Starting phenix.real_space_refine on Mon Dec 30 06:53:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrr_36603/12_2024/8jrr_36603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrr_36603/12_2024/8jrr_36603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jrr_36603/12_2024/8jrr_36603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrr_36603/12_2024/8jrr_36603.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrr_36603/12_2024/8jrr_36603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrr_36603/12_2024/8jrr_36603.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 70 5.16 5 C 7868 2.51 5 N 2108 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5087 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 27, 'TRANS': 617} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1096 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5263 SG CYS B 37 62.978 32.443 94.524 1.00178.25 S ATOM 5537 SG CYS B 70 60.683 35.235 93.633 1.00162.28 S ATOM 5560 SG CYS B 73 63.463 37.412 93.236 1.00146.37 S ATOM 5901 SG CYS B 113 59.383 34.814 78.871 1.00162.87 S ATOM 6163 SG CYS B 143 58.033 35.303 75.513 1.00192.52 S Restraints were copied for chains: D, C Time building chain proxies: 10.87, per 1000 atoms: 0.88 Number of scatterers: 12370 At special positions: 0 Unit cell: (138.159, 108.171, 111.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 70 16.00 O 2320 8.00 N 2108 7.00 C 7868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 73 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 73 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 10 sheets defined 50.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 146 through 152 removed outlier: 3.609A pdb=" N ILE A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.693A pdb=" N SER A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.246A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.254A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Proline residue: A 265 - end of helix removed outlier: 3.575A pdb=" N GLU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.974A pdb=" N ARG A 279 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 removed outlier: 3.568A pdb=" N LEU A 286 " --> pdb=" O TYR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.357A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.586A pdb=" N GLU A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix removed outlier: 3.624A pdb=" N LYS A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 removed outlier: 5.070A pdb=" N LEU A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 4.059A pdb=" N GLU A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.928A pdb=" N ILE A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.795A pdb=" N CYS A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.760A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.216A pdb=" N VAL A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 506 removed outlier: 5.158A pdb=" N LEU A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 4.351A pdb=" N SER A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 3.757A pdb=" N ASP A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.588A pdb=" N GLU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 611 through 623 removed outlier: 3.980A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 4.034A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 655 through 668 removed outlier: 3.895A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.888A pdb=" N PHE A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 742 removed outlier: 3.764A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 766 through 771 removed outlier: 4.333A pdb=" N LEU A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 766 through 771' Processing helix chain 'A' and resid 786 through 795 removed outlier: 3.914A pdb=" N TRP A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU A 792 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 removed outlier: 3.596A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 863 " --> pdb=" O LYS A 859 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 4.501A pdb=" N THR B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.566A pdb=" N TYR B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.651A pdb=" N SER B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 4.434A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 96' Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.749A pdb=" N LEU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.609A pdb=" N ILE C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.693A pdb=" N SER C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 246 removed outlier: 4.246A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 4.254A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 270 Proline residue: C 265 - end of helix removed outlier: 3.575A pdb=" N GLU C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.974A pdb=" N ARG C 279 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 286 removed outlier: 3.568A pdb=" N LEU C 286 " --> pdb=" O TYR C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.357A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 315 removed outlier: 3.586A pdb=" N GLU C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.624A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 5.070A pdb=" N LEU C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 4.059A pdb=" N GLU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.928A pdb=" N ILE C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 349 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.795A pdb=" N CYS C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 381 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.760A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 removed outlier: 4.216A pdb=" N VAL C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 506 removed outlier: 5.158A pdb=" N LEU C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 492 " --> pdb=" O THR C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 removed outlier: 4.351A pdb=" N SER C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 removed outlier: 3.757A pdb=" N ASP C 535 " --> pdb=" O HIS C 531 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 540 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 removed outlier: 3.588A pdb=" N GLU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 610 Processing helix chain 'C' and resid 611 through 623 removed outlier: 3.980A pdb=" N ILE C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 617 " --> pdb=" O THR C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 4.034A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 655 through 668 removed outlier: 3.895A pdb=" N SER C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 3.888A pdb=" N PHE C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 717 " --> pdb=" O PHE C 713 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 742 removed outlier: 3.764A pdb=" N GLY C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 766 through 771 removed outlier: 4.333A pdb=" N LEU C 770 " --> pdb=" O ASP C 766 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 771 " --> pdb=" O PHE C 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 766 through 771' Processing helix chain 'C' and resid 786 through 795 removed outlier: 3.914A pdb=" N TRP C 791 " --> pdb=" O ILE C 787 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C 792 " --> pdb=" O ARG C 788 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 868 removed outlier: 3.596A pdb=" N LEU C 858 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 861 " --> pdb=" O LYS C 857 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU C 863 " --> pdb=" O LYS C 859 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 865 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 removed outlier: 4.501A pdb=" N THR D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.566A pdb=" N TYR D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 51' Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.651A pdb=" N SER D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 4.434A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.749A pdb=" N LEU D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 526 removed outlier: 5.513A pdb=" N LEU A 523 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A 558 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU A 525 " --> pdb=" O GLU A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 590 through 593 removed outlier: 4.044A pdb=" N TRP A 600 " --> pdb=" O THR A 591 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 682 through 684 removed outlier: 3.834A pdb=" N ILE A 682 " --> pdb=" O TYR A 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 694 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 91 removed outlier: 7.279A pdb=" N ASN B 134 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B 89 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE B 132 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 135 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 523 through 526 removed outlier: 5.513A pdb=" N LEU C 523 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C 558 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 525 " --> pdb=" O GLU C 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 590 through 593 removed outlier: 4.044A pdb=" N TRP C 600 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 682 through 684 removed outlier: 3.834A pdb=" N ILE C 682 " --> pdb=" O TYR C 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR C 694 " --> pdb=" O ILE C 682 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 91 removed outlier: 7.279A pdb=" N ASN D 134 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER D 89 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE D 132 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 135 " --> pdb=" O ARG D 138 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 960 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: 3.70 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4008 1.34 - 1.46: 2618 1.46 - 1.58: 5850 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 12580 Sorted by residual: bond pdb=" CB PHE C 599 " pdb=" CG PHE C 599 " ideal model delta sigma weight residual 1.502 1.440 0.062 2.30e-02 1.89e+03 7.22e+00 bond pdb=" CB PHE A 599 " pdb=" CG PHE A 599 " ideal model delta sigma weight residual 1.502 1.440 0.062 2.30e-02 1.89e+03 7.22e+00 bond pdb=" CD LYS A 553 " pdb=" CE LYS A 553 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.17e+00 bond pdb=" CD LYS C 553 " pdb=" CE LYS C 553 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.17e+00 bond pdb=" CD2 PHE C 599 " pdb=" CE2 PHE C 599 " ideal model delta sigma weight residual 1.382 1.313 0.069 3.00e-02 1.11e+03 5.32e+00 ... (remaining 12575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 15972 2.03 - 4.07: 844 4.07 - 6.10: 116 6.10 - 8.14: 40 8.14 - 10.17: 8 Bond angle restraints: 16980 Sorted by residual: angle pdb=" N GLY A 433 " pdb=" CA GLY A 433 " pdb=" C GLY A 433 " ideal model delta sigma weight residual 114.25 109.09 5.16 1.30e+00 5.92e-01 1.58e+01 angle pdb=" N GLY C 433 " pdb=" CA GLY C 433 " pdb=" C GLY C 433 " ideal model delta sigma weight residual 114.25 109.09 5.16 1.30e+00 5.92e-01 1.58e+01 angle pdb=" CB LYS C 553 " pdb=" CG LYS C 553 " pdb=" CD LYS C 553 " ideal model delta sigma weight residual 111.30 103.44 7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB LYS A 553 " pdb=" CG LYS A 553 " pdb=" CD LYS A 553 " ideal model delta sigma weight residual 111.30 103.44 7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" C ILE B 135 " pdb=" N ARG B 136 " pdb=" CA ARG B 136 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 ... (remaining 16975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 6520 17.33 - 34.65: 968 34.65 - 51.98: 182 51.98 - 69.30: 38 69.30 - 86.63: 8 Dihedral angle restraints: 7716 sinusoidal: 3124 harmonic: 4592 Sorted by residual: dihedral pdb=" CA ALA C 320 " pdb=" C ALA C 320 " pdb=" N GLN C 321 " pdb=" CA GLN C 321 " ideal model delta harmonic sigma weight residual 180.00 148.23 31.77 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA ALA A 320 " pdb=" C ALA A 320 " pdb=" N GLN A 321 " pdb=" CA GLN A 321 " ideal model delta harmonic sigma weight residual 180.00 148.23 31.77 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA VAL A 509 " pdb=" C VAL A 509 " pdb=" N LEU A 510 " pdb=" CA LEU A 510 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 7713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1342 0.064 - 0.127: 482 0.127 - 0.190: 80 0.190 - 0.254: 4 0.254 - 0.317: 4 Chirality restraints: 1912 Sorted by residual: chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL C 234 " pdb=" CA VAL C 234 " pdb=" CG1 VAL C 234 " pdb=" CG2 VAL C 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE A 532 " pdb=" CA ILE A 532 " pdb=" CG1 ILE A 532 " pdb=" CG2 ILE A 532 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1909 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 582 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ILE A 582 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE A 582 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 583 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 582 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ILE C 582 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE C 582 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE C 583 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 19 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.67e+00 pdb=" N PRO B 20 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 20 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 20 " -0.036 5.00e-02 4.00e+02 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2646 2.76 - 3.30: 12628 3.30 - 3.83: 22008 3.83 - 4.37: 26504 4.37 - 4.90: 40111 Nonbonded interactions: 103897 Sorted by model distance: nonbonded pdb=" O GLY A 610 " pdb=" OG1 THR A 613 " model vdw 2.229 3.040 nonbonded pdb=" O GLY C 610 " pdb=" OG1 THR C 613 " model vdw 2.229 3.040 nonbonded pdb=" O SER A 476 " pdb=" OG1 THR A 479 " model vdw 2.249 3.040 nonbonded pdb=" O SER C 476 " pdb=" OG1 THR C 479 " model vdw 2.249 3.040 nonbonded pdb=" O ARG A 240 " pdb=" OG1 THR A 244 " model vdw 2.270 3.040 ... (remaining 103892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.910 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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 : 0.008 0.082 12580 Z= 0.529 Angle : 1.082 10.174 16980 Z= 0.584 Chirality : 0.063 0.317 1912 Planarity : 0.007 0.065 2186 Dihedral : 16.683 86.629 4720 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 1.66 % Allowed : 16.64 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.20), residues: 1496 helix: -4.04 (0.13), residues: 594 sheet: -1.99 (1.12), residues: 16 loop : -2.03 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 791 HIS 0.011 0.002 HIS A 655 PHE 0.027 0.004 PHE C 633 TYR 0.024 0.003 TYR C 592 ARG 0.009 0.001 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 453 time to evaluate : 1.472 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: 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 241 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7993 (mmp80) REVERT: A 287 PHE cc_start: 0.7461 (m-80) cc_final: 0.6954 (m-80) REVERT: A 313 MET cc_start: 0.7854 (tpp) cc_final: 0.7621 (tpp) REVERT: A 323 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8225 (mmtm) REVERT: A 328 TRP cc_start: 0.8479 (m-10) cc_final: 0.8012 (m-10) REVERT: A 339 MET cc_start: 0.8832 (ptp) cc_final: 0.8141 (ptp) REVERT: A 340 MET cc_start: 0.7518 (ptm) cc_final: 0.7150 (ptt) REVERT: A 345 GLN cc_start: 0.7717 (mt0) cc_final: 0.7082 (mt0) REVERT: A 354 ASN cc_start: 0.8127 (m-40) cc_final: 0.7868 (p0) REVERT: A 373 LYS cc_start: 0.8605 (tttp) cc_final: 0.8110 (mmmm) REVERT: A 397 ASP cc_start: 0.7125 (m-30) cc_final: 0.6845 (m-30) REVERT: A 403 GLU cc_start: 0.7481 (tp30) cc_final: 0.7213 (tm-30) REVERT: A 454 LEU cc_start: 0.8640 (tp) cc_final: 0.8404 (tt) REVERT: A 472 GLU cc_start: 0.8469 (pt0) cc_final: 0.8205 (pm20) REVERT: A 477 PHE cc_start: 0.8128 (m-80) cc_final: 0.7808 (m-80) REVERT: A 478 MET cc_start: 0.7861 (tpp) cc_final: 0.7486 (tpp) REVERT: A 507 ILE cc_start: 0.7956 (tp) cc_final: 0.7673 (tp) REVERT: A 510 LEU cc_start: 0.8252 (mp) cc_final: 0.7893 (mt) REVERT: A 515 GLN cc_start: 0.7559 (mp10) cc_final: 0.7300 (mp10) REVERT: A 537 LEU cc_start: 0.8320 (tp) cc_final: 0.7957 (tp) REVERT: A 539 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7505 (tpp80) REVERT: A 558 GLU cc_start: 0.8029 (pt0) cc_final: 0.7695 (pm20) REVERT: A 578 VAL cc_start: 0.8078 (t) cc_final: 0.7528 (t) REVERT: A 580 GLU cc_start: 0.7595 (tp30) cc_final: 0.7187 (tp30) REVERT: A 593 ASP cc_start: 0.8209 (t0) cc_final: 0.7873 (t0) REVERT: A 597 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8696 (mtpp) REVERT: A 621 LEU cc_start: 0.8694 (mm) cc_final: 0.8454 (mm) REVERT: A 625 ASN cc_start: 0.6998 (p0) cc_final: 0.6712 (p0) REVERT: A 635 MET cc_start: 0.7679 (mpp) cc_final: 0.7035 (mmp) REVERT: A 639 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7005 (mmm-85) REVERT: A 640 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7947 (mtmt) REVERT: A 649 ARG cc_start: 0.7660 (ppt170) cc_final: 0.7349 (ptt90) REVERT: A 663 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8093 (ptpp) REVERT: A 684 GLN cc_start: 0.7349 (tp40) cc_final: 0.5893 (tm-30) REVERT: A 694 TYR cc_start: 0.6839 (t80) cc_final: 0.6627 (t80) REVERT: A 730 PHE cc_start: 0.7215 (t80) cc_final: 0.6672 (t80) REVERT: A 739 MET cc_start: 0.7858 (ttm) cc_final: 0.7624 (ttm) REVERT: A 754 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 822 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8114 (mmtm) REVERT: B 25 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7754 (mp0) REVERT: B 38 VAL cc_start: 0.7628 (p) cc_final: 0.7228 (m) REVERT: B 58 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7112 (t) REVERT: B 59 ILE cc_start: 0.7017 (mm) cc_final: 0.5625 (mm) REVERT: B 107 LEU cc_start: 0.8132 (tp) cc_final: 0.7919 (mm) REVERT: B 121 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6576 (mm-30) REVERT: B 122 LYS cc_start: 0.7817 (mttp) cc_final: 0.7520 (mttp) REVERT: B 124 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6296 (mmm160) REVERT: C 146 TYR cc_start: 0.7902 (p90) cc_final: 0.6944 (p90) REVERT: C 235 ASP cc_start: 0.7024 (m-30) cc_final: 0.6819 (m-30) REVERT: C 241 ARG cc_start: 0.8400 (mmp80) cc_final: 0.7981 (mmp80) REVERT: C 287 PHE cc_start: 0.7626 (m-80) cc_final: 0.7086 (m-80) REVERT: C 323 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8294 (mmtm) REVERT: C 324 LEU cc_start: 0.8693 (mt) cc_final: 0.8318 (mt) REVERT: C 328 TRP cc_start: 0.8504 (m-10) cc_final: 0.8135 (m-10) REVERT: C 335 GLN cc_start: 0.8328 (mm110) cc_final: 0.8072 (mm110) REVERT: C 336 ILE cc_start: 0.8683 (mt) cc_final: 0.8201 (mt) REVERT: C 340 MET cc_start: 0.7315 (ptm) cc_final: 0.7002 (ptt) REVERT: C 345 GLN cc_start: 0.7773 (mt0) cc_final: 0.7166 (mt0) REVERT: C 394 GLU cc_start: 0.7176 (tt0) cc_final: 0.5602 (tt0) REVERT: C 397 ASP cc_start: 0.7808 (m-30) cc_final: 0.7602 (m-30) REVERT: C 450 ILE cc_start: 0.8325 (mt) cc_final: 0.8046 (mt) REVERT: C 478 MET cc_start: 0.7851 (tpp) cc_final: 0.7407 (tpp) REVERT: C 507 ILE cc_start: 0.8079 (tp) cc_final: 0.7831 (tp) REVERT: C 511 TYR cc_start: 0.7259 (m-80) cc_final: 0.7013 (m-80) REVERT: C 531 HIS cc_start: 0.7443 (m90) cc_final: 0.7093 (m90) REVERT: C 537 LEU cc_start: 0.8393 (tp) cc_final: 0.8058 (tp) REVERT: C 539 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7605 (tpp80) REVERT: C 545 MET cc_start: 0.7485 (ptt) cc_final: 0.7281 (ptt) REVERT: C 558 GLU cc_start: 0.8015 (pt0) cc_final: 0.7723 (pm20) REVERT: C 580 GLU cc_start: 0.7685 (tp30) cc_final: 0.7032 (tp30) REVERT: C 597 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8726 (mtpp) REVERT: C 639 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7096 (mmm-85) REVERT: C 648 PHE cc_start: 0.7629 (t80) cc_final: 0.7299 (t80) REVERT: C 649 ARG cc_start: 0.7374 (ppt170) cc_final: 0.6910 (tmm160) REVERT: C 651 LEU cc_start: 0.8484 (tp) cc_final: 0.8275 (tp) REVERT: C 663 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8362 (ptpp) REVERT: C 684 GLN cc_start: 0.7845 (tp40) cc_final: 0.7079 (tm-30) REVERT: C 712 GLU cc_start: 0.8486 (tt0) cc_final: 0.7343 (tp30) REVERT: C 731 LYS cc_start: 0.7706 (tptt) cc_final: 0.7407 (tptt) REVERT: C 734 ARG cc_start: 0.6790 (ttt180) cc_final: 0.6283 (ttt90) REVERT: C 739 MET cc_start: 0.7974 (ttm) cc_final: 0.7646 (ttm) REVERT: C 751 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7139 (tpt170) REVERT: C 801 GLN cc_start: 0.7911 (mt0) cc_final: 0.7702 (mt0) REVERT: C 822 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7971 (tptp) REVERT: D 38 VAL cc_start: 0.7675 (p) cc_final: 0.7293 (m) REVERT: D 55 ARG cc_start: 0.8223 (mpt-90) cc_final: 0.7937 (mmt-90) REVERT: D 58 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7482 (t) REVERT: D 121 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 122 LYS cc_start: 0.7846 (mttp) cc_final: 0.7534 (mttp) REVERT: D 124 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6351 (tpt90) outliers start: 22 outliers final: 10 residues processed: 465 average time/residue: 0.3410 time to fit residues: 208.5089 Evaluate side-chains 405 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 393 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 114 GLN C 517 GLN C 738 HIS ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 114 GLN D 125 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12580 Z= 0.210 Angle : 0.727 11.815 16980 Z= 0.378 Chirality : 0.047 0.260 1912 Planarity : 0.006 0.057 2186 Dihedral : 6.600 23.730 1688 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.23 % Allowed : 5.22 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.21), residues: 1496 helix: -3.15 (0.16), residues: 642 sheet: -2.16 (0.83), residues: 40 loop : -1.59 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 328 HIS 0.003 0.001 HIS B 85 PHE 0.032 0.002 PHE A 343 TYR 0.028 0.002 TYR C 464 ARG 0.009 0.001 ARG C 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 437 time to evaluate : 1.468 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: 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 138 GLU cc_start: 0.8085 (tp30) cc_final: 0.7547 (tp30) REVERT: A 146 TYR cc_start: 0.7874 (p90) cc_final: 0.7612 (p90) REVERT: A 241 ARG cc_start: 0.8550 (mmp80) cc_final: 0.7994 (mmp80) REVERT: A 245 ARG cc_start: 0.6948 (mtt90) cc_final: 0.6685 (mtt-85) REVERT: A 282 ASN cc_start: 0.8098 (t0) cc_final: 0.7795 (t0) REVERT: A 313 MET cc_start: 0.7540 (tpp) cc_final: 0.7294 (tpp) REVERT: A 323 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7481 (tptt) REVERT: A 324 LEU cc_start: 0.8456 (mt) cc_final: 0.7951 (mt) REVERT: A 328 TRP cc_start: 0.8474 (m-10) cc_final: 0.8203 (m-10) REVERT: A 336 ILE cc_start: 0.8931 (mt) cc_final: 0.8381 (mt) REVERT: A 339 MET cc_start: 0.8849 (ptp) cc_final: 0.8362 (ptp) REVERT: A 344 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7591 (tp-100) REVERT: A 354 ASN cc_start: 0.8189 (m-40) cc_final: 0.7869 (p0) REVERT: A 380 TYR cc_start: 0.7253 (t80) cc_final: 0.7046 (t80) REVERT: A 410 GLN cc_start: 0.8651 (pt0) cc_final: 0.8324 (pt0) REVERT: A 424 ARG cc_start: 0.7682 (ttt-90) cc_final: 0.7281 (tpt-90) REVERT: A 460 MET cc_start: 0.6079 (mpp) cc_final: 0.5144 (mpp) REVERT: A 472 GLU cc_start: 0.8393 (pt0) cc_final: 0.8183 (pp20) REVERT: A 477 PHE cc_start: 0.7903 (m-80) cc_final: 0.7478 (m-80) REVERT: A 478 MET cc_start: 0.7676 (tpp) cc_final: 0.7344 (tpp) REVERT: A 494 TYR cc_start: 0.6782 (t80) cc_final: 0.6536 (t80) REVERT: A 507 ILE cc_start: 0.8117 (tp) cc_final: 0.7827 (tp) REVERT: A 510 LEU cc_start: 0.8530 (mp) cc_final: 0.8078 (mm) REVERT: A 533 ILE cc_start: 0.8680 (mp) cc_final: 0.8240 (tp) REVERT: A 537 LEU cc_start: 0.7900 (tp) cc_final: 0.6981 (tp) REVERT: A 538 VAL cc_start: 0.8305 (p) cc_final: 0.7966 (p) REVERT: A 539 ARG cc_start: 0.8320 (tpp80) cc_final: 0.7600 (tpp80) REVERT: A 553 LYS cc_start: 0.6616 (tttp) cc_final: 0.6374 (tttp) REVERT: A 558 GLU cc_start: 0.7686 (pt0) cc_final: 0.7369 (pm20) REVERT: A 576 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6587 (tm-30) REVERT: A 578 VAL cc_start: 0.7779 (t) cc_final: 0.7519 (t) REVERT: A 597 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8863 (mtpp) REVERT: A 635 MET cc_start: 0.7691 (mpp) cc_final: 0.6772 (mpp) REVERT: A 639 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.6817 (mmm-85) REVERT: A 640 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7562 (mtmt) REVERT: A 648 PHE cc_start: 0.7370 (t80) cc_final: 0.7138 (t80) REVERT: A 651 LEU cc_start: 0.7835 (tp) cc_final: 0.7518 (tp) REVERT: A 663 LYS cc_start: 0.8621 (ptmm) cc_final: 0.8103 (ptpp) REVERT: A 684 GLN cc_start: 0.7234 (tp40) cc_final: 0.6255 (tm-30) REVERT: A 730 PHE cc_start: 0.6654 (t80) cc_final: 0.6171 (t80) REVERT: A 739 MET cc_start: 0.7942 (ttm) cc_final: 0.7681 (ttm) REVERT: A 754 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 801 GLN cc_start: 0.8150 (mt0) cc_final: 0.7874 (mt0) REVERT: A 822 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8014 (mmtm) REVERT: B 47 ARG cc_start: 0.6255 (tmt-80) cc_final: 0.6023 (tmt-80) REVERT: B 79 LYS cc_start: 0.8544 (tptt) cc_final: 0.8053 (tptt) REVERT: B 82 GLU cc_start: 0.7121 (pp20) cc_final: 0.6732 (pp20) REVERT: B 121 GLU cc_start: 0.7822 (mm-30) cc_final: 0.6712 (tp30) REVERT: B 124 ARG cc_start: 0.8000 (tpt170) cc_final: 0.7067 (mmm160) REVERT: B 133 HIS cc_start: 0.7084 (m-70) cc_final: 0.6695 (m-70) REVERT: C 240 ARG cc_start: 0.8900 (mtt180) cc_final: 0.8504 (mtt180) REVERT: C 241 ARG cc_start: 0.8486 (mmp80) cc_final: 0.8177 (mmp80) REVERT: C 251 LYS cc_start: 0.6974 (ptpp) cc_final: 0.6424 (mtmm) REVERT: C 282 ASN cc_start: 0.7888 (t0) cc_final: 0.7645 (t0) REVERT: C 287 PHE cc_start: 0.7330 (m-80) cc_final: 0.6750 (m-80) REVERT: C 290 VAL cc_start: 0.7361 (m) cc_final: 0.6905 (t) REVERT: C 323 LYS cc_start: 0.8377 (mmmt) cc_final: 0.7520 (tptt) REVERT: C 328 TRP cc_start: 0.8447 (m-10) cc_final: 0.8212 (m-10) REVERT: C 335 GLN cc_start: 0.7899 (mm110) cc_final: 0.7695 (mm110) REVERT: C 336 ILE cc_start: 0.8707 (mt) cc_final: 0.8500 (mt) REVERT: C 339 MET cc_start: 0.8741 (ptp) cc_final: 0.8420 (ptt) REVERT: C 340 MET cc_start: 0.7379 (ptm) cc_final: 0.7163 (ptt) REVERT: C 345 GLN cc_start: 0.7688 (mt0) cc_final: 0.6853 (mt0) REVERT: C 373 LYS cc_start: 0.8553 (tttp) cc_final: 0.7989 (tptp) REVERT: C 376 LYS cc_start: 0.8455 (tttm) cc_final: 0.8206 (tttm) REVERT: C 398 GLU cc_start: 0.8489 (mp0) cc_final: 0.7505 (mp0) REVERT: C 429 GLU cc_start: 0.7903 (mp0) cc_final: 0.7276 (pm20) REVERT: C 454 LEU cc_start: 0.8543 (tt) cc_final: 0.8169 (tp) REVERT: C 458 LEU cc_start: 0.6945 (mt) cc_final: 0.6719 (mt) REVERT: C 472 GLU cc_start: 0.8143 (pm20) cc_final: 0.7875 (pm20) REVERT: C 473 ASN cc_start: 0.8490 (m-40) cc_final: 0.8260 (m-40) REVERT: C 478 MET cc_start: 0.7616 (tpp) cc_final: 0.7325 (tpp) REVERT: C 494 TYR cc_start: 0.6879 (t80) cc_final: 0.6670 (t80) REVERT: C 511 TYR cc_start: 0.7563 (m-80) cc_final: 0.7019 (m-80) REVERT: C 533 ILE cc_start: 0.8382 (tp) cc_final: 0.8132 (tp) REVERT: C 537 LEU cc_start: 0.8009 (tp) cc_final: 0.7200 (tp) REVERT: C 538 VAL cc_start: 0.8290 (p) cc_final: 0.7944 (p) REVERT: C 539 ARG cc_start: 0.8225 (tpp80) cc_final: 0.7546 (ttt180) REVERT: C 542 MET cc_start: 0.7238 (mmp) cc_final: 0.7036 (mmp) REVERT: C 576 GLN cc_start: 0.7299 (tm-30) cc_final: 0.6729 (tm-30) REVERT: C 578 VAL cc_start: 0.8051 (t) cc_final: 0.7668 (t) REVERT: C 592 TYR cc_start: 0.7731 (t80) cc_final: 0.6514 (t80) REVERT: C 625 ASN cc_start: 0.7010 (p0) cc_final: 0.6355 (p0) REVERT: C 635 MET cc_start: 0.7741 (mpp) cc_final: 0.6788 (mpp) REVERT: C 639 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.6784 (mmm-85) REVERT: C 640 LYS cc_start: 0.8446 (mtmt) cc_final: 0.7879 (mtmt) REVERT: C 648 PHE cc_start: 0.7359 (t80) cc_final: 0.7089 (t80) REVERT: C 651 LEU cc_start: 0.8017 (tp) cc_final: 0.7705 (tp) REVERT: C 663 LYS cc_start: 0.8922 (ptmm) cc_final: 0.8232 (ptpp) REVERT: C 684 GLN cc_start: 0.7920 (tp40) cc_final: 0.7233 (tm-30) REVERT: C 739 MET cc_start: 0.7969 (ttm) cc_final: 0.7615 (ttm) REVERT: C 754 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8089 (mt-10) REVERT: C 784 SER cc_start: 0.6932 (t) cc_final: 0.6332 (m) REVERT: C 801 GLN cc_start: 0.7955 (mt0) cc_final: 0.7562 (mt0) REVERT: C 802 LYS cc_start: 0.7716 (mttp) cc_final: 0.7396 (mptt) REVERT: C 822 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7859 (tptp) REVERT: C 861 ARG cc_start: 0.6925 (ttp-110) cc_final: 0.6288 (mtp85) REVERT: D 47 ARG cc_start: 0.6274 (tmt-80) cc_final: 0.6035 (tpt170) REVERT: D 79 LYS cc_start: 0.8534 (tptt) cc_final: 0.7911 (tptt) REVERT: D 82 GLU cc_start: 0.7210 (pp20) cc_final: 0.6612 (pp20) REVERT: D 121 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6716 (mm-30) REVERT: D 124 ARG cc_start: 0.7952 (tpt170) cc_final: 0.6963 (mmm160) REVERT: D 133 HIS cc_start: 0.6963 (m-70) cc_final: 0.6546 (m-70) outliers start: 3 outliers final: 1 residues processed: 440 average time/residue: 0.3422 time to fit residues: 197.8381 Evaluate side-chains 394 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 chunk 116 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 47 optimal weight: 0.0970 chunk 112 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 611 GLN ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12580 Z= 0.181 Angle : 0.671 12.860 16980 Z= 0.344 Chirality : 0.045 0.221 1912 Planarity : 0.005 0.072 2186 Dihedral : 5.912 23.322 1688 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.21), residues: 1496 helix: -2.78 (0.16), residues: 660 sheet: -0.68 (1.16), residues: 16 loop : -1.46 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 791 HIS 0.004 0.001 HIS B 85 PHE 0.024 0.002 PHE A 633 TYR 0.028 0.001 TYR C 464 ARG 0.016 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.585 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: 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 164 VAL cc_start: 0.7462 (t) cc_final: 0.7237 (p) REVERT: A 235 ASP cc_start: 0.7834 (p0) cc_final: 0.7539 (m-30) REVERT: A 241 ARG cc_start: 0.8537 (mmp80) cc_final: 0.8086 (mmp80) REVERT: A 287 PHE cc_start: 0.7247 (m-80) cc_final: 0.6770 (m-80) REVERT: A 290 VAL cc_start: 0.7278 (m) cc_final: 0.6728 (t) REVERT: A 323 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7997 (tttm) REVERT: A 324 LEU cc_start: 0.8611 (mt) cc_final: 0.7736 (mt) REVERT: A 328 TRP cc_start: 0.8439 (m-10) cc_final: 0.8211 (m-10) REVERT: A 335 GLN cc_start: 0.7481 (mp10) cc_final: 0.6943 (mp10) REVERT: A 336 ILE cc_start: 0.8566 (mt) cc_final: 0.7942 (mm) REVERT: A 337 ARG cc_start: 0.7773 (mmp80) cc_final: 0.6773 (mmm160) REVERT: A 340 MET cc_start: 0.7509 (ptm) cc_final: 0.6755 (ptm) REVERT: A 344 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7467 (tp-100) REVERT: A 410 GLN cc_start: 0.8513 (pt0) cc_final: 0.8005 (pt0) REVERT: A 424 ARG cc_start: 0.7679 (ttt-90) cc_final: 0.7336 (ttm-80) REVERT: A 472 GLU cc_start: 0.8448 (pt0) cc_final: 0.8160 (pp20) REVERT: A 473 ASN cc_start: 0.8781 (m110) cc_final: 0.8114 (m110) REVERT: A 477 PHE cc_start: 0.7996 (m-80) cc_final: 0.7590 (m-80) REVERT: A 478 MET cc_start: 0.7478 (tpp) cc_final: 0.7199 (tpp) REVERT: A 507 ILE cc_start: 0.8161 (tp) cc_final: 0.7886 (tp) REVERT: A 543 ILE cc_start: 0.7357 (tp) cc_final: 0.7119 (tp) REVERT: A 597 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8900 (mtpp) REVERT: A 635 MET cc_start: 0.7655 (mpp) cc_final: 0.6788 (mpp) REVERT: A 639 ARG cc_start: 0.7734 (mmm-85) cc_final: 0.6845 (mmm-85) REVERT: A 651 LEU cc_start: 0.7829 (tp) cc_final: 0.7526 (tp) REVERT: A 663 LYS cc_start: 0.8552 (ptmm) cc_final: 0.7755 (ptpp) REVERT: A 684 GLN cc_start: 0.7153 (tp40) cc_final: 0.6028 (tm-30) REVERT: A 693 MET cc_start: 0.7420 (tpt) cc_final: 0.7193 (tpt) REVERT: A 711 LYS cc_start: 0.8679 (mptt) cc_final: 0.8447 (mptt) REVERT: A 739 MET cc_start: 0.7850 (ttm) cc_final: 0.7564 (ttm) REVERT: A 754 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 801 GLN cc_start: 0.8120 (mt0) cc_final: 0.7850 (mt0) REVERT: A 807 GLN cc_start: 0.8461 (mt0) cc_final: 0.8134 (mm110) REVERT: A 822 LYS cc_start: 0.8294 (mmtm) cc_final: 0.7951 (mmtm) REVERT: B 25 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7533 (mp0) REVERT: B 47 ARG cc_start: 0.6291 (tmt-80) cc_final: 0.5958 (tpt170) REVERT: B 58 CYS cc_start: 0.6526 (t) cc_final: 0.6168 (t) REVERT: B 79 LYS cc_start: 0.8549 (tptt) cc_final: 0.7991 (tptt) REVERT: B 82 GLU cc_start: 0.7309 (pp20) cc_final: 0.6701 (pp20) REVERT: B 121 GLU cc_start: 0.7657 (mm-30) cc_final: 0.6697 (tp30) REVERT: B 124 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7172 (mmm160) REVERT: C 241 ARG cc_start: 0.8359 (mmp80) cc_final: 0.7541 (mmp80) REVERT: C 287 PHE cc_start: 0.7358 (m-80) cc_final: 0.6737 (m-80) REVERT: C 323 LYS cc_start: 0.8417 (mmmt) cc_final: 0.7819 (tptt) REVERT: C 324 LEU cc_start: 0.8483 (mt) cc_final: 0.7534 (mt) REVERT: C 334 ASP cc_start: 0.7919 (p0) cc_final: 0.6786 (p0) REVERT: C 335 GLN cc_start: 0.7858 (mm110) cc_final: 0.7098 (mm110) REVERT: C 340 MET cc_start: 0.7253 (ptm) cc_final: 0.6934 (ptt) REVERT: C 344 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7206 (tp40) REVERT: C 345 GLN cc_start: 0.7719 (mt0) cc_final: 0.6813 (mt0) REVERT: C 354 ASN cc_start: 0.8284 (m-40) cc_final: 0.8072 (p0) REVERT: C 395 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7037 (tm-30) REVERT: C 404 SER cc_start: 0.6964 (t) cc_final: 0.6676 (t) REVERT: C 428 LEU cc_start: 0.8220 (tp) cc_final: 0.8019 (tp) REVERT: C 460 MET cc_start: 0.6283 (mpp) cc_final: 0.5784 (mpp) REVERT: C 472 GLU cc_start: 0.8230 (pm20) cc_final: 0.7892 (pm20) REVERT: C 478 MET cc_start: 0.7439 (tpp) cc_final: 0.7002 (tpp) REVERT: C 507 ILE cc_start: 0.8252 (tp) cc_final: 0.7943 (tp) REVERT: C 511 TYR cc_start: 0.7505 (m-80) cc_final: 0.7180 (m-80) REVERT: C 538 VAL cc_start: 0.8104 (p) cc_final: 0.7882 (p) REVERT: C 539 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7419 (ttt180) REVERT: C 553 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7088 (ttpp) REVERT: C 589 MET cc_start: 0.4981 (mtt) cc_final: 0.4681 (tpp) REVERT: C 592 TYR cc_start: 0.7037 (t80) cc_final: 0.6243 (t80) REVERT: C 597 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8017 (mmmt) REVERT: C 625 ASN cc_start: 0.7078 (p0) cc_final: 0.6580 (p0) REVERT: C 635 MET cc_start: 0.7650 (mpp) cc_final: 0.6824 (mpp) REVERT: C 639 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7119 (mmm-85) REVERT: C 640 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7930 (mtmt) REVERT: C 651 LEU cc_start: 0.8029 (tp) cc_final: 0.7694 (tp) REVERT: C 663 LYS cc_start: 0.8616 (ptmm) cc_final: 0.8177 (ptpp) REVERT: C 684 GLN cc_start: 0.7973 (tp40) cc_final: 0.6994 (tm-30) REVERT: C 711 LYS cc_start: 0.8621 (mptt) cc_final: 0.8413 (mptt) REVERT: C 739 MET cc_start: 0.7958 (ttm) cc_final: 0.7674 (ttm) REVERT: C 754 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7795 (mt-10) REVERT: C 801 GLN cc_start: 0.8048 (mt0) cc_final: 0.7727 (mt0) REVERT: C 822 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7863 (tptp) REVERT: D 25 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7382 (mp0) REVERT: D 47 ARG cc_start: 0.6134 (tmt-80) cc_final: 0.5886 (tpt170) REVERT: D 79 LYS cc_start: 0.8601 (tptt) cc_final: 0.7993 (tptt) REVERT: D 82 GLU cc_start: 0.7335 (pp20) cc_final: 0.6782 (pp20) REVERT: D 101 LYS cc_start: 0.6076 (tptp) cc_final: 0.5836 (tptp) REVERT: D 121 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6916 (mm-30) REVERT: D 124 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7115 (mmm160) REVERT: D 133 HIS cc_start: 0.6990 (m-70) cc_final: 0.6551 (m-70) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.3439 time to fit residues: 193.8190 Evaluate side-chains 382 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12580 Z= 0.183 Angle : 0.648 11.093 16980 Z= 0.329 Chirality : 0.044 0.162 1912 Planarity : 0.005 0.074 2186 Dihedral : 5.467 20.953 1688 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.15 % Allowed : 3.33 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.21), residues: 1496 helix: -2.34 (0.17), residues: 672 sheet: -0.25 (1.26), residues: 16 loop : -1.32 (0.24), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 328 HIS 0.004 0.001 HIS B 85 PHE 0.025 0.002 PHE B 52 TYR 0.011 0.001 TYR D 91 ARG 0.014 0.001 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 404 time to evaluate : 1.466 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: 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 235 ASP cc_start: 0.7762 (p0) cc_final: 0.7501 (m-30) REVERT: A 287 PHE cc_start: 0.7169 (m-80) cc_final: 0.6943 (m-80) REVERT: A 324 LEU cc_start: 0.8485 (mt) cc_final: 0.7463 (mt) REVERT: A 337 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7235 (mmm160) REVERT: A 339 MET cc_start: 0.8769 (ptp) cc_final: 0.8165 (ptp) REVERT: A 340 MET cc_start: 0.7599 (ptm) cc_final: 0.6611 (ptm) REVERT: A 344 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7406 (tp-100) REVERT: A 373 LYS cc_start: 0.8469 (mttm) cc_final: 0.7902 (mttm) REVERT: A 464 TYR cc_start: 0.6321 (t80) cc_final: 0.5888 (t80) REVERT: A 472 GLU cc_start: 0.8439 (pt0) cc_final: 0.8109 (pp20) REVERT: A 473 ASN cc_start: 0.8807 (m110) cc_final: 0.8382 (m110) REVERT: A 477 PHE cc_start: 0.8068 (m-80) cc_final: 0.7570 (m-80) REVERT: A 507 ILE cc_start: 0.8196 (tp) cc_final: 0.7967 (tp) REVERT: A 539 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7863 (tpp80) REVERT: A 597 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8948 (mtpp) REVERT: A 635 MET cc_start: 0.7646 (mpp) cc_final: 0.6808 (mpp) REVERT: A 639 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.6900 (mmm-85) REVERT: A 640 LYS cc_start: 0.8231 (mttt) cc_final: 0.7878 (mttt) REVERT: A 651 LEU cc_start: 0.7738 (tp) cc_final: 0.7432 (tp) REVERT: A 663 LYS cc_start: 0.8313 (ptmm) cc_final: 0.7868 (ptpp) REVERT: A 692 MET cc_start: 0.5679 (mpp) cc_final: 0.5229 (mpp) REVERT: A 711 LYS cc_start: 0.8746 (mptt) cc_final: 0.8542 (mptt) REVERT: A 734 ARG cc_start: 0.6331 (ttt180) cc_final: 0.5932 (ttm-80) REVERT: A 739 MET cc_start: 0.7886 (ttm) cc_final: 0.7619 (ttm) REVERT: A 801 GLN cc_start: 0.8108 (mt0) cc_final: 0.7835 (mt0) REVERT: A 822 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7954 (mmtm) REVERT: B 55 ARG cc_start: 0.8199 (mmt90) cc_final: 0.7897 (mmt90) REVERT: B 58 CYS cc_start: 0.6601 (t) cc_final: 0.6019 (t) REVERT: B 59 ILE cc_start: 0.6405 (mm) cc_final: 0.6008 (mm) REVERT: B 79 LYS cc_start: 0.8542 (tptt) cc_final: 0.7941 (tptt) REVERT: B 82 GLU cc_start: 0.7241 (pp20) cc_final: 0.6964 (pp20) REVERT: B 88 TYR cc_start: 0.4793 (p90) cc_final: 0.4496 (p90) REVERT: B 121 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7185 (tp30) REVERT: B 124 ARG cc_start: 0.8138 (tpt170) cc_final: 0.7242 (mmm160) REVERT: C 240 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8430 (mtt180) REVERT: C 241 ARG cc_start: 0.8333 (mmp80) cc_final: 0.7690 (mmp80) REVERT: C 287 PHE cc_start: 0.7420 (m-80) cc_final: 0.6943 (m-80) REVERT: C 321 GLN cc_start: 0.8354 (mt0) cc_final: 0.8138 (mm-40) REVERT: C 324 LEU cc_start: 0.8436 (mt) cc_final: 0.7342 (mt) REVERT: C 340 MET cc_start: 0.7348 (ptm) cc_final: 0.6985 (ptt) REVERT: C 344 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7242 (tp40) REVERT: C 345 GLN cc_start: 0.7639 (mt0) cc_final: 0.6759 (mt0) REVERT: C 395 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6993 (tm-30) REVERT: C 478 MET cc_start: 0.7449 (tpp) cc_final: 0.6806 (tpp) REVERT: C 507 ILE cc_start: 0.8320 (tp) cc_final: 0.8103 (tp) REVERT: C 511 TYR cc_start: 0.7534 (m-80) cc_final: 0.7294 (m-80) REVERT: C 533 ILE cc_start: 0.8397 (tp) cc_final: 0.8171 (tp) REVERT: C 539 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7481 (ttt180) REVERT: C 554 GLN cc_start: 0.7369 (tt0) cc_final: 0.7092 (tt0) REVERT: C 580 GLU cc_start: 0.7860 (tp30) cc_final: 0.7609 (tp30) REVERT: C 592 TYR cc_start: 0.7186 (t80) cc_final: 0.6456 (t80) REVERT: C 597 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8226 (mmmt) REVERT: C 607 GLU cc_start: 0.8038 (pm20) cc_final: 0.7781 (pm20) REVERT: C 635 MET cc_start: 0.7681 (mpp) cc_final: 0.6919 (mpp) REVERT: C 639 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7130 (mmm-85) REVERT: C 640 LYS cc_start: 0.8411 (mtmt) cc_final: 0.7898 (mtmt) REVERT: C 651 LEU cc_start: 0.8012 (tp) cc_final: 0.7688 (tp) REVERT: C 663 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8161 (ptpp) REVERT: C 684 GLN cc_start: 0.7873 (tp40) cc_final: 0.6975 (tm-30) REVERT: C 739 MET cc_start: 0.7913 (ttm) cc_final: 0.7624 (ttm) REVERT: C 742 ASN cc_start: 0.8666 (p0) cc_final: 0.8104 (p0) REVERT: C 752 PRO cc_start: 0.8096 (OUTLIER) cc_final: 0.7846 (Cg_endo) REVERT: C 754 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 801 GLN cc_start: 0.7924 (mt0) cc_final: 0.7567 (mt0) REVERT: C 807 GLN cc_start: 0.7916 (mm110) cc_final: 0.7647 (mm-40) REVERT: C 822 LYS cc_start: 0.8233 (mmtm) cc_final: 0.7890 (tptp) REVERT: C 861 ARG cc_start: 0.7060 (ttm170) cc_final: 0.6854 (mtp85) REVERT: D 25 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7394 (mp0) REVERT: D 79 LYS cc_start: 0.8609 (tptt) cc_final: 0.7912 (tptt) REVERT: D 82 GLU cc_start: 0.7327 (pp20) cc_final: 0.6774 (pp20) REVERT: D 121 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7213 (mm-30) REVERT: D 124 ARG cc_start: 0.8170 (tpt170) cc_final: 0.7210 (mmm160) REVERT: D 133 HIS cc_start: 0.7122 (m-70) cc_final: 0.6761 (m-70) outliers start: 2 outliers final: 1 residues processed: 405 average time/residue: 0.3354 time to fit residues: 178.9201 Evaluate side-chains 373 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 chunk 2 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 715 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 660 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12580 Z= 0.168 Angle : 0.647 13.541 16980 Z= 0.322 Chirality : 0.044 0.169 1912 Planarity : 0.004 0.059 2186 Dihedral : 5.093 22.545 1688 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.22), residues: 1496 helix: -2.01 (0.18), residues: 680 sheet: -1.69 (0.82), residues: 40 loop : -1.23 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 328 HIS 0.004 0.001 HIS A 738 PHE 0.024 0.002 PHE A 737 TYR 0.021 0.001 TYR A 464 ARG 0.007 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.448 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: 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 164 VAL cc_start: 0.7311 (t) cc_final: 0.7089 (p) REVERT: A 266 ASN cc_start: 0.7029 (t0) cc_final: 0.6579 (m-40) REVERT: A 287 PHE cc_start: 0.7360 (m-80) cc_final: 0.7006 (m-80) REVERT: A 290 VAL cc_start: 0.7202 (m) cc_final: 0.6610 (t) REVERT: A 309 PHE cc_start: 0.7746 (t80) cc_final: 0.7525 (t80) REVERT: A 321 GLN cc_start: 0.8334 (mt0) cc_final: 0.8134 (mt0) REVERT: A 324 LEU cc_start: 0.8490 (mt) cc_final: 0.7474 (mt) REVERT: A 335 GLN cc_start: 0.7404 (mp10) cc_final: 0.6824 (mp10) REVERT: A 336 ILE cc_start: 0.8532 (mm) cc_final: 0.7849 (mm) REVERT: A 337 ARG cc_start: 0.7882 (mmp80) cc_final: 0.6899 (mmm160) REVERT: A 340 MET cc_start: 0.7656 (ptm) cc_final: 0.6685 (ptm) REVERT: A 344 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7433 (tp-100) REVERT: A 373 LYS cc_start: 0.8275 (mttm) cc_final: 0.7895 (mttm) REVERT: A 472 GLU cc_start: 0.8438 (pt0) cc_final: 0.8084 (pp20) REVERT: A 473 ASN cc_start: 0.8792 (m110) cc_final: 0.8478 (m110) REVERT: A 491 LEU cc_start: 0.8658 (mt) cc_final: 0.8366 (mt) REVERT: A 507 ILE cc_start: 0.8229 (tp) cc_final: 0.7986 (tp) REVERT: A 540 LEU cc_start: 0.8660 (pp) cc_final: 0.8321 (pp) REVERT: A 635 MET cc_start: 0.7610 (mpp) cc_final: 0.6928 (mpp) REVERT: A 639 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7060 (mmm-85) REVERT: A 640 LYS cc_start: 0.8197 (mttt) cc_final: 0.7961 (mttt) REVERT: A 651 LEU cc_start: 0.7811 (tp) cc_final: 0.7503 (tp) REVERT: A 663 LYS cc_start: 0.8380 (ptmm) cc_final: 0.7648 (mtmm) REVERT: A 710 ARG cc_start: 0.7232 (ptt180) cc_final: 0.6981 (ptt180) REVERT: A 730 PHE cc_start: 0.6677 (t80) cc_final: 0.6318 (t80) REVERT: A 739 MET cc_start: 0.7707 (ttm) cc_final: 0.7421 (ttm) REVERT: A 754 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8120 (mt-10) REVERT: A 801 GLN cc_start: 0.8005 (mt0) cc_final: 0.7684 (mt0) REVERT: A 802 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7591 (mmtm) REVERT: A 822 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7855 (mmtm) REVERT: B 18 LYS cc_start: 0.8170 (mttt) cc_final: 0.7898 (mttt) REVERT: B 58 CYS cc_start: 0.6542 (t) cc_final: 0.6117 (t) REVERT: B 79 LYS cc_start: 0.8508 (tptt) cc_final: 0.7782 (tptt) REVERT: B 82 GLU cc_start: 0.7402 (pp20) cc_final: 0.6795 (pp20) REVERT: B 121 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6982 (tp30) REVERT: B 124 ARG cc_start: 0.8098 (tpt170) cc_final: 0.7118 (mmm160) REVERT: C 138 GLU cc_start: 0.8054 (tp30) cc_final: 0.7585 (tp30) REVERT: C 240 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8410 (mtt180) REVERT: C 241 ARG cc_start: 0.8336 (mmp80) cc_final: 0.7746 (mmp80) REVERT: C 242 VAL cc_start: 0.8699 (t) cc_final: 0.8403 (t) REVERT: C 282 ASN cc_start: 0.8097 (t0) cc_final: 0.7769 (t0) REVERT: C 287 PHE cc_start: 0.7384 (m-80) cc_final: 0.7062 (m-80) REVERT: C 313 MET cc_start: 0.7442 (mmm) cc_final: 0.7065 (tpp) REVERT: C 321 GLN cc_start: 0.8224 (mt0) cc_final: 0.7915 (mm-40) REVERT: C 324 LEU cc_start: 0.8395 (mt) cc_final: 0.7332 (mt) REVERT: C 334 ASP cc_start: 0.7829 (p0) cc_final: 0.6550 (p0) REVERT: C 335 GLN cc_start: 0.7883 (mm110) cc_final: 0.7118 (mm110) REVERT: C 336 ILE cc_start: 0.8707 (mt) cc_final: 0.8211 (mt) REVERT: C 340 MET cc_start: 0.7322 (ptm) cc_final: 0.6951 (ptt) REVERT: C 344 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7215 (tp40) REVERT: C 345 GLN cc_start: 0.7661 (mt0) cc_final: 0.7139 (mt0) REVERT: C 373 LYS cc_start: 0.8476 (mttm) cc_final: 0.8254 (mttm) REVERT: C 395 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6903 (tm-30) REVERT: C 398 GLU cc_start: 0.8023 (mp0) cc_final: 0.7807 (mp0) REVERT: C 472 GLU cc_start: 0.8344 (pm20) cc_final: 0.8108 (pm20) REVERT: C 478 MET cc_start: 0.7260 (tpp) cc_final: 0.6852 (tpp) REVERT: C 491 LEU cc_start: 0.8655 (mt) cc_final: 0.8324 (mt) REVERT: C 507 ILE cc_start: 0.8311 (tp) cc_final: 0.8095 (tp) REVERT: C 539 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7428 (ttt180) REVERT: C 580 GLU cc_start: 0.7773 (tp30) cc_final: 0.7497 (tp30) REVERT: C 592 TYR cc_start: 0.7079 (t80) cc_final: 0.6827 (t80) REVERT: C 597 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8166 (mmmt) REVERT: C 605 SER cc_start: 0.8030 (p) cc_final: 0.7540 (t) REVERT: C 607 GLU cc_start: 0.8141 (pm20) cc_final: 0.7876 (pm20) REVERT: C 627 CYS cc_start: 0.6315 (p) cc_final: 0.6110 (p) REVERT: C 629 LEU cc_start: 0.7471 (mp) cc_final: 0.6587 (mt) REVERT: C 635 MET cc_start: 0.7622 (mpp) cc_final: 0.6867 (mpp) REVERT: C 639 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.6928 (mmm-85) REVERT: C 640 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7922 (mtmt) REVERT: C 651 LEU cc_start: 0.8095 (tp) cc_final: 0.7743 (tp) REVERT: C 663 LYS cc_start: 0.8640 (ptmm) cc_final: 0.8086 (ptpp) REVERT: C 664 ASP cc_start: 0.8805 (p0) cc_final: 0.8584 (p0) REVERT: C 667 GLU cc_start: 0.8601 (mp0) cc_final: 0.8289 (mp0) REVERT: C 684 GLN cc_start: 0.7944 (tp40) cc_final: 0.6715 (tm-30) REVERT: C 710 ARG cc_start: 0.7468 (ptt180) cc_final: 0.7015 (mtm180) REVERT: C 739 MET cc_start: 0.7869 (ttm) cc_final: 0.7607 (ttm) REVERT: C 754 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7796 (mt-10) REVERT: C 784 SER cc_start: 0.6754 (t) cc_final: 0.6145 (m) REVERT: C 801 GLN cc_start: 0.8022 (mt0) cc_final: 0.7593 (mt0) REVERT: C 802 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7644 (mmtm) REVERT: C 807 GLN cc_start: 0.7896 (mm110) cc_final: 0.7632 (mm-40) REVERT: D 25 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7424 (mt-10) REVERT: D 58 CYS cc_start: 0.6367 (t) cc_final: 0.6114 (t) REVERT: D 79 LYS cc_start: 0.8566 (tptt) cc_final: 0.7765 (tptt) REVERT: D 82 GLU cc_start: 0.7390 (pp20) cc_final: 0.6868 (pp20) REVERT: D 121 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7189 (tp30) REVERT: D 124 ARG cc_start: 0.8299 (tpt170) cc_final: 0.7498 (mmm160) REVERT: D 133 HIS cc_start: 0.7127 (m-70) cc_final: 0.6714 (m-70) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.3433 time to fit residues: 187.5154 Evaluate side-chains 380 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12580 Z= 0.174 Angle : 0.635 10.699 16980 Z= 0.318 Chirality : 0.044 0.193 1912 Planarity : 0.005 0.054 2186 Dihedral : 4.963 21.000 1688 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1496 helix: -1.86 (0.18), residues: 692 sheet: -1.94 (0.75), residues: 40 loop : -1.16 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 328 HIS 0.004 0.001 HIS D 85 PHE 0.025 0.002 PHE C 466 TYR 0.019 0.001 TYR A 624 ARG 0.007 0.001 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.518 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: 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 164 VAL cc_start: 0.7300 (t) cc_final: 0.7081 (p) REVERT: A 241 ARG cc_start: 0.8762 (mmp80) cc_final: 0.8401 (mmp80) REVERT: A 266 ASN cc_start: 0.7068 (t0) cc_final: 0.6675 (m-40) REVERT: A 287 PHE cc_start: 0.7401 (m-80) cc_final: 0.6998 (m-80) REVERT: A 290 VAL cc_start: 0.7343 (m) cc_final: 0.6818 (t) REVERT: A 321 GLN cc_start: 0.8403 (mt0) cc_final: 0.8165 (mt0) REVERT: A 324 LEU cc_start: 0.8499 (mt) cc_final: 0.7495 (mt) REVERT: A 335 GLN cc_start: 0.7453 (mp10) cc_final: 0.7067 (mp10) REVERT: A 336 ILE cc_start: 0.8565 (mm) cc_final: 0.8024 (mm) REVERT: A 337 ARG cc_start: 0.7950 (mmp80) cc_final: 0.6972 (mmm160) REVERT: A 339 MET cc_start: 0.8672 (ptp) cc_final: 0.8449 (ptp) REVERT: A 340 MET cc_start: 0.7781 (ptm) cc_final: 0.6706 (ptm) REVERT: A 344 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7433 (tp-100) REVERT: A 373 LYS cc_start: 0.8209 (mttm) cc_final: 0.7881 (mttm) REVERT: A 441 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7530 (mmtp) REVERT: A 470 GLU cc_start: 0.7137 (tt0) cc_final: 0.6825 (pm20) REVERT: A 472 GLU cc_start: 0.8350 (pt0) cc_final: 0.8131 (pp20) REVERT: A 473 ASN cc_start: 0.8840 (m110) cc_final: 0.8318 (m110) REVERT: A 477 PHE cc_start: 0.7782 (m-80) cc_final: 0.6990 (m-80) REVERT: A 491 LEU cc_start: 0.8598 (mt) cc_final: 0.8300 (mt) REVERT: A 503 SER cc_start: 0.7576 (t) cc_final: 0.6812 (p) REVERT: A 507 ILE cc_start: 0.8268 (tp) cc_final: 0.8047 (tp) REVERT: A 539 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7785 (tpp80) REVERT: A 543 ILE cc_start: 0.7759 (tp) cc_final: 0.7420 (pt) REVERT: A 597 LYS cc_start: 0.9032 (mmmt) cc_final: 0.8585 (mmmt) REVERT: A 635 MET cc_start: 0.7598 (mpp) cc_final: 0.6886 (mpp) REVERT: A 639 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7101 (mmm-85) REVERT: A 640 LYS cc_start: 0.8280 (mttt) cc_final: 0.7928 (mttt) REVERT: A 651 LEU cc_start: 0.7767 (tp) cc_final: 0.7445 (tp) REVERT: A 663 LYS cc_start: 0.8280 (ptmm) cc_final: 0.7763 (mtmm) REVERT: A 710 ARG cc_start: 0.7234 (ptt180) cc_final: 0.7008 (ptt180) REVERT: A 730 PHE cc_start: 0.6821 (t80) cc_final: 0.6540 (t80) REVERT: A 754 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 801 GLN cc_start: 0.7974 (mt0) cc_final: 0.7615 (mt0) REVERT: A 807 GLN cc_start: 0.8406 (mt0) cc_final: 0.8153 (mm110) REVERT: B 18 LYS cc_start: 0.8165 (mttt) cc_final: 0.7939 (mttt) REVERT: B 25 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 52 PHE cc_start: 0.6608 (t80) cc_final: 0.6357 (t80) REVERT: B 58 CYS cc_start: 0.6580 (t) cc_final: 0.6157 (t) REVERT: B 59 ILE cc_start: 0.6946 (mm) cc_final: 0.6594 (mm) REVERT: B 74 LEU cc_start: 0.7893 (tp) cc_final: 0.7692 (tp) REVERT: B 79 LYS cc_start: 0.8503 (tptt) cc_final: 0.7843 (tptt) REVERT: B 82 GLU cc_start: 0.7494 (pp20) cc_final: 0.6910 (pp20) REVERT: B 121 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7026 (tp30) REVERT: B 124 ARG cc_start: 0.8265 (tpt170) cc_final: 0.7377 (mmm160) REVERT: C 241 ARG cc_start: 0.8325 (mmp80) cc_final: 0.7800 (mmp80) REVERT: C 242 VAL cc_start: 0.8731 (t) cc_final: 0.8490 (t) REVERT: C 287 PHE cc_start: 0.7422 (m-80) cc_final: 0.7121 (m-80) REVERT: C 324 LEU cc_start: 0.8415 (mt) cc_final: 0.7307 (mt) REVERT: C 336 ILE cc_start: 0.8736 (mt) cc_final: 0.8390 (mt) REVERT: C 340 MET cc_start: 0.7406 (ptm) cc_final: 0.7022 (ptt) REVERT: C 344 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7215 (tp40) REVERT: C 345 GLN cc_start: 0.7686 (mt0) cc_final: 0.7182 (mt0) REVERT: C 373 LYS cc_start: 0.8424 (mttm) cc_final: 0.8151 (mttm) REVERT: C 395 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6884 (tm-30) REVERT: C 398 GLU cc_start: 0.7980 (mp0) cc_final: 0.7711 (mp0) REVERT: C 411 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8088 (mt-10) REVERT: C 440 ARG cc_start: 0.6828 (mtp85) cc_final: 0.6016 (mtp85) REVERT: C 460 MET cc_start: 0.6273 (mpp) cc_final: 0.5999 (mpp) REVERT: C 472 GLU cc_start: 0.8227 (pm20) cc_final: 0.7996 (pm20) REVERT: C 478 MET cc_start: 0.7185 (tpp) cc_final: 0.6811 (tpp) REVERT: C 491 LEU cc_start: 0.8614 (mt) cc_final: 0.8343 (mt) REVERT: C 533 ILE cc_start: 0.8228 (tp) cc_final: 0.8014 (tp) REVERT: C 539 ARG cc_start: 0.7984 (tpp80) cc_final: 0.7539 (ttt180) REVERT: C 580 GLU cc_start: 0.7815 (tp30) cc_final: 0.7533 (tp30) REVERT: C 597 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8395 (mmmt) REVERT: C 607 GLU cc_start: 0.8111 (pm20) cc_final: 0.7834 (pm20) REVERT: C 629 LEU cc_start: 0.7345 (mp) cc_final: 0.6484 (mt) REVERT: C 635 MET cc_start: 0.7615 (mpp) cc_final: 0.6849 (mpp) REVERT: C 639 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.6939 (mmm-85) REVERT: C 640 LYS cc_start: 0.8453 (mtmt) cc_final: 0.7994 (mtmt) REVERT: C 651 LEU cc_start: 0.8099 (tp) cc_final: 0.7723 (tp) REVERT: C 663 LYS cc_start: 0.8780 (ptmm) cc_final: 0.8220 (ptpp) REVERT: C 684 GLN cc_start: 0.7944 (tp40) cc_final: 0.6950 (tm-30) REVERT: C 731 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8102 (mmtm) REVERT: C 739 MET cc_start: 0.7847 (ttm) cc_final: 0.7621 (ttm) REVERT: C 752 PRO cc_start: 0.8293 (Cg_exo) cc_final: 0.8082 (Cg_endo) REVERT: C 754 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7760 (mt-10) REVERT: C 801 GLN cc_start: 0.8014 (mt0) cc_final: 0.7549 (mt0) REVERT: C 802 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7624 (mmtm) REVERT: C 807 GLN cc_start: 0.7927 (mm110) cc_final: 0.7550 (mm110) REVERT: C 861 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6761 (mtp85) REVERT: D 25 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7276 (mt-10) REVERT: D 79 LYS cc_start: 0.8523 (tptt) cc_final: 0.7791 (tptt) REVERT: D 82 GLU cc_start: 0.7438 (pp20) cc_final: 0.6892 (pp20) REVERT: D 133 HIS cc_start: 0.7149 (m-70) cc_final: 0.6772 (m-70) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3542 time to fit residues: 192.2963 Evaluate side-chains 373 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 0.0670 chunk 148 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 114 GLN C 249 ASN C 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12580 Z= 0.178 Angle : 0.663 11.785 16980 Z= 0.331 Chirality : 0.044 0.197 1912 Planarity : 0.005 0.063 2186 Dihedral : 4.905 23.174 1688 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1496 helix: -1.81 (0.18), residues: 704 sheet: -2.07 (0.73), residues: 40 loop : -1.16 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 791 HIS 0.005 0.001 HIS D 85 PHE 0.043 0.002 PHE A 633 TYR 0.028 0.001 TYR B 91 ARG 0.007 0.001 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.396 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: 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 240 ARG cc_start: 0.8950 (mtt180) cc_final: 0.8532 (mtt180) REVERT: A 266 ASN cc_start: 0.7108 (t0) cc_final: 0.6724 (m-40) REVERT: A 287 PHE cc_start: 0.7388 (m-80) cc_final: 0.7038 (m-80) REVERT: A 324 LEU cc_start: 0.8481 (mt) cc_final: 0.7419 (mt) REVERT: A 335 GLN cc_start: 0.7433 (mp10) cc_final: 0.7084 (mp10) REVERT: A 336 ILE cc_start: 0.8593 (mm) cc_final: 0.7898 (tp) REVERT: A 337 ARG cc_start: 0.8011 (mmp80) cc_final: 0.7009 (mmm160) REVERT: A 339 MET cc_start: 0.8615 (ptp) cc_final: 0.8268 (ptp) REVERT: A 340 MET cc_start: 0.7846 (ptm) cc_final: 0.6602 (ptm) REVERT: A 373 LYS cc_start: 0.8217 (mttm) cc_final: 0.7908 (mttm) REVERT: A 441 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7770 (mmtp) REVERT: A 464 TYR cc_start: 0.6516 (t80) cc_final: 0.5787 (t80) REVERT: A 469 VAL cc_start: 0.7767 (t) cc_final: 0.7428 (t) REVERT: A 472 GLU cc_start: 0.8297 (pt0) cc_final: 0.8030 (pp20) REVERT: A 473 ASN cc_start: 0.8913 (m110) cc_final: 0.8511 (m110) REVERT: A 491 LEU cc_start: 0.8481 (mt) cc_final: 0.8242 (mt) REVERT: A 528 ARG cc_start: 0.7143 (ttp-110) cc_final: 0.6450 (ttp-110) REVERT: A 531 HIS cc_start: 0.7284 (m90) cc_final: 0.7000 (m90) REVERT: A 539 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7785 (tpp80) REVERT: A 542 MET cc_start: 0.7085 (mmt) cc_final: 0.6767 (mmt) REVERT: A 576 GLN cc_start: 0.7189 (tm-30) cc_final: 0.5582 (tm-30) REVERT: A 597 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8579 (mmmt) REVERT: A 635 MET cc_start: 0.7526 (mpp) cc_final: 0.6928 (mpp) REVERT: A 640 LYS cc_start: 0.8337 (mttt) cc_final: 0.7897 (mttt) REVERT: A 651 LEU cc_start: 0.7847 (tp) cc_final: 0.7586 (tp) REVERT: A 663 LYS cc_start: 0.8402 (ptmm) cc_final: 0.7900 (ptpp) REVERT: A 710 ARG cc_start: 0.7232 (ptt180) cc_final: 0.6988 (ptt180) REVERT: A 730 PHE cc_start: 0.6776 (t80) cc_final: 0.6537 (t80) REVERT: A 742 ASN cc_start: 0.8318 (p0) cc_final: 0.8007 (p0) REVERT: A 754 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 801 GLN cc_start: 0.8003 (mt0) cc_final: 0.7626 (mt0) REVERT: A 802 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7622 (mmtt) REVERT: A 807 GLN cc_start: 0.8393 (mt0) cc_final: 0.8136 (mm110) REVERT: A 822 LYS cc_start: 0.7844 (tptp) cc_final: 0.7481 (tptp) REVERT: B 18 LYS cc_start: 0.8172 (mttt) cc_final: 0.7906 (mttt) REVERT: B 25 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 52 PHE cc_start: 0.6594 (t80) cc_final: 0.6301 (t80) REVERT: B 58 CYS cc_start: 0.6647 (t) cc_final: 0.5864 (t) REVERT: B 59 ILE cc_start: 0.6868 (mm) cc_final: 0.6587 (mm) REVERT: B 88 TYR cc_start: 0.4865 (p90) cc_final: 0.4626 (p90) REVERT: B 121 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6971 (tp30) REVERT: B 124 ARG cc_start: 0.8120 (tpt170) cc_final: 0.7076 (mmm160) REVERT: C 241 ARG cc_start: 0.8366 (mmp80) cc_final: 0.7808 (mmp80) REVERT: C 242 VAL cc_start: 0.8742 (t) cc_final: 0.8517 (t) REVERT: C 309 PHE cc_start: 0.7889 (t80) cc_final: 0.7600 (t80) REVERT: C 313 MET cc_start: 0.7230 (mmm) cc_final: 0.6971 (mmm) REVERT: C 324 LEU cc_start: 0.8356 (mt) cc_final: 0.8060 (mt) REVERT: C 336 ILE cc_start: 0.8712 (mt) cc_final: 0.8216 (mt) REVERT: C 340 MET cc_start: 0.7419 (ptm) cc_final: 0.7047 (ptt) REVERT: C 344 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7586 (tp-100) REVERT: C 345 GLN cc_start: 0.7659 (mt0) cc_final: 0.7082 (mt0) REVERT: C 373 LYS cc_start: 0.8341 (mttm) cc_final: 0.8087 (mttm) REVERT: C 395 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6889 (tm-30) REVERT: C 398 GLU cc_start: 0.7956 (mp0) cc_final: 0.7751 (mp0) REVERT: C 472 GLU cc_start: 0.8257 (pm20) cc_final: 0.8035 (pm20) REVERT: C 478 MET cc_start: 0.7118 (tpp) cc_final: 0.6788 (tpp) REVERT: C 491 LEU cc_start: 0.8601 (mt) cc_final: 0.8383 (mt) REVERT: C 494 TYR cc_start: 0.7102 (t80) cc_final: 0.6823 (t80) REVERT: C 539 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7658 (ttp80) REVERT: C 554 GLN cc_start: 0.7375 (tt0) cc_final: 0.7113 (tt0) REVERT: C 597 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8552 (mmmt) REVERT: C 607 GLU cc_start: 0.8104 (pm20) cc_final: 0.7774 (pm20) REVERT: C 635 MET cc_start: 0.7545 (mpp) cc_final: 0.6862 (mpp) REVERT: C 639 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7318 (mmm-85) REVERT: C 640 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8000 (mtmt) REVERT: C 651 LEU cc_start: 0.8115 (tp) cc_final: 0.7728 (tp) REVERT: C 663 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8184 (ptpp) REVERT: C 684 GLN cc_start: 0.8032 (tp40) cc_final: 0.6833 (tm-30) REVERT: C 739 MET cc_start: 0.7800 (ttm) cc_final: 0.7550 (ttm) REVERT: C 752 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7971 (Cg_endo) REVERT: C 754 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 801 GLN cc_start: 0.8000 (mt0) cc_final: 0.7530 (mt0) REVERT: C 802 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7667 (mmtm) REVERT: C 807 GLN cc_start: 0.7907 (mm110) cc_final: 0.7667 (mm-40) REVERT: C 822 LYS cc_start: 0.7872 (tptt) cc_final: 0.7417 (tptp) REVERT: C 861 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6655 (mtp85) REVERT: D 25 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7215 (mt-10) REVERT: D 47 ARG cc_start: 0.5851 (tpt170) cc_final: 0.5427 (tpm170) REVERT: D 58 CYS cc_start: 0.6380 (t) cc_final: 0.5598 (t) REVERT: D 59 ILE cc_start: 0.6610 (mm) cc_final: 0.6314 (mm) REVERT: D 121 GLU cc_start: 0.7450 (tp30) cc_final: 0.7153 (tp30) REVERT: D 124 ARG cc_start: 0.8180 (tpt170) cc_final: 0.7691 (mmm160) REVERT: D 133 HIS cc_start: 0.6988 (m-70) cc_final: 0.6753 (m-70) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3465 time to fit residues: 181.9478 Evaluate side-chains 367 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.2980 chunk 94 optimal weight: 0.0010 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** C 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12580 Z= 0.177 Angle : 0.672 12.144 16980 Z= 0.332 Chirality : 0.044 0.198 1912 Planarity : 0.005 0.059 2186 Dihedral : 4.937 24.159 1688 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.21), residues: 1496 helix: -1.82 (0.18), residues: 736 sheet: -2.12 (0.68), residues: 36 loop : -1.20 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 791 HIS 0.005 0.001 HIS C 632 PHE 0.036 0.002 PHE C 633 TYR 0.028 0.001 TYR C 464 ARG 0.007 0.001 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.650 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: 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 239 ILE cc_start: 0.8714 (tp) cc_final: 0.8376 (tp) REVERT: A 240 ARG cc_start: 0.8889 (mtt180) cc_final: 0.8567 (mtt180) REVERT: A 241 ARG cc_start: 0.8692 (mmp80) cc_final: 0.8280 (mmp80) REVERT: A 266 ASN cc_start: 0.6931 (t0) cc_final: 0.6688 (m110) REVERT: A 287 PHE cc_start: 0.7529 (m-80) cc_final: 0.7064 (m-80) REVERT: A 324 LEU cc_start: 0.8461 (mt) cc_final: 0.7436 (mt) REVERT: A 335 GLN cc_start: 0.7497 (mp10) cc_final: 0.7254 (mp10) REVERT: A 336 ILE cc_start: 0.8687 (mm) cc_final: 0.8296 (mm) REVERT: A 337 ARG cc_start: 0.8020 (mmp80) cc_final: 0.7174 (mmm160) REVERT: A 339 MET cc_start: 0.8615 (ptp) cc_final: 0.8350 (ptp) REVERT: A 340 MET cc_start: 0.7853 (ptm) cc_final: 0.6683 (ptm) REVERT: A 373 LYS cc_start: 0.8163 (mttm) cc_final: 0.7811 (mttm) REVERT: A 412 LEU cc_start: 0.8538 (tt) cc_final: 0.8314 (tt) REVERT: A 419 ASN cc_start: 0.7490 (m-40) cc_final: 0.7289 (m-40) REVERT: A 428 LEU cc_start: 0.8572 (tt) cc_final: 0.7931 (mp) REVERT: A 441 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7737 (mmtp) REVERT: A 472 GLU cc_start: 0.8333 (pt0) cc_final: 0.7854 (pp20) REVERT: A 473 ASN cc_start: 0.8882 (m110) cc_final: 0.8291 (m110) REVERT: A 477 PHE cc_start: 0.7648 (m-80) cc_final: 0.6929 (m-80) REVERT: A 491 LEU cc_start: 0.8418 (mt) cc_final: 0.7938 (mt) REVERT: A 528 ARG cc_start: 0.7290 (ttp-110) cc_final: 0.6676 (ttp-110) REVERT: A 531 HIS cc_start: 0.7374 (m90) cc_final: 0.6971 (m90) REVERT: A 539 ARG cc_start: 0.8088 (tpp80) cc_final: 0.7317 (ttt180) REVERT: A 541 GLU cc_start: 0.7626 (mp0) cc_final: 0.7337 (pm20) REVERT: A 589 MET cc_start: 0.4475 (ttm) cc_final: 0.4174 (ttm) REVERT: A 597 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8551 (mmmt) REVERT: A 635 MET cc_start: 0.7513 (mpp) cc_final: 0.6920 (mpp) REVERT: A 639 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7549 (mmm-85) REVERT: A 640 LYS cc_start: 0.8287 (mttt) cc_final: 0.7742 (mttt) REVERT: A 651 LEU cc_start: 0.7865 (tp) cc_final: 0.7622 (tp) REVERT: A 663 LYS cc_start: 0.8421 (ptmm) cc_final: 0.8087 (ptpp) REVERT: A 730 PHE cc_start: 0.6875 (t80) cc_final: 0.6617 (t80) REVERT: A 739 MET cc_start: 0.7681 (ttm) cc_final: 0.7406 (ttm) REVERT: A 754 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8014 (mt-10) REVERT: A 801 GLN cc_start: 0.8033 (mt0) cc_final: 0.7685 (mt0) REVERT: A 802 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7736 (mmtt) REVERT: A 822 LYS cc_start: 0.7843 (tptp) cc_final: 0.7464 (tptp) REVERT: B 18 LYS cc_start: 0.8198 (mttt) cc_final: 0.7922 (mttt) REVERT: B 25 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7390 (mt-10) REVERT: B 52 PHE cc_start: 0.6593 (t80) cc_final: 0.6373 (t80) REVERT: B 59 ILE cc_start: 0.6965 (mm) cc_final: 0.6727 (mm) REVERT: B 74 LEU cc_start: 0.7852 (tp) cc_final: 0.7613 (tp) REVERT: B 121 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6951 (tp30) REVERT: B 124 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7215 (mmm160) REVERT: C 138 GLU cc_start: 0.7974 (tp30) cc_final: 0.7463 (tp30) REVERT: C 241 ARG cc_start: 0.8339 (mmp80) cc_final: 0.7636 (mmp80) REVERT: C 242 VAL cc_start: 0.8753 (t) cc_final: 0.8550 (t) REVERT: C 303 GLU cc_start: 0.7626 (mp0) cc_final: 0.7420 (mp0) REVERT: C 309 PHE cc_start: 0.7914 (t80) cc_final: 0.7673 (t80) REVERT: C 324 LEU cc_start: 0.8448 (mt) cc_final: 0.8142 (mt) REVERT: C 334 ASP cc_start: 0.7841 (p0) cc_final: 0.6557 (p0) REVERT: C 335 GLN cc_start: 0.7977 (mm110) cc_final: 0.7145 (mm110) REVERT: C 336 ILE cc_start: 0.8756 (mt) cc_final: 0.8253 (mt) REVERT: C 340 MET cc_start: 0.7443 (ptm) cc_final: 0.7080 (ptt) REVERT: C 344 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7591 (tp-100) REVERT: C 345 GLN cc_start: 0.7706 (mt0) cc_final: 0.7115 (mt0) REVERT: C 373 LYS cc_start: 0.8322 (mttm) cc_final: 0.8064 (mttm) REVERT: C 389 ASP cc_start: 0.7461 (p0) cc_final: 0.6986 (p0) REVERT: C 395 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6969 (tm-30) REVERT: C 441 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7905 (mmtt) REVERT: C 460 MET cc_start: 0.5847 (mpp) cc_final: 0.5623 (mpp) REVERT: C 462 LYS cc_start: 0.7092 (mmpt) cc_final: 0.6884 (mmpt) REVERT: C 464 TYR cc_start: 0.6628 (t80) cc_final: 0.6104 (t80) REVERT: C 478 MET cc_start: 0.7174 (tpp) cc_final: 0.6870 (tpp) REVERT: C 491 LEU cc_start: 0.8566 (mt) cc_final: 0.8324 (mt) REVERT: C 494 TYR cc_start: 0.7123 (t80) cc_final: 0.6823 (t80) REVERT: C 501 MET cc_start: 0.6654 (mmp) cc_final: 0.6411 (mmp) REVERT: C 539 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7328 (ttt180) REVERT: C 541 GLU cc_start: 0.7596 (pm20) cc_final: 0.6643 (pm20) REVERT: C 542 MET cc_start: 0.7184 (mmt) cc_final: 0.6880 (mmt) REVERT: C 554 GLN cc_start: 0.7382 (tt0) cc_final: 0.7095 (tt0) REVERT: C 607 GLU cc_start: 0.8110 (pm20) cc_final: 0.7747 (pm20) REVERT: C 635 MET cc_start: 0.7557 (mpp) cc_final: 0.6829 (mpp) REVERT: C 639 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7082 (mmm-85) REVERT: C 640 LYS cc_start: 0.8434 (mtmt) cc_final: 0.7928 (mtmt) REVERT: C 651 LEU cc_start: 0.8015 (tp) cc_final: 0.7661 (tp) REVERT: C 659 TYR cc_start: 0.7883 (t80) cc_final: 0.7381 (t80) REVERT: C 663 LYS cc_start: 0.8671 (ptmm) cc_final: 0.8401 (ptpp) REVERT: C 684 GLN cc_start: 0.7564 (tp40) cc_final: 0.5850 (tm-30) REVERT: C 694 TYR cc_start: 0.5603 (t80) cc_final: 0.5095 (t80) REVERT: C 720 TYR cc_start: 0.6906 (t80) cc_final: 0.6599 (t80) REVERT: C 739 MET cc_start: 0.7681 (ttm) cc_final: 0.7459 (ttm) REVERT: C 744 SER cc_start: 0.8667 (t) cc_final: 0.8221 (p) REVERT: C 754 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 801 GLN cc_start: 0.7983 (mt0) cc_final: 0.7518 (mt0) REVERT: C 807 GLN cc_start: 0.7803 (mm110) cc_final: 0.7581 (mm-40) REVERT: C 822 LYS cc_start: 0.8027 (tptt) cc_final: 0.7521 (tptp) REVERT: C 861 ARG cc_start: 0.7055 (mtt180) cc_final: 0.6601 (mtp85) REVERT: D 25 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7339 (mt-10) REVERT: D 58 CYS cc_start: 0.6597 (t) cc_final: 0.5948 (t) REVERT: D 124 ARG cc_start: 0.8256 (tpt170) cc_final: 0.7737 (mmm160) REVERT: D 133 HIS cc_start: 0.7123 (m-70) cc_final: 0.6844 (m-70) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3286 time to fit residues: 176.1117 Evaluate side-chains 362 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 130 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN C 275 ASN C 382 ASN C 632 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12580 Z= 0.204 Angle : 0.695 11.275 16980 Z= 0.349 Chirality : 0.046 0.231 1912 Planarity : 0.005 0.072 2186 Dihedral : 5.018 21.453 1688 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.08 % Allowed : 0.83 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.22), residues: 1496 helix: -1.77 (0.18), residues: 728 sheet: -1.97 (0.69), residues: 36 loop : -1.04 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP C 791 HIS 0.006 0.001 HIS D 85 PHE 0.033 0.002 PHE A 633 TYR 0.021 0.001 TYR A 464 ARG 0.012 0.001 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 403 time to evaluate : 1.413 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: 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 241 ARG cc_start: 0.8720 (mmp80) cc_final: 0.8222 (mmp80) REVERT: A 266 ASN cc_start: 0.7053 (t0) cc_final: 0.6823 (m110) REVERT: A 272 THR cc_start: 0.7230 (t) cc_final: 0.6779 (p) REVERT: A 321 GLN cc_start: 0.8533 (mt0) cc_final: 0.8259 (mt0) REVERT: A 324 LEU cc_start: 0.8446 (mt) cc_final: 0.8150 (mt) REVERT: A 336 ILE cc_start: 0.8761 (mm) cc_final: 0.8353 (mm) REVERT: A 337 ARG cc_start: 0.8092 (mmp80) cc_final: 0.7255 (mmm160) REVERT: A 339 MET cc_start: 0.8552 (ptp) cc_final: 0.8268 (ptp) REVERT: A 340 MET cc_start: 0.7996 (ptm) cc_final: 0.6803 (ptm) REVERT: A 373 LYS cc_start: 0.8143 (mttm) cc_final: 0.7826 (mttm) REVERT: A 412 LEU cc_start: 0.8365 (tt) cc_final: 0.8134 (tt) REVERT: A 428 LEU cc_start: 0.8560 (tt) cc_final: 0.7910 (mp) REVERT: A 441 LYS cc_start: 0.8338 (mmtp) cc_final: 0.7975 (mmtp) REVERT: A 472 GLU cc_start: 0.8309 (pt0) cc_final: 0.7823 (pp20) REVERT: A 473 ASN cc_start: 0.8845 (m110) cc_final: 0.8234 (m110) REVERT: A 477 PHE cc_start: 0.7816 (m-80) cc_final: 0.7146 (m-80) REVERT: A 491 LEU cc_start: 0.8461 (mt) cc_final: 0.8234 (mt) REVERT: A 528 ARG cc_start: 0.7420 (ttp-110) cc_final: 0.6896 (ttp-110) REVERT: A 531 HIS cc_start: 0.7505 (m90) cc_final: 0.7176 (m90) REVERT: A 539 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7675 (tpp80) REVERT: A 541 GLU cc_start: 0.7542 (mp0) cc_final: 0.7320 (pm20) REVERT: A 580 GLU cc_start: 0.7827 (tp30) cc_final: 0.7464 (tp30) REVERT: A 589 MET cc_start: 0.4408 (ttm) cc_final: 0.4046 (ttm) REVERT: A 597 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8661 (mmmt) REVERT: A 635 MET cc_start: 0.7621 (mpp) cc_final: 0.6959 (mpp) REVERT: A 639 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7552 (mmm-85) REVERT: A 640 LYS cc_start: 0.8242 (mttt) cc_final: 0.7906 (mttt) REVERT: A 648 PHE cc_start: 0.7241 (t80) cc_final: 0.7015 (t80) REVERT: A 651 LEU cc_start: 0.7933 (tp) cc_final: 0.7729 (tp) REVERT: A 663 LYS cc_start: 0.8656 (ptmm) cc_final: 0.8244 (ptpp) REVERT: A 694 TYR cc_start: 0.6331 (t80) cc_final: 0.5463 (t80) REVERT: A 720 TYR cc_start: 0.6965 (t80) cc_final: 0.6483 (t80) REVERT: A 739 MET cc_start: 0.7727 (ttm) cc_final: 0.7430 (ttm) REVERT: A 742 ASN cc_start: 0.8447 (p0) cc_final: 0.8153 (p0) REVERT: A 752 PRO cc_start: 0.8392 (Cg_endo) cc_final: 0.8132 (Cg_exo) REVERT: A 754 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 801 GLN cc_start: 0.8107 (mt0) cc_final: 0.7861 (mt0) REVERT: A 802 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7828 (mmtt) REVERT: A 807 GLN cc_start: 0.8357 (mt0) cc_final: 0.8144 (mm110) REVERT: A 822 LYS cc_start: 0.7814 (tptp) cc_final: 0.7430 (tptp) REVERT: B 18 LYS cc_start: 0.8221 (mttt) cc_final: 0.7943 (mttt) REVERT: B 25 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7491 (mt-10) REVERT: B 52 PHE cc_start: 0.6635 (t80) cc_final: 0.6370 (t80) REVERT: B 58 CYS cc_start: 0.6742 (t) cc_final: 0.6202 (t) REVERT: B 59 ILE cc_start: 0.7086 (mm) cc_final: 0.6745 (mm) REVERT: B 79 LYS cc_start: 0.8654 (tptt) cc_final: 0.7856 (tptt) REVERT: C 138 GLU cc_start: 0.8050 (tp30) cc_final: 0.7529 (tp30) REVERT: C 240 ARG cc_start: 0.8728 (mtt180) cc_final: 0.8031 (tpp-160) REVERT: C 241 ARG cc_start: 0.8307 (mmp80) cc_final: 0.8004 (mmp80) REVERT: C 303 GLU cc_start: 0.7697 (mp0) cc_final: 0.7486 (mp0) REVERT: C 309 PHE cc_start: 0.7863 (t80) cc_final: 0.7634 (t80) REVERT: C 324 LEU cc_start: 0.8426 (mt) cc_final: 0.8104 (mt) REVERT: C 334 ASP cc_start: 0.7880 (p0) cc_final: 0.6633 (p0) REVERT: C 335 GLN cc_start: 0.8047 (mm110) cc_final: 0.7201 (mm110) REVERT: C 336 ILE cc_start: 0.8786 (mt) cc_final: 0.8291 (mt) REVERT: C 340 MET cc_start: 0.7617 (ptm) cc_final: 0.7312 (ptt) REVERT: C 344 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7654 (tp-100) REVERT: C 345 GLN cc_start: 0.7675 (mt0) cc_final: 0.7087 (mt0) REVERT: C 373 LYS cc_start: 0.8275 (mttm) cc_final: 0.8050 (mttm) REVERT: C 389 ASP cc_start: 0.7507 (p0) cc_final: 0.6875 (p0) REVERT: C 395 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6943 (tm-30) REVERT: C 398 GLU cc_start: 0.7867 (mp0) cc_final: 0.7540 (mp0) REVERT: C 441 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7810 (mmtt) REVERT: C 460 MET cc_start: 0.5727 (mpp) cc_final: 0.5302 (mpp) REVERT: C 478 MET cc_start: 0.7297 (tpp) cc_final: 0.6970 (tpp) REVERT: C 491 LEU cc_start: 0.8573 (mt) cc_final: 0.8325 (mt) REVERT: C 494 TYR cc_start: 0.7253 (t80) cc_final: 0.6951 (t80) REVERT: C 539 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7507 (ttt180) REVERT: C 554 GLN cc_start: 0.7426 (tt0) cc_final: 0.7137 (tt0) REVERT: C 597 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8659 (mmmt) REVERT: C 607 GLU cc_start: 0.8076 (pm20) cc_final: 0.7721 (pm20) REVERT: C 635 MET cc_start: 0.7681 (mpp) cc_final: 0.6902 (mmp) REVERT: C 639 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7093 (mmm-85) REVERT: C 640 LYS cc_start: 0.8442 (mtmt) cc_final: 0.7914 (mtmt) REVERT: C 651 LEU cc_start: 0.8082 (tp) cc_final: 0.7711 (tp) REVERT: C 659 TYR cc_start: 0.7905 (t80) cc_final: 0.7516 (t80) REVERT: C 663 LYS cc_start: 0.8702 (ptmm) cc_final: 0.8407 (ptpp) REVERT: C 684 GLN cc_start: 0.7597 (tp40) cc_final: 0.6115 (tm-30) REVERT: C 694 TYR cc_start: 0.5639 (t80) cc_final: 0.5361 (t80) REVERT: C 720 TYR cc_start: 0.7123 (t80) cc_final: 0.6876 (t80) REVERT: C 739 MET cc_start: 0.7837 (ttm) cc_final: 0.7573 (ttm) REVERT: C 744 SER cc_start: 0.8664 (t) cc_final: 0.8247 (p) REVERT: C 754 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 801 GLN cc_start: 0.7839 (mt0) cc_final: 0.7415 (mt0) REVERT: C 807 GLN cc_start: 0.7995 (mm110) cc_final: 0.7635 (mm110) REVERT: C 822 LYS cc_start: 0.8010 (tptt) cc_final: 0.7802 (tptp) REVERT: C 861 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6693 (mtp85) REVERT: D 25 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7316 (mt-10) REVERT: D 58 CYS cc_start: 0.6693 (t) cc_final: 0.6122 (t) REVERT: D 59 ILE cc_start: 0.7058 (mm) cc_final: 0.6853 (mm) REVERT: D 124 ARG cc_start: 0.8288 (tpt170) cc_final: 0.7767 (tpt90) REVERT: D 133 HIS cc_start: 0.7167 (m-70) cc_final: 0.6943 (m-70) outliers start: 1 outliers final: 1 residues processed: 403 average time/residue: 0.3307 time to fit residues: 176.2513 Evaluate side-chains 365 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 97 optimal weight: 2.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS C 382 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12580 Z= 0.212 Angle : 0.711 10.793 16980 Z= 0.355 Chirality : 0.046 0.206 1912 Planarity : 0.005 0.057 2186 Dihedral : 5.052 23.188 1688 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.21), residues: 1496 helix: -1.80 (0.18), residues: 744 sheet: -1.74 (0.71), residues: 36 loop : -1.15 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 791 HIS 0.008 0.001 HIS C 632 PHE 0.025 0.002 PHE A 737 TYR 0.026 0.002 TYR A 464 ARG 0.009 0.001 ARG A 861 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.511 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: 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: symmetry clash REVERT: A 240 ARG cc_start: 0.8783 (mtt180) cc_final: 0.8316 (mtt180) REVERT: A 241 ARG cc_start: 0.8681 (mmp80) cc_final: 0.8178 (mmp80) REVERT: A 266 ASN cc_start: 0.7166 (t0) cc_final: 0.6854 (m-40) REVERT: A 272 THR cc_start: 0.7152 (t) cc_final: 0.6713 (p) REVERT: A 287 PHE cc_start: 0.7662 (m-80) cc_final: 0.7088 (m-80) REVERT: A 321 GLN cc_start: 0.8458 (mt0) cc_final: 0.8072 (mt0) REVERT: A 324 LEU cc_start: 0.8425 (mt) cc_final: 0.8071 (mt) REVERT: A 335 GLN cc_start: 0.7512 (mp10) cc_final: 0.7208 (mp10) REVERT: A 336 ILE cc_start: 0.8802 (mm) cc_final: 0.8376 (mt) REVERT: A 337 ARG cc_start: 0.8132 (mmp80) cc_final: 0.7301 (mmm160) REVERT: A 339 MET cc_start: 0.8532 (ptp) cc_final: 0.8292 (ptp) REVERT: A 340 MET cc_start: 0.8070 (ptm) cc_final: 0.7078 (ptm) REVERT: A 373 LYS cc_start: 0.8103 (mttm) cc_final: 0.7794 (mttm) REVERT: A 399 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 412 LEU cc_start: 0.8583 (tt) cc_final: 0.8330 (tt) REVERT: A 428 LEU cc_start: 0.8494 (tt) cc_final: 0.7796 (mp) REVERT: A 441 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8030 (mmtp) REVERT: A 472 GLU cc_start: 0.8289 (pt0) cc_final: 0.7795 (pp20) REVERT: A 473 ASN cc_start: 0.8841 (m110) cc_final: 0.8128 (m110) REVERT: A 491 LEU cc_start: 0.8472 (mt) cc_final: 0.8213 (mt) REVERT: A 539 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7390 (ttt180) REVERT: A 541 GLU cc_start: 0.7542 (mp0) cc_final: 0.7288 (pm20) REVERT: A 580 GLU cc_start: 0.7834 (tp30) cc_final: 0.7496 (tp30) REVERT: A 589 MET cc_start: 0.4536 (ttm) cc_final: 0.4214 (ttm) REVERT: A 597 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8636 (mmmt) REVERT: A 639 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7602 (mmm-85) REVERT: A 640 LYS cc_start: 0.8293 (mttt) cc_final: 0.7739 (mttt) REVERT: A 642 MET cc_start: 0.7758 (mmp) cc_final: 0.7542 (mmp) REVERT: A 648 PHE cc_start: 0.7381 (t80) cc_final: 0.7138 (t80) REVERT: A 651 LEU cc_start: 0.7995 (tp) cc_final: 0.7678 (tp) REVERT: A 659 TYR cc_start: 0.7505 (t80) cc_final: 0.7176 (t80) REVERT: A 663 LYS cc_start: 0.8602 (ptmm) cc_final: 0.7948 (mtmm) REVERT: A 694 TYR cc_start: 0.6439 (t80) cc_final: 0.5567 (t80) REVERT: A 720 TYR cc_start: 0.6964 (t80) cc_final: 0.6685 (t80) REVERT: A 739 MET cc_start: 0.7872 (ttm) cc_final: 0.7562 (ttm) REVERT: A 742 ASN cc_start: 0.8510 (p0) cc_final: 0.8136 (p0) REVERT: A 752 PRO cc_start: 0.8390 (Cg_endo) cc_final: 0.8080 (Cg_exo) REVERT: A 754 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7997 (mt-10) REVERT: A 764 ASN cc_start: 0.8247 (p0) cc_final: 0.7971 (p0) REVERT: A 801 GLN cc_start: 0.8092 (mt0) cc_final: 0.7826 (mt0) REVERT: A 822 LYS cc_start: 0.7711 (tptp) cc_final: 0.7468 (tptp) REVERT: A 861 ARG cc_start: 0.7045 (mtm180) cc_final: 0.6642 (mtm110) REVERT: B 18 LYS cc_start: 0.8257 (mttt) cc_final: 0.7972 (mttt) REVERT: B 25 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 52 PHE cc_start: 0.6648 (t80) cc_final: 0.6422 (t80) REVERT: B 55 ARG cc_start: 0.8141 (mmt90) cc_final: 0.7554 (mmt90) REVERT: B 58 CYS cc_start: 0.6643 (t) cc_final: 0.6404 (t) REVERT: B 59 ILE cc_start: 0.7110 (mm) cc_final: 0.6751 (mm) REVERT: B 74 LEU cc_start: 0.7892 (tp) cc_final: 0.7488 (tp) REVERT: B 82 GLU cc_start: 0.7411 (pp20) cc_final: 0.6636 (pp20) REVERT: C 240 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8153 (tpp-160) REVERT: C 241 ARG cc_start: 0.8307 (mmp80) cc_final: 0.8011 (mmp80) REVERT: C 303 GLU cc_start: 0.7824 (mp0) cc_final: 0.7620 (mp0) REVERT: C 309 PHE cc_start: 0.8010 (t80) cc_final: 0.7080 (t80) REVERT: C 324 LEU cc_start: 0.8340 (mt) cc_final: 0.8037 (mt) REVERT: C 334 ASP cc_start: 0.7900 (p0) cc_final: 0.6626 (p0) REVERT: C 335 GLN cc_start: 0.8089 (mm110) cc_final: 0.7252 (mm110) REVERT: C 336 ILE cc_start: 0.8854 (mt) cc_final: 0.8346 (mt) REVERT: C 340 MET cc_start: 0.7689 (ptm) cc_final: 0.7419 (ptt) REVERT: C 344 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7642 (tp-100) REVERT: C 345 GLN cc_start: 0.7555 (mt0) cc_final: 0.7037 (mt0) REVERT: C 373 LYS cc_start: 0.8251 (mttm) cc_final: 0.7921 (mttm) REVERT: C 389 ASP cc_start: 0.7541 (p0) cc_final: 0.6770 (p0) REVERT: C 395 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7030 (tm-30) REVERT: C 460 MET cc_start: 0.5767 (mpp) cc_final: 0.5378 (mpp) REVERT: C 478 MET cc_start: 0.7337 (tpp) cc_final: 0.7000 (tpp) REVERT: C 491 LEU cc_start: 0.8584 (mt) cc_final: 0.8335 (mt) REVERT: C 494 TYR cc_start: 0.7243 (t80) cc_final: 0.6887 (t80) REVERT: C 539 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7517 (tpp80) REVERT: C 542 MET cc_start: 0.7215 (mmt) cc_final: 0.6884 (mmt) REVERT: C 554 GLN cc_start: 0.7470 (tt0) cc_final: 0.7265 (tt0) REVERT: C 589 MET cc_start: 0.5055 (ttm) cc_final: 0.4840 (ttm) REVERT: C 597 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8640 (mmmt) REVERT: C 607 GLU cc_start: 0.8058 (pm20) cc_final: 0.7665 (pm20) REVERT: C 633 PHE cc_start: 0.8271 (m-80) cc_final: 0.8013 (m-80) REVERT: C 635 MET cc_start: 0.7681 (mpp) cc_final: 0.7051 (mmp) REVERT: C 640 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8002 (mtmt) REVERT: C 651 LEU cc_start: 0.8104 (tp) cc_final: 0.7728 (tp) REVERT: C 659 TYR cc_start: 0.7881 (t80) cc_final: 0.7580 (t80) REVERT: C 684 GLN cc_start: 0.7424 (tp40) cc_final: 0.5741 (tm-30) REVERT: C 694 TYR cc_start: 0.5826 (t80) cc_final: 0.5176 (t80) REVERT: C 720 TYR cc_start: 0.7101 (t80) cc_final: 0.6758 (t80) REVERT: C 739 MET cc_start: 0.7772 (ttm) cc_final: 0.7563 (ttm) REVERT: C 744 SER cc_start: 0.8547 (t) cc_final: 0.8133 (p) REVERT: C 749 LEU cc_start: 0.8259 (mt) cc_final: 0.8015 (pp) REVERT: C 754 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7666 (mt-10) REVERT: C 801 GLN cc_start: 0.7924 (mt0) cc_final: 0.7628 (mt0) REVERT: C 807 GLN cc_start: 0.7840 (mm110) cc_final: 0.7585 (mm110) REVERT: C 861 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6779 (mtt-85) REVERT: D 25 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 36 GLU cc_start: 0.7390 (mp0) cc_final: 0.6899 (pm20) REVERT: D 74 LEU cc_start: 0.7830 (tp) cc_final: 0.7606 (tp) REVERT: D 124 ARG cc_start: 0.8407 (tpt170) cc_final: 0.7668 (tpt90) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3370 time to fit residues: 179.7329 Evaluate side-chains 368 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 133 HIS C 285 ASN C 382 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.154684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.125117 restraints weight = 28836.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.129882 restraints weight = 19785.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133659 restraints weight = 14660.953| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12580 Z= 0.204 Angle : 0.715 10.449 16980 Z= 0.358 Chirality : 0.046 0.249 1912 Planarity : 0.005 0.090 2186 Dihedral : 5.075 23.088 1688 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.21), residues: 1496 helix: -1.72 (0.18), residues: 714 sheet: -1.62 (0.75), residues: 36 loop : -1.13 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 791 HIS 0.005 0.001 HIS C 632 PHE 0.023 0.002 PHE A 737 TYR 0.024 0.002 TYR A 464 ARG 0.014 0.001 ARG A 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3582.56 seconds wall clock time: 65 minutes 57.39 seconds (3957.39 seconds total)