHE D 612 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 12665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2321 0.037 - 0.075: 669 0.075 - 0.112: 245 0.112 - 0.149: 54 0.149 - 0.186: 5 Chirality restraints: 3294 Sorted by residual: chirality pdb=" CA VAL D 253 " pdb=" N VAL D 253 " pdb=" C VAL D 253 " pdb=" CB VAL D 253 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CA LEU D 552 " pdb=" N LEU D 552 " pdb=" C LEU D 552 " pdb=" CB LEU D 552 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA VAL D 68 " pdb=" N VAL D 68 " pdb=" C VAL D 68 " pdb=" CB VAL D 68 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 3291 not shown) Planarity restraints: 3516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 247 " 0.015 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C LEU B 247 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU B 247 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 248 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 596 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C TYR D 596 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR D 596 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR D 597 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 596 " -0.007 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C TYR B 596 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR B 596 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR B 597 " -0.009 2.00e-02 2.50e+03 ... (remaining 3513 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3834 2.78 - 3.31: 19368 3.31 - 3.84: 32575 3.84 - 4.37: 38379 4.37 - 4.90: 67209 Nonbonded interactions: 161365 Sorted by model distance: nonbonded pdb=" OE2 GLU D 501 " pdb="MG MG D 903 " model vdw 2.248 2.170 nonbonded pdb=" OE2 GLU B 501 " pdb="MG MG B 903 " model vdw 2.305 2.170 nonbonded pdb=" OE2 GLU A 501 " pdb="MG MG A 903 " model vdw 2.320 2.170 nonbonded pdb=" OE2 GLU C 501 " pdb="MG MG C 903 " model vdw 2.346 2.170 nonbonded pdb=" N THR D 633 " pdb=" OG1 THR D 633 " model vdw 2.464 2.496 ... (remaining 161360 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 518 or (resid 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 or (resid 521 through 523 and (name N o \ r name CA or name C or name O or name CB )) or resid 524 through 525 or (resid 5 \ 26 through 527 and (name N or name CA or name C or name O or name CB )) or resid \ 528 or (resid 529 through 530 and (name N or name CA or name C or name O or nam \ e CB )) or resid 531 through 647 or resid 693 through 905)) selection = chain 'B' selection = (chain 'C' and (resid 44 through 518 or (resid 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 or (resid 521 through 523 and (name N o \ r name CA or name C or name O or name CB )) or resid 524 through 525 or (resid 5 \ 26 through 527 and (name N or name CA or name C or name O or name CB )) or resid \ 528 or (resid 529 through 530 and (name N or name CA or name C or name O or nam \ e CB )) or resid 531 through 647 or resid 693 through 905)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 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: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.850 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20716 Z= 0.196 Angle : 0.525 6.078 28060 Z= 0.299 Chirality : 0.042 0.186 3294 Planarity : 0.003 0.032 3516 Dihedral : 9.900 89.149 7808 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.23 % Allowed : 4.30 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2528 helix: 1.78 (0.16), residues: 1030 sheet: -0.42 (0.27), residues: 376 loop : 0.03 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 215 TYR 0.012 0.001 TYR B 603 PHE 0.020 0.002 PHE C 612 TRP 0.014 0.001 TRP C 183 HIS 0.003 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (20708) covalent geometry : angle 0.52543 / 0.30 (28044) SS BOND : bond 0.00253 / 0.17 ( 8) SS BOND : angle 0.50679 / 0.29 ( 16) hydrogen bonds : bond 0.12213 / 8.60 ( 972) hydrogen bonds : angle 6.45970 / 4.68 ( 2850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 338 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6720 (t-170) REVERT: B 633 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8455 (m) REVERT: C 192 LEU cc_start: 0.7741 (mt) cc_final: 0.7538 (mt) REVERT: C 477 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7195 (ttpp) REVERT: D 264 LEU cc_start: 0.6664 (tp) cc_final: 0.6435 (tp) REVERT: D 633 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8516 (m) outliers start: 28 outliers final: 3 residues processed: 366 average time/residue: 0.1669 time to fit residues: 91.3046 Evaluate side-chains 189 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 477 LYS Chi-restraints excluded: chain D residue 633 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 447 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN C 85 ASN C 352 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.074645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.057649 restraints weight = 115376.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.056341 restraints weight = 72068.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.056836 restraints weight = 58839.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057162 restraints weight = 45971.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.057222 restraints weight = 42502.674| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20716 Z= 0.224 Angle : 0.636 10.848 28060 Z= 0.324 Chirality : 0.042 0.159 3294 Planarity : 0.004 0.052 3516 Dihedral : 6.657 77.468 2894 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.03 % Allowed : 9.79 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2528 helix: 1.88 (0.16), residues: 1042 sheet: -0.23 (0.28), residues: 368 loop : 0.17 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 724 TYR 0.019 0.001 TYR A 597 PHE 0.019 0.002 PHE C 612 TRP 0.014 0.002 TRP A 183 HIS 0.004 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (20708) covalent geometry : angle 0.63574 / 0.32 (28044) SS BOND : bond 0.00404 / 0.26 ( 8) SS BOND : angle 0.60629 / 0.35 ( 16) hydrogen bonds : bond 0.04046 / 2.76 ( 972) hydrogen bonds : angle 5.07224 / 3.67 ( 2850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 183 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ARG cc_start: 0.9295 (ttm170) cc_final: 0.9082 (ttm110) REVERT: B 349 GLU cc_start: 0.9335 (tt0) cc_final: 0.8926 (tp30) REVERT: B 581 TYR cc_start: 0.8458 (t80) cc_final: 0.8253 (t80) REVERT: B 633 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8790 (p) REVERT: B 642 MET cc_start: 0.8196 (tpp) cc_final: 0.7852 (tpp) REVERT: C 344 MET cc_start: 0.9484 (tmm) cc_final: 0.9094 (tmm) REVERT: C 725 MET cc_start: 0.8902 (tmm) cc_final: 0.8666 (ppp) REVERT: D 145 MET cc_start: 0.8627 (mpp) cc_final: 0.8410 (mmm) REVERT: D 200 SER cc_start: 0.9367 (m) cc_final: 0.9122 (p) REVERT: D 248 LEU cc_start: 0.9615 (tp) cc_final: 0.9179 (tt) REVERT: D 256 SER cc_start: 0.9116 (m) cc_final: 0.8647 (p) REVERT: D 270 MET cc_start: 0.4173 (pmm) cc_final: 0.2183 (tmm) REVERT: D 349 GLU cc_start: 0.9347 (tt0) cc_final: 0.8876 (tp30) REVERT: D 401 MET cc_start: 0.9046 (mmm) cc_final: 0.8800 (mmm) REVERT: D 619 LYS cc_start: 0.9168 (ptmt) cc_final: 0.8941 (ptpp) REVERT: D 633 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8875 (p) REVERT: D 642 MET cc_start: 0.8181 (tpp) cc_final: 0.7874 (tpp) outliers start: 69 outliers final: 39 residues processed: 244 average time/residue: 0.1342 time to fit residues: 52.2848 Evaluate side-chains 198 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 593 HIS Chi-restraints excluded: chain D residue 633 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 169 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 135 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.074898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.057867 restraints weight = 115678.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056929 restraints weight = 71098.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.057377 restraints weight = 54577.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.057853 restraints weight = 43815.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057839 restraints weight = 39983.051| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20716 Z= 0.147 Angle : 0.561 10.828 28060 Z= 0.281 Chirality : 0.041 0.174 3294 Planarity : 0.003 0.039 3516 Dihedral : 6.328 67.137 2882 Min Nonbonded Distance : 1.536 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.46 % Allowed : 10.71 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.17), residues: 2528 helix: 2.01 (0.16), residues: 1056 sheet: -0.11 (0.28), residues: 368 loop : 0.30 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 236 TYR 0.024 0.001 TYR B 81 PHE 0.015 0.001 PHE D 67 TRP 0.010 0.001 TRP A 183 HIS 0.002 0.000 HIS C 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (20708) covalent geometry : angle 0.56079 / 0.28 (28044) SS BOND : bond 0.00238 / 0.15 ( 8) SS BOND : angle 0.43034 / 0.27 ( 16) hydrogen bonds : bond 0.03539 / 2.39 ( 972) hydrogen bonds : angle 4.84762 / 3.50 ( 2850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9585 (tmm) cc_final: 0.9352 (tmm) REVERT: A 514 MET cc_start: 0.8830 (tpp) cc_final: 0.8413 (tpp) REVERT: B 349 GLU cc_start: 0.9303 (tt0) cc_final: 0.8868 (tp30) REVERT: B 401 MET cc_start: 0.9071 (mmm) cc_final: 0.8822 (mmm) REVERT: B 633 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 642 MET cc_start: 0.8265 (tpp) cc_final: 0.7770 (tpp) REVERT: C 172 MET cc_start: 0.3330 (tpp) cc_final: 0.3064 (tpt) REVERT: C 203 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8102 (t0) REVERT: C 344 MET cc_start: 0.9539 (tmm) cc_final: 0.9094 (tmm) REVERT: D 160 TRP cc_start: 0.8463 (m100) cc_final: 0.8145 (m100) REVERT: D 200 SER cc_start: 0.9341 (m) cc_final: 0.8762 (p) REVERT: D 248 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9155 (tt) REVERT: D 270 MET cc_start: 0.4143 (pmm) cc_final: 0.2771 (ppp) REVERT: D 349 GLU cc_start: 0.9315 (tt0) cc_final: 0.8834 (tp30) REVERT: D 401 MET cc_start: 0.9056 (mmm) cc_final: 0.8736 (mmm) REVERT: D 630 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8660 (mmmm) REVERT: D 642 MET cc_start: 0.8175 (tpp) cc_final: 0.7711 (tpp) outliers start: 56 outliers final: 29 residues processed: 209 average time/residue: 0.1223 time to fit residues: 41.3679 Evaluate side-chains 184 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 593 HIS Chi-restraints excluded: chain D residue 630 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 103 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** 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 = 0.3804 r_free = 0.3804 target = 0.073372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055811 restraints weight = 117386.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.055061 restraints weight = 71538.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055719 restraints weight = 54092.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055971 restraints weight = 43908.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055982 restraints weight = 41657.141| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20716 Z= 0.204 Angle : 0.597 8.607 28060 Z= 0.304 Chirality : 0.041 0.154 3294 Planarity : 0.003 0.039 3516 Dihedral : 6.410 71.659 2881 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.94 % Allowed : 10.36 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.17), residues: 2528 helix: 1.99 (0.16), residues: 1046 sheet: 0.07 (0.28), residues: 384 loop : 0.36 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 226 TYR 0.018 0.001 TYR A 597 PHE 0.022 0.002 PHE A 171 TRP 0.010 0.001 TRP C 183 HIS 0.004 0.001 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (20708) covalent geometry : angle 0.59717 / 0.30 (28044) SS BOND : bond 0.00306 / 0.21 ( 8) SS BOND : angle 0.58756 / 0.36 ( 16) hydrogen bonds : bond 0.03721 / 2.53 ( 972) hydrogen bonds : angle 4.96251 / 3.58 ( 2850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 164 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8031 (ptp) cc_final: 0.7671 (ptp) REVERT: A 344 MET cc_start: 0.9601 (tmm) cc_final: 0.9200 (tmm) REVERT: A 345 LEU cc_start: 0.9714 (mt) cc_final: 0.9433 (mt) REVERT: A 514 MET cc_start: 0.8869 (tpp) cc_final: 0.8517 (tpp) REVERT: B 256 SER cc_start: 0.9406 (m) cc_final: 0.8989 (p) REVERT: B 349 GLU cc_start: 0.9348 (tt0) cc_final: 0.8923 (tp30) REVERT: B 401 MET cc_start: 0.9190 (mmm) cc_final: 0.8951 (mmm) REVERT: B 552 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8790 (tt) REVERT: B 581 TYR cc_start: 0.8640 (t80) cc_final: 0.8338 (t80) REVERT: B 633 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 642 MET cc_start: 0.8332 (tpp) cc_final: 0.7772 (tpp) REVERT: C 172 MET cc_start: 0.3339 (tpp) cc_final: 0.3061 (tpt) REVERT: C 310 MET cc_start: 0.7984 (ptp) cc_final: 0.7687 (ptp) REVERT: C 344 MET cc_start: 0.9559 (tmm) cc_final: 0.9134 (tmm) REVERT: D 160 TRP cc_start: 0.8732 (m100) cc_final: 0.8339 (m100) REVERT: D 200 SER cc_start: 0.9269 (m) cc_final: 0.8990 (p) REVERT: D 248 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9212 (tt) REVERT: D 270 MET cc_start: 0.4433 (pmm) cc_final: 0.3835 (ppp) REVERT: D 284 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8076 (tp30) REVERT: D 349 GLU cc_start: 0.9328 (tt0) cc_final: 0.8923 (tp30) REVERT: D 401 MET cc_start: 0.9127 (mmm) cc_final: 0.8854 (mmm) REVERT: D 642 MET cc_start: 0.8326 (tpp) cc_final: 0.7773 (tpp) outliers start: 67 outliers final: 45 residues processed: 219 average time/residue: 0.1208 time to fit residues: 43.6672 Evaluate side-chains 198 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 583 ASP Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 593 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 136 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.071382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.053402 restraints weight = 108653.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052404 restraints weight = 59878.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052924 restraints weight = 47541.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053594 restraints weight = 37156.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053526 restraints weight = 32980.804| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20716 Z= 0.157 Angle : 0.564 10.124 28060 Z= 0.284 Chirality : 0.040 0.147 3294 Planarity : 0.003 0.040 3516 Dihedral : 6.312 69.948 2881 Min Nonbonded Distance : 1.159 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.37 % Allowed : 11.85 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.17), residues: 2528 helix: 2.11 (0.16), residues: 1048 sheet: -0.04 (0.27), residues: 406 loop : 0.41 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 226 TYR 0.022 0.001 TYR D 581 PHE 0.029 0.001 PHE A 171 TRP 0.009 0.001 TRP C 183 HIS 0.002 0.001 HIS B 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (20708) covalent geometry : angle 0.56368 / 0.28 (28044) SS BOND : bond 0.00229 / 0.15 ( 8) SS BOND : angle 0.46026 / 0.29 ( 16) hydrogen bonds : bond 0.03311 / 2.24 ( 972) hydrogen bonds : angle 4.81351 / 3.46 ( 2850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8053 (ptp) cc_final: 0.7672 (ptp) REVERT: A 344 MET cc_start: 0.9639 (tmm) cc_final: 0.9290 (tmm) REVERT: A 345 LEU cc_start: 0.9705 (mt) cc_final: 0.9462 (mt) REVERT: A 540 ASN cc_start: 0.8936 (m-40) cc_final: 0.8622 (t0) REVERT: B 248 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9181 (tt) REVERT: B 256 SER cc_start: 0.9388 (m) cc_final: 0.8979 (p) REVERT: B 349 GLU cc_start: 0.9379 (tt0) cc_final: 0.8926 (tp30) REVERT: B 401 MET cc_start: 0.9219 (mmm) cc_final: 0.8992 (mmm) REVERT: B 418 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8984 (mp) REVERT: B 552 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8807 (tt) REVERT: B 581 TYR cc_start: 0.8616 (t80) cc_final: 0.8354 (t80) REVERT: B 633 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8686 (p) REVERT: B 642 MET cc_start: 0.8355 (tpp) cc_final: 0.7748 (tpp) REVERT: C 172 MET cc_start: 0.3158 (tpp) cc_final: 0.2876 (tpt) REVERT: C 310 MET cc_start: 0.8092 (ptp) cc_final: 0.7731 (ptp) REVERT: C 344 MET cc_start: 0.9593 (tmm) cc_final: 0.9204 (tmm) REVERT: C 345 LEU cc_start: 0.9678 (mt) cc_final: 0.9459 (mt) REVERT: D 160 TRP cc_start: 0.8774 (m100) cc_final: 0.8427 (m100) REVERT: D 248 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9197 (tt) REVERT: D 256 SER cc_start: 0.9261 (m) cc_final: 0.8842 (p) REVERT: D 270 MET cc_start: 0.4377 (pmm) cc_final: 0.3979 (ppp) REVERT: D 349 GLU cc_start: 0.9383 (tt0) cc_final: 0.8922 (tp30) REVERT: D 401 MET cc_start: 0.9128 (mmm) cc_final: 0.8853 (mmm) REVERT: D 418 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9015 (mp) REVERT: D 642 MET cc_start: 0.8267 (tpp) cc_final: 0.7667 (tpp) outliers start: 54 outliers final: 36 residues processed: 193 average time/residue: 0.1244 time to fit residues: 40.0912 Evaluate side-chains 181 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 583 ASP Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 593 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 128 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 138 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 242 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.071735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.052062 restraints weight = 108080.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052156 restraints weight = 68552.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.052907 restraints weight = 46242.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.052949 restraints weight = 35135.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053095 restraints weight = 33640.517| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20716 Z= 0.116 Angle : 0.548 10.317 28060 Z= 0.274 Chirality : 0.040 0.165 3294 Planarity : 0.003 0.047 3516 Dihedral : 6.196 69.028 2881 Min Nonbonded Distance : 1.178 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 13.13 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.18), residues: 2528 helix: 2.30 (0.16), residues: 1036 sheet: 0.14 (0.28), residues: 396 loop : 0.46 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 387 TYR 0.020 0.001 TYR D 581 PHE 0.028 0.001 PHE A 171 TRP 0.008 0.001 TRP C 183 HIS 0.005 0.000 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (20708) covalent geometry : angle 0.54764 / 0.27 (28044) SS BOND : bond 0.00179 / 0.12 ( 8) SS BOND : angle 0.37728 / 0.24 ( 16) hydrogen bonds : bond 0.03107 / 2.10 ( 972) hydrogen bonds : angle 4.67667 / 3.36 ( 2850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8168 (ptp) cc_final: 0.7832 (ptp) REVERT: A 342 MET cc_start: 0.8838 (mtt) cc_final: 0.8261 (mmm) REVERT: A 344 MET cc_start: 0.9653 (tmm) cc_final: 0.9280 (tmm) REVERT: A 345 LEU cc_start: 0.9699 (mt) cc_final: 0.9424 (mt) REVERT: A 540 ASN cc_start: 0.8928 (m-40) cc_final: 0.8587 (t0) REVERT: B 248 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9171 (tt) REVERT: B 256 SER cc_start: 0.9376 (m) cc_final: 0.8982 (p) REVERT: B 349 GLU cc_start: 0.9404 (tt0) cc_final: 0.8934 (tp30) REVERT: B 401 MET cc_start: 0.9229 (mmm) cc_final: 0.8990 (mmm) REVERT: B 581 TYR cc_start: 0.8687 (t80) cc_final: 0.8459 (t80) REVERT: B 633 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8773 (p) REVERT: C 310 MET cc_start: 0.8111 (ptp) cc_final: 0.7714 (ptp) REVERT: C 344 MET cc_start: 0.9600 (tmm) cc_final: 0.9381 (tmm) REVERT: C 474 ILE cc_start: 0.9399 (mt) cc_final: 0.9154 (tt) REVERT: D 160 TRP cc_start: 0.9236 (m100) cc_final: 0.8882 (m100) REVERT: D 248 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9184 (tt) REVERT: D 256 SER cc_start: 0.9271 (m) cc_final: 0.8837 (p) REVERT: D 270 MET cc_start: 0.4239 (pmm) cc_final: 0.3993 (ppp) REVERT: D 342 MET cc_start: 0.9229 (ppp) cc_final: 0.9010 (ppp) REVERT: D 349 GLU cc_start: 0.9371 (tt0) cc_final: 0.8903 (tp30) REVERT: D 401 MET cc_start: 0.9162 (mmm) cc_final: 0.8864 (mmm) REVERT: D 418 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8984 (mp) REVERT: D 725 MET cc_start: 0.9184 (mmp) cc_final: 0.8720 (ppp) outliers start: 37 outliers final: 28 residues processed: 178 average time/residue: 0.1171 time to fit residues: 34.8266 Evaluate side-chains 174 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 593 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 145 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 112 optimal weight: 0.0010 chunk 121 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 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 = 0.3758 r_free = 0.3758 target = 0.071771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.050695 restraints weight = 107157.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051788 restraints weight = 62378.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.052273 restraints weight = 41119.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052326 restraints weight = 41780.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.053165 restraints weight = 34043.405| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20716 Z= 0.133 Angle : 0.565 13.024 28060 Z= 0.279 Chirality : 0.040 0.193 3294 Planarity : 0.003 0.038 3516 Dihedral : 6.221 69.052 2881 Min Nonbonded Distance : 1.191 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.84 % Allowed : 13.78 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.18), residues: 2528 helix: 2.29 (0.16), residues: 1044 sheet: 0.21 (0.28), residues: 396 loop : 0.52 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 387 TYR 0.018 0.001 TYR B 597 PHE 0.041 0.001 PHE A 171 TRP 0.007 0.001 TRP C 183 HIS 0.006 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (20708) covalent geometry : angle 0.56461 / 0.28 (28044) SS BOND : bond 0.00204 / 0.14 ( 8) SS BOND : angle 0.41261 / 0.26 ( 16) hydrogen bonds : bond 0.03132 / 2.13 ( 972) hydrogen bonds : angle 4.69641 / 3.38 ( 2850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 212 MET cc_start: 0.9270 (mpp) cc_final: 0.8865 (mtm) REVERT: A 310 MET cc_start: 0.8180 (ptp) cc_final: 0.7848 (ptp) REVERT: A 342 MET cc_start: 0.8826 (mtt) cc_final: 0.8275 (mmm) REVERT: A 344 MET cc_start: 0.9655 (tmm) cc_final: 0.9432 (tmm) REVERT: A 540 ASN cc_start: 0.8739 (m-40) cc_final: 0.8399 (t0) REVERT: B 50 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8176 (tpp80) REVERT: B 170 LEU cc_start: 0.7884 (mt) cc_final: 0.7384 (tp) REVERT: B 248 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9186 (tt) REVERT: B 256 SER cc_start: 0.9362 (m) cc_final: 0.8953 (p) REVERT: B 401 MET cc_start: 0.9221 (mmm) cc_final: 0.8977 (mmm) REVERT: B 581 TYR cc_start: 0.8683 (t80) cc_final: 0.8468 (t80) REVERT: B 633 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8773 (p) REVERT: B 725 MET cc_start: 0.9026 (mmp) cc_final: 0.8585 (ppp) REVERT: C 145 MET cc_start: 0.6635 (tpp) cc_final: 0.6013 (tpp) REVERT: C 172 MET cc_start: 0.3281 (tpt) cc_final: 0.3054 (tpt) REVERT: C 310 MET cc_start: 0.8131 (ptp) cc_final: 0.7723 (ptp) REVERT: C 344 MET cc_start: 0.9537 (tmm) cc_final: 0.9302 (tmm) REVERT: D 160 TRP cc_start: 0.9253 (m100) cc_final: 0.8909 (m100) REVERT: D 248 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9191 (tt) REVERT: D 256 SER cc_start: 0.9377 (m) cc_final: 0.8929 (p) REVERT: D 270 MET cc_start: 0.4582 (pmm) cc_final: 0.4180 (ppp) REVERT: D 377 MET cc_start: 0.8862 (tmm) cc_final: 0.8615 (tmm) REVERT: D 401 MET cc_start: 0.9160 (mmm) cc_final: 0.8843 (mmm) REVERT: D 418 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9030 (mp) REVERT: D 642 MET cc_start: 0.8289 (tpp) cc_final: 0.7911 (tpp) outliers start: 42 outliers final: 32 residues processed: 179 average time/residue: 0.1170 time to fit residues: 35.5649 Evaluate side-chains 176 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 593 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 190 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.070943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.053093 restraints weight = 118685.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.051999 restraints weight = 73582.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052360 restraints weight = 60763.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.052612 restraints weight = 50323.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052668 restraints weight = 45790.125| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 20716 Z= 0.346 Angle : 0.772 15.385 28060 Z= 0.386 Chirality : 0.044 0.182 3294 Planarity : 0.004 0.044 3516 Dihedral : 7.343 75.725 2881 Min Nonbonded Distance : 1.192 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.72 % Allowed : 13.78 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2528 helix: 1.48 (0.16), residues: 1046 sheet: 0.14 (0.29), residues: 372 loop : 0.05 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 724 TYR 0.027 0.002 TYR A 597 PHE 0.025 0.002 PHE D 67 TRP 0.011 0.001 TRP C 183 HIS 0.009 0.002 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.35 (20708) covalent geometry : angle 0.77197 / 0.39 (28044) SS BOND : bond 0.00458 / 0.32 ( 8) SS BOND : angle 1.06370 / 0.68 ( 16) hydrogen bonds : bond 0.04477 / 3.05 ( 972) hydrogen bonds : angle 5.43002 / 3.89 ( 2850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 142 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 294 HIS cc_start: 0.8329 (OUTLIER) cc_final: 0.7759 (m-70) REVERT: A 310 MET cc_start: 0.8256 (ptp) cc_final: 0.7895 (ptp) REVERT: A 344 MET cc_start: 0.9643 (tmm) cc_final: 0.9439 (tmm) REVERT: B 50 ARG cc_start: 0.8330 (tpp80) cc_final: 0.8123 (tpp80) REVERT: B 170 LEU cc_start: 0.8049 (mt) cc_final: 0.7474 (tp) REVERT: B 248 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9250 (tt) REVERT: B 256 SER cc_start: 0.9417 (m) cc_final: 0.8984 (p) REVERT: B 401 MET cc_start: 0.9260 (mmm) cc_final: 0.9005 (mmm) REVERT: B 552 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9058 (tp) REVERT: B 633 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8776 (p) REVERT: C 310 MET cc_start: 0.8207 (ptp) cc_final: 0.7869 (ptp) REVERT: C 344 MET cc_start: 0.9572 (tmm) cc_final: 0.9294 (tmm) REVERT: D 160 TRP cc_start: 0.9148 (m100) cc_final: 0.8797 (m100) REVERT: D 248 LEU cc_start: 0.9663 (tp) cc_final: 0.9282 (tt) REVERT: D 256 SER cc_start: 0.9343 (m) cc_final: 0.8915 (p) REVERT: D 270 MET cc_start: 0.4372 (pmm) cc_final: 0.3924 (ppp) REVERT: D 642 MET cc_start: 0.8613 (tpp) cc_final: 0.8137 (tpp) REVERT: D 725 MET cc_start: 0.9181 (mmp) cc_final: 0.8798 (ppp) outliers start: 62 outliers final: 44 residues processed: 191 average time/residue: 0.1079 time to fit residues: 35.4563 Evaluate side-chains 179 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 593 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 178 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 564 GLN ** B 185 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 = 0.3765 r_free = 0.3765 target = 0.071313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.051728 restraints weight = 109247.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.052167 restraints weight = 66873.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.052739 restraints weight = 46706.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.052661 restraints weight = 42440.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052974 restraints weight = 35744.174| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20716 Z= 0.114 Angle : 0.609 14.011 28060 Z= 0.299 Chirality : 0.041 0.205 3294 Planarity : 0.003 0.040 3516 Dihedral : 6.650 70.493 2881 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.32 % Allowed : 15.19 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2528 helix: 2.09 (0.16), residues: 1032 sheet: 0.13 (0.29), residues: 386 loop : 0.40 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.023 0.001 TYR A 597 PHE 0.022 0.001 PHE D 309 TRP 0.012 0.001 TRP C 183 HIS 0.005 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20708) covalent geometry : angle 0.60888 / 0.30 (28044) SS BOND : bond 0.00178 / 0.12 ( 8) SS BOND : angle 0.43628 / 0.27 ( 16) hydrogen bonds : bond 0.03311 / 2.23 ( 972) hydrogen bonds : angle 4.82282 / 3.46 ( 2850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8214 (ptp) cc_final: 0.7823 (ptp) REVERT: A 342 MET cc_start: 0.8966 (mtt) cc_final: 0.8368 (mmm) REVERT: A 344 MET cc_start: 0.9668 (tmm) cc_final: 0.9381 (tmm) REVERT: A 540 ASN cc_start: 0.9037 (m-40) cc_final: 0.8637 (t0) REVERT: B 170 LEU cc_start: 0.7860 (mt) cc_final: 0.7332 (tp) REVERT: B 172 MET cc_start: 0.4329 (ttt) cc_final: 0.3922 (ttt) REVERT: B 248 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9184 (tt) REVERT: B 256 SER cc_start: 0.9369 (m) cc_final: 0.8960 (p) REVERT: B 401 MET cc_start: 0.9236 (mmm) cc_final: 0.9002 (mmm) REVERT: B 633 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (p) REVERT: C 294 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7826 (m-70) REVERT: C 310 MET cc_start: 0.8079 (ptp) cc_final: 0.7691 (ptp) REVERT: C 344 MET cc_start: 0.9573 (tmm) cc_final: 0.9330 (tmm) REVERT: C 474 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9153 (tt) REVERT: C 540 ASN cc_start: 0.9015 (m-40) cc_final: 0.8612 (t0) REVERT: D 160 TRP cc_start: 0.9332 (m100) cc_final: 0.9023 (m100) REVERT: D 248 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9194 (tt) REVERT: D 256 SER cc_start: 0.9390 (m) cc_final: 0.8963 (p) REVERT: D 725 MET cc_start: 0.9153 (mmp) cc_final: 0.8741 (ppp) outliers start: 30 outliers final: 23 residues processed: 162 average time/residue: 0.1211 time to fit residues: 33.1402 Evaluate side-chains 166 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 593 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 162 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.0470 chunk 172 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 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 = 0.3752 r_free = 0.3752 target = 0.070720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.049727 restraints weight = 109787.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.051338 restraints weight = 58501.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052375 restraints weight = 39725.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053088 restraints weight = 31000.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.053524 restraints weight = 26222.042| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20716 Z= 0.147 Angle : 0.615 14.250 28060 Z= 0.300 Chirality : 0.041 0.178 3294 Planarity : 0.003 0.039 3516 Dihedral : 6.616 70.320 2881 Min Nonbonded Distance : 1.135 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.49 % Allowed : 15.28 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.18), residues: 2528 helix: 2.05 (0.16), residues: 1046 sheet: 0.36 (0.29), residues: 384 loop : 0.45 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 387 TYR 0.022 0.001 TYR A 597 PHE 0.028 0.001 PHE D 309 TRP 0.008 0.001 TRP C 183 HIS 0.007 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (20708) covalent geometry : angle 0.61526 / 0.30 (28044) SS BOND : bond 0.00249 / 0.17 ( 8) SS BOND : angle 0.56283 / 0.35 ( 16) hydrogen bonds : bond 0.03376 / 2.28 ( 972) hydrogen bonds : angle 4.82403 / 3.46 ( 2850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 MET cc_start: 0.8929 (mtt) cc_final: 0.8347 (mmm) REVERT: A 540 ASN cc_start: 0.8782 (m-40) cc_final: 0.8373 (t0) REVERT: A 642 MET cc_start: 0.8303 (mmt) cc_final: 0.8101 (mmp) REVERT: B 170 LEU cc_start: 0.7679 (mt) cc_final: 0.7257 (tp) REVERT: B 172 MET cc_start: 0.4887 (ttt) cc_final: 0.4634 (ttt) REVERT: B 248 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9195 (tt) REVERT: B 256 SER cc_start: 0.9353 (m) cc_final: 0.8945 (p) REVERT: B 377 MET cc_start: 0.8773 (tmm) cc_final: 0.7878 (tmm) REVERT: C 294 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7753 (m-70) REVERT: C 310 MET cc_start: 0.8013 (ptp) cc_final: 0.7611 (ptp) REVERT: C 344 MET cc_start: 0.9559 (tmm) cc_final: 0.9303 (tmm) REVERT: C 540 ASN cc_start: 0.8760 (m-40) cc_final: 0.8371 (t0) REVERT: D 160 TRP cc_start: 0.9510 (m100) cc_final: 0.9255 (m100) REVERT: D 207 MET cc_start: 0.9000 (mmt) cc_final: 0.8578 (mmm) REVERT: D 248 LEU cc_start: 0.9579 (tp) cc_final: 0.9190 (tt) REVERT: D 256 SER cc_start: 0.9388 (m) cc_final: 0.8964 (p) REVERT: D 377 MET cc_start: 0.8864 (tmm) cc_final: 0.7997 (tmm) outliers start: 34 outliers final: 29 residues processed: 164 average time/residue: 0.1099 time to fit residues: 30.7647 Evaluate side-chains 164 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 593 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 142 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 88 optimal weight: 0.0050 chunk 117 optimal weight: 0.0870 chunk 242 optimal weight: 0.8980 chunk 195 optimal weight: 40.0000 chunk 202 optimal weight: 0.0980 chunk 80 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.2310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 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 = 0.3796 r_free = 0.3796 target = 0.072418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.054036 restraints weight = 109299.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.054018 restraints weight = 56897.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054464 restraints weight = 47325.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054486 restraints weight = 39364.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.054683 restraints weight = 35442.279| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20716 Z= 0.099 Angle : 0.611 14.383 28060 Z= 0.294 Chirality : 0.041 0.161 3294 Planarity : 0.003 0.038 3516 Dihedral : 6.239 68.351 2880 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.10 % Allowed : 15.67 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.18), residues: 2528 helix: 2.24 (0.16), residues: 1034 sheet: 0.07 (0.28), residues: 388 loop : 0.56 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 599 TYR 0.026 0.001 TYR A 597 PHE 0.025 0.001 PHE A 171 TRP 0.007 0.001 TRP C 183 HIS 0.004 0.000 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (20708) covalent geometry : angle 0.61153 / 0.29 (28044) SS BOND : bond 0.00129 / 0.09 ( 8) SS BOND : angle 0.34506 / 0.20 ( 16) hydrogen bonds : bond 0.03019 / 2.04 ( 972) hydrogen bonds : angle 4.63621 / 3.32 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3005.78 seconds wall clock time: 52 minutes 56.33 seconds (3176.33 seconds total)