Starting phenix.real_space_refine on Sat Aug 23 13:50:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrr_36603/08_2025/8jrr_36603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrr_36603/08_2025/8jrr_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jrr_36603/08_2025/8jrr_36603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrr_36603/08_2025/8jrr_36603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jrr_36603/08_2025/8jrr_36603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrr_36603/08_2025/8jrr_36603.map" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TYR:plan': 5, 'ARG:plan': 6, 'PHE:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 7, 'HIS:plan': 1} 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: C, D Time building chain proxies: 4.57, per 1000 atoms: 0.37 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: 0.78 Conformation dependent library (CDL) restraints added in 579.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.49 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: 1.70 Time building geometry restraints manager: 1.08 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: 0.03 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.340 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- 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 : 0.013 0.639 12590 Z= 0.515 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 : 14.91 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 649 TYR 0.024 0.003 TYR C 592 PHE 0.027 0.004 PHE C 633 TRP 0.012 0.003 TRP A 791 HIS 0.011 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00833 (12580) covalent geometry : angle 1.08160 (16980) hydrogen bonds : bond 0.33405 ( 334) hydrogen bonds : angle 11.53968 ( 960) metal coordination : bond 0.35722 ( 10) *********************** 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 : 0.500 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 241 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7994 (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: 0.8224 (mmtm) REVERT: A 328 TRP cc_start: 0.8479 (m-10) cc_final: 0.8013 (m-10) REVERT: A 335 GLN cc_start: 0.8360 (mm110) cc_final: 0.8159 (mm110) REVERT: A 339 MET cc_start: 0.8832 (ptp) cc_final: 0.8143 (ptp) REVERT: A 340 MET cc_start: 0.7518 (ptm) cc_final: 0.7153 (ptt) REVERT: A 345 GLN cc_start: 0.7717 (mt0) cc_final: 0.7084 (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: 0.8109 (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: 0.7212 (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: 0.7807 (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: 0.7894 (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: 0.7506 (tpp80) REVERT: A 558 GLU cc_start: 0.8029 (pt0) cc_final: 0.7696 (pm20) REVERT: A 578 VAL cc_start: 0.8078 (t) cc_final: 0.7527 (t) REVERT: A 580 GLU cc_start: 0.7595 (tp30) cc_final: 0.7188 (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: 0.7006 (mmm-85) REVERT: A 640 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7945 (mtmt) REVERT: A 649 ARG cc_start: 0.7660 (ppt170) cc_final: 0.7351 (ptt90) REVERT: A 663 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8094 (ptpp) REVERT: A 684 GLN cc_start: 0.7349 (tp40) cc_final: 0.5892 (tm-30) REVERT: A 694 TYR cc_start: 0.6839 (t80) cc_final: 0.6628 (t80) REVERT: A 730 PHE cc_start: 0.7215 (t80) cc_final: 0.6673 (t80) REVERT: A 739 MET cc_start: 0.7858 (ttm) cc_final: 0.7623 (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: 0.8113 (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: 0.7114 (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: 0.6577 (mm-30) REVERT: B 122 LYS cc_start: 0.7817 (mttp) cc_final: 0.7521 (mttp) REVERT: B 124 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6295 (mmm160) REVERT: C 146 TYR cc_start: 0.7902 (p90) cc_final: 0.6943 (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: 0.8295 (mmtm) REVERT: C 324 LEU cc_start: 0.8693 (mt) cc_final: 0.8320 (mt) REVERT: C 328 TRP cc_start: 0.8504 (m-10) cc_final: 0.8136 (m-10) REVERT: C 335 GLN cc_start: 0.8328 (mm110) cc_final: 0.8075 (mm110) REVERT: C 336 ILE cc_start: 0.8683 (mt) cc_final: 0.8202 (mt) REVERT: C 340 MET cc_start: 0.7315 (ptm) cc_final: 0.7000 (ptt) REVERT: C 345 GLN cc_start: 0.7773 (mt0) cc_final: 0.7165 (mt0) REVERT: C 394 GLU cc_start: 0.7176 (tt0) cc_final: 0.5597 (tt0) REVERT: C 397 ASP cc_start: 0.7808 (m-30) cc_final: 0.7607 (m-30) REVERT: C 450 ILE cc_start: 0.8325 (mt) cc_final: 0.8047 (mt) REVERT: C 478 MET cc_start: 0.7851 (tpp) cc_final: 0.7409 (tpp) REVERT: C 507 ILE cc_start: 0.8079 (tp) cc_final: 0.7830 (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: 0.7096 (m90) REVERT: C 537 LEU cc_start: 0.8393 (tp) cc_final: 0.8054 (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: 0.7279 (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: 0.7033 (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: 0.7105 (mmm-85) REVERT: C 648 PHE cc_start: 0.7629 (t80) cc_final: 0.7309 (t80) REVERT: C 649 ARG cc_start: 0.7374 (ppt170) cc_final: 0.6920 (tmm160) REVERT: C 651 LEU cc_start: 0.8484 (tp) cc_final: 0.8271 (tp) REVERT: C 663 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8361 (ptpp) REVERT: C 684 GLN cc_start: 0.7845 (tp40) cc_final: 0.7099 (tm-30) REVERT: C 712 GLU cc_start: 0.8486 (tt0) cc_final: 0.7347 (tp30) REVERT: C 731 LYS cc_start: 0.7706 (tptt) cc_final: 0.7405 (tptt) REVERT: C 734 ARG cc_start: 0.6790 (ttt180) cc_final: 0.6282 (ttt90) REVERT: C 739 MET cc_start: 0.7974 (ttm) cc_final: 0.7649 (ttm) REVERT: C 751 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7138 (tpt170) REVERT: C 801 GLN cc_start: 0.7911 (mt0) cc_final: 0.7700 (mt0) REVERT: C 822 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7970 (tptp) REVERT: D 38 VAL cc_start: 0.7675 (p) cc_final: 0.7292 (m) REVERT: D 55 ARG cc_start: 0.8223 (mpt-90) cc_final: 0.7938 (mmt-90) REVERT: D 58 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7483 (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: 0.7535 (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: 0.1622 time to fit residues: 99.8270 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 : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 392 HIS C 517 GLN C 738 HIS D 85 HIS D 98 GLN D 114 GLN D 125 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.154951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.126126 restraints weight = 27603.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.131240 restraints weight = 18272.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.135178 restraints weight = 13111.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.138029 restraints weight = 9869.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.139848 restraints weight = 7737.392| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12590 Z= 0.163 Angle : 0.726 11.909 16980 Z= 0.377 Chirality : 0.046 0.233 1912 Planarity : 0.006 0.058 2186 Dihedral : 6.602 23.727 1688 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.23 % Allowed : 5.37 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.20), residues: 1496 helix: -3.21 (0.15), residues: 660 sheet: -2.47 (0.78), residues: 40 loop : -1.66 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 440 TYR 0.028 0.002 TYR C 464 PHE 0.032 0.002 PHE A 343 TRP 0.017 0.002 TRP C 328 HIS 0.003 0.001 HIS C 531 Details of bonding type rmsd covalent geometry : bond 0.00338 (12580) covalent geometry : angle 0.72646 (16980) hydrogen bonds : bond 0.05700 ( 334) hydrogen bonds : angle 7.57319 ( 960) metal coordination : bond 0.00858 ( 10) *********************** 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 435 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.504 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 138 GLU cc_start: 0.8030 (tp30) cc_final: 0.7485 (tp30) REVERT: A 241 ARG cc_start: 0.8609 (mmp80) cc_final: 0.8039 (mmp80) REVERT: A 245 ARG cc_start: 0.6967 (mtt90) cc_final: 0.6684 (mtt-85) REVERT: A 266 ASN cc_start: 0.6891 (t0) cc_final: 0.6464 (m110) REVERT: A 282 ASN cc_start: 0.7981 (t0) cc_final: 0.7665 (t0) REVERT: A 323 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7616 (tptt) REVERT: A 324 LEU cc_start: 0.8504 (mt) cc_final: 0.8075 (mt) REVERT: A 328 TRP cc_start: 0.8584 (m-10) cc_final: 0.8316 (m-10) REVERT: A 336 ILE cc_start: 0.9022 (mt) cc_final: 0.8433 (mt) REVERT: A 339 MET cc_start: 0.8978 (ptp) cc_final: 0.8543 (ptp) REVERT: A 344 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7827 (tp-100) REVERT: A 354 ASN cc_start: 0.8241 (m-40) cc_final: 0.7876 (p0) REVERT: A 394 GLU cc_start: 0.7757 (tt0) cc_final: 0.7423 (tm-30) REVERT: A 410 GLN cc_start: 0.8612 (pt0) cc_final: 0.8312 (pt0) REVERT: A 424 ARG cc_start: 0.7780 (ttt-90) cc_final: 0.7542 (tpt-90) REVERT: A 472 GLU cc_start: 0.8406 (pt0) cc_final: 0.8145 (pp20) REVERT: A 477 PHE cc_start: 0.8377 (m-80) cc_final: 0.7657 (m-80) REVERT: A 478 MET cc_start: 0.8132 (tpp) cc_final: 0.7673 (tpp) REVERT: A 491 LEU cc_start: 0.8618 (tp) cc_final: 0.8407 (tp) REVERT: A 507 ILE cc_start: 0.8509 (tp) cc_final: 0.8301 (tp) REVERT: A 510 LEU cc_start: 0.8576 (mp) cc_final: 0.8107 (mm) REVERT: A 531 HIS cc_start: 0.8065 (m90) cc_final: 0.7791 (m90) REVERT: A 533 ILE cc_start: 0.8686 (mp) cc_final: 0.8358 (tp) REVERT: A 537 LEU cc_start: 0.8099 (tp) cc_final: 0.7155 (tp) REVERT: A 538 VAL cc_start: 0.8354 (p) cc_final: 0.8135 (p) REVERT: A 539 ARG cc_start: 0.8712 (tpp80) cc_final: 0.7830 (tpp80) REVERT: A 542 MET cc_start: 0.7855 (mmp) cc_final: 0.7409 (mmp) REVERT: A 558 GLU cc_start: 0.8180 (pt0) cc_final: 0.7668 (pm20) REVERT: A 576 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 580 GLU cc_start: 0.8268 (tp30) cc_final: 0.8040 (mm-30) REVERT: A 594 GLU cc_start: 0.8224 (pm20) cc_final: 0.7986 (pm20) REVERT: A 597 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8855 (mtpp) REVERT: A 635 MET cc_start: 0.7919 (mpp) cc_final: 0.6931 (mpp) REVERT: A 639 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7329 (mmm-85) REVERT: A 640 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7724 (mtmt) REVERT: A 648 PHE cc_start: 0.7652 (t80) cc_final: 0.7338 (t80) REVERT: A 651 LEU cc_start: 0.8072 (tp) cc_final: 0.7851 (tp) REVERT: A 663 LYS cc_start: 0.8429 (ptmm) cc_final: 0.7980 (ptpp) REVERT: A 684 GLN cc_start: 0.6931 (tp40) cc_final: 0.5978 (tm-30) REVERT: A 711 LYS cc_start: 0.8657 (mptt) cc_final: 0.8456 (mptt) REVERT: A 730 PHE cc_start: 0.7887 (t80) cc_final: 0.7416 (t80) REVERT: A 739 MET cc_start: 0.8288 (ttm) cc_final: 0.8003 (ttm) REVERT: A 742 ASN cc_start: 0.8513 (p0) cc_final: 0.8206 (p0) REVERT: A 754 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8475 (mt-10) REVERT: A 801 GLN cc_start: 0.8129 (mt0) cc_final: 0.7882 (mt0) REVERT: A 822 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8082 (mmtm) REVERT: B 47 ARG cc_start: 0.6100 (tmt-80) cc_final: 0.5886 (tmt-80) REVERT: B 55 ARG cc_start: 0.8081 (mpt-90) cc_final: 0.7812 (mmt-90) REVERT: B 79 LYS cc_start: 0.8569 (tptt) cc_final: 0.8144 (tptt) REVERT: B 82 GLU cc_start: 0.7704 (pp20) cc_final: 0.7257 (pp20) REVERT: B 121 GLU cc_start: 0.7820 (mm-30) cc_final: 0.6767 (tp30) REVERT: B 124 ARG cc_start: 0.7869 (tpt170) cc_final: 0.6965 (mmm160) REVERT: B 133 HIS cc_start: 0.7345 (m-70) cc_final: 0.6914 (m-70) REVERT: C 146 TYR cc_start: 0.8042 (p90) cc_final: 0.7788 (p90) REVERT: C 240 ARG cc_start: 0.9014 (mtt180) cc_final: 0.8694 (mtt180) REVERT: C 241 ARG cc_start: 0.8518 (mmp80) cc_final: 0.8180 (mmp80) REVERT: C 287 PHE cc_start: 0.7439 (m-80) cc_final: 0.6819 (m-80) REVERT: C 290 VAL cc_start: 0.7439 (m) cc_final: 0.7005 (t) REVERT: C 323 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7698 (tptt) REVERT: C 328 TRP cc_start: 0.8589 (m-10) cc_final: 0.8316 (m-10) REVERT: C 339 MET cc_start: 0.8813 (ptp) cc_final: 0.8532 (ptt) REVERT: C 340 MET cc_start: 0.7734 (ptm) cc_final: 0.7498 (ptt) REVERT: C 345 GLN cc_start: 0.7567 (mt0) cc_final: 0.6792 (mt0) REVERT: C 373 LYS cc_start: 0.8536 (tttp) cc_final: 0.7977 (tptp) REVERT: C 391 ASN cc_start: 0.7779 (t0) cc_final: 0.7570 (t0) REVERT: C 395 GLU cc_start: 0.7628 (pm20) cc_final: 0.7389 (pp20) REVERT: C 429 GLU cc_start: 0.8195 (mp0) cc_final: 0.7660 (pm20) REVERT: C 446 PHE cc_start: 0.8663 (m-80) cc_final: 0.8432 (m-10) REVERT: C 449 PHE cc_start: 0.8086 (m-80) cc_final: 0.7642 (m-80) REVERT: C 454 LEU cc_start: 0.8719 (tt) cc_final: 0.8492 (tp) REVERT: C 472 GLU cc_start: 0.8126 (pm20) cc_final: 0.7857 (pm20) REVERT: C 478 MET cc_start: 0.8045 (tpp) cc_final: 0.7649 (tpp) REVERT: C 491 LEU cc_start: 0.8670 (tp) cc_final: 0.8466 (tp) REVERT: C 511 TYR cc_start: 0.8114 (m-80) cc_final: 0.7712 (m-80) REVERT: C 533 ILE cc_start: 0.8419 (tp) cc_final: 0.8185 (tp) REVERT: C 539 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8042 (tpt-90) REVERT: C 542 MET cc_start: 0.7917 (mmp) cc_final: 0.7545 (mmp) REVERT: C 545 MET cc_start: 0.7891 (ptt) cc_final: 0.7685 (ptt) REVERT: C 556 TYR cc_start: 0.6725 (t80) cc_final: 0.6488 (t80) REVERT: C 576 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7457 (tp40) REVERT: C 580 GLU cc_start: 0.8429 (tp30) cc_final: 0.8082 (mm-30) REVERT: C 589 MET cc_start: 0.5904 (mtt) cc_final: 0.5701 (mtt) REVERT: C 592 TYR cc_start: 0.7881 (t80) cc_final: 0.6584 (t80) REVERT: C 597 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8954 (mtpp) REVERT: C 631 VAL cc_start: 0.8421 (t) cc_final: 0.8175 (p) REVERT: C 635 MET cc_start: 0.8008 (mpp) cc_final: 0.7032 (mpp) REVERT: C 639 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.7327 (mmm-85) REVERT: C 640 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8016 (mtmt) REVERT: C 648 PHE cc_start: 0.7660 (t80) cc_final: 0.7316 (t80) REVERT: C 651 LEU cc_start: 0.8205 (tp) cc_final: 0.7968 (tp) REVERT: C 663 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8156 (ptpp) REVERT: C 684 GLN cc_start: 0.7816 (tp40) cc_final: 0.7248 (tm-30) REVERT: C 694 TYR cc_start: 0.7860 (t80) cc_final: 0.7600 (t80) REVERT: C 739 MET cc_start: 0.8394 (ttm) cc_final: 0.8058 (ttm) REVERT: C 742 ASN cc_start: 0.8503 (p0) cc_final: 0.8217 (p0) REVERT: C 751 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7906 (tpp-160) REVERT: C 754 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8243 (mt-10) REVERT: C 784 SER cc_start: 0.7337 (t) cc_final: 0.6729 (m) REVERT: C 801 GLN cc_start: 0.7996 (mt0) cc_final: 0.7636 (mt0) REVERT: C 822 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7811 (tptp) REVERT: C 861 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6295 (mtp85) REVERT: D 47 ARG cc_start: 0.6137 (tmt-80) cc_final: 0.5874 (tpt170) REVERT: D 55 ARG cc_start: 0.8009 (mpt-90) cc_final: 0.7716 (mmt-90) REVERT: D 79 LYS cc_start: 0.8598 (tptt) cc_final: 0.8121 (tptt) REVERT: D 81 SER cc_start: 0.8445 (p) cc_final: 0.8123 (t) REVERT: D 82 GLU cc_start: 0.7701 (pp20) cc_final: 0.7066 (pp20) REVERT: D 121 GLU cc_start: 0.7647 (mm-30) cc_final: 0.6921 (mm-30) REVERT: D 124 ARG cc_start: 0.7778 (tpt170) cc_final: 0.6863 (mmm160) REVERT: D 133 HIS cc_start: 0.7199 (m-70) cc_final: 0.6757 (m-70) outliers start: 3 outliers final: 1 residues processed: 435 average time/residue: 0.1594 time to fit residues: 91.4966 Evaluate side-chains 387 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 chunk 26 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 25 optimal weight: 0.0060 chunk 98 optimal weight: 3.9990 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 497 ASN A 611 GLN A 655 HIS ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.125793 restraints weight = 28840.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.130692 restraints weight = 19697.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.134380 restraints weight = 14506.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.137262 restraints weight = 11217.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.139496 restraints weight = 8971.311| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12590 Z= 0.133 Angle : 0.649 12.049 16980 Z= 0.332 Chirality : 0.044 0.169 1912 Planarity : 0.005 0.066 2186 Dihedral : 5.804 22.308 1688 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.15 % Allowed : 5.90 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.21), residues: 1496 helix: -2.71 (0.16), residues: 666 sheet: -1.44 (1.08), residues: 16 loop : -1.41 (0.24), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 861 TYR 0.028 0.001 TYR C 464 PHE 0.023 0.002 PHE A 633 TRP 0.006 0.001 TRP A 791 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00287 (12580) covalent geometry : angle 0.64850 (16980) hydrogen bonds : bond 0.04551 ( 334) hydrogen bonds : angle 6.96625 ( 960) metal coordination : bond 0.00300 ( 10) *********************** 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 419 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 417 time to evaluate : 0.562 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 235 ASP cc_start: 0.7896 (p0) cc_final: 0.7585 (m-30) REVERT: A 266 ASN cc_start: 0.6851 (t0) cc_final: 0.6502 (m110) REVERT: A 287 PHE cc_start: 0.7400 (m-80) cc_final: 0.6842 (m-80) REVERT: A 290 VAL cc_start: 0.7312 (m) cc_final: 0.6766 (t) REVERT: A 309 PHE cc_start: 0.7928 (t80) cc_final: 0.7654 (t80) REVERT: A 321 GLN cc_start: 0.8575 (mt0) cc_final: 0.8350 (mm-40) REVERT: A 323 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8107 (tttp) REVERT: A 324 LEU cc_start: 0.8685 (mt) cc_final: 0.7820 (mt) REVERT: A 337 ARG cc_start: 0.7803 (mmp80) cc_final: 0.7207 (mmm160) REVERT: A 339 MET cc_start: 0.8871 (ptp) cc_final: 0.8325 (ptp) REVERT: A 340 MET cc_start: 0.7915 (ptm) cc_final: 0.7103 (ptm) REVERT: A 344 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7669 (tp-100) REVERT: A 354 ASN cc_start: 0.8194 (m-40) cc_final: 0.7980 (p0) REVERT: A 428 LEU cc_start: 0.8837 (tp) cc_final: 0.8626 (tt) REVERT: A 464 TYR cc_start: 0.7001 (t80) cc_final: 0.6702 (t80) REVERT: A 472 GLU cc_start: 0.8460 (pt0) cc_final: 0.8165 (pp20) REVERT: A 473 ASN cc_start: 0.8812 (m110) cc_final: 0.8211 (m110) REVERT: A 477 PHE cc_start: 0.8348 (m-80) cc_final: 0.7484 (m-80) REVERT: A 478 MET cc_start: 0.7977 (tpp) cc_final: 0.7554 (tpp) REVERT: A 491 LEU cc_start: 0.8621 (tp) cc_final: 0.8414 (tp) REVERT: A 531 HIS cc_start: 0.8073 (m90) cc_final: 0.7371 (m90) REVERT: A 539 ARG cc_start: 0.8825 (tpp80) cc_final: 0.8116 (tpp80) REVERT: A 542 MET cc_start: 0.7915 (mmp) cc_final: 0.7660 (mmt) REVERT: A 543 ILE cc_start: 0.7819 (tp) cc_final: 0.7609 (tp) REVERT: A 558 GLU cc_start: 0.8102 (pt0) cc_final: 0.7864 (pm20) REVERT: A 611 GLN cc_start: 0.8150 (mp10) cc_final: 0.7915 (mp10) REVERT: A 635 MET cc_start: 0.7948 (mpp) cc_final: 0.7025 (mpp) REVERT: A 639 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7369 (mmm-85) REVERT: A 651 LEU cc_start: 0.8114 (tp) cc_final: 0.7894 (tp) REVERT: A 663 LYS cc_start: 0.8360 (ptmm) cc_final: 0.7703 (ptpp) REVERT: A 684 GLN cc_start: 0.6784 (tp40) cc_final: 0.5746 (tm-30) REVERT: A 711 LYS cc_start: 0.8657 (mptt) cc_final: 0.8443 (mptt) REVERT: A 739 MET cc_start: 0.8265 (ttm) cc_final: 0.7989 (ttm) REVERT: A 742 ASN cc_start: 0.8410 (p0) cc_final: 0.8190 (p0) REVERT: A 751 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7787 (tpp-160) REVERT: A 754 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8380 (mt-10) REVERT: A 801 GLN cc_start: 0.8101 (mt0) cc_final: 0.7873 (mt0) REVERT: A 802 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7768 (mmtm) REVERT: A 822 LYS cc_start: 0.8356 (mmtm) cc_final: 0.8027 (mmtm) REVERT: B 25 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7583 (mp0) REVERT: B 52 PHE cc_start: 0.7098 (t80) cc_final: 0.6893 (t80) REVERT: B 79 LYS cc_start: 0.8600 (tptt) cc_final: 0.8105 (tptt) REVERT: B 82 GLU cc_start: 0.7721 (pp20) cc_final: 0.7121 (pp20) REVERT: B 121 GLU cc_start: 0.7719 (mm-30) cc_final: 0.6777 (tp30) REVERT: B 124 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7079 (mmm160) REVERT: B 133 HIS cc_start: 0.7236 (m-70) cc_final: 0.6988 (m-70) REVERT: C 240 ARG cc_start: 0.8967 (mtt180) cc_final: 0.7712 (tpp80) REVERT: C 241 ARG cc_start: 0.8411 (mmp80) cc_final: 0.7673 (mmp80) REVERT: C 287 PHE cc_start: 0.7411 (m-80) cc_final: 0.6999 (m-80) REVERT: C 290 VAL cc_start: 0.7307 (m) cc_final: 0.6998 (t) REVERT: C 323 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8116 (mmtt) REVERT: C 324 LEU cc_start: 0.8578 (mt) cc_final: 0.7653 (mt) REVERT: C 339 MET cc_start: 0.8791 (ptp) cc_final: 0.8475 (ptt) REVERT: C 340 MET cc_start: 0.7634 (ptm) cc_final: 0.7228 (ptt) REVERT: C 344 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7463 (tp40) REVERT: C 345 GLN cc_start: 0.7659 (mt0) cc_final: 0.6750 (mt0) REVERT: C 354 ASN cc_start: 0.8325 (m-40) cc_final: 0.8084 (p0) REVERT: C 373 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7881 (tptp) REVERT: C 391 ASN cc_start: 0.7668 (t0) cc_final: 0.7389 (t0) REVERT: C 398 GLU cc_start: 0.8150 (mp0) cc_final: 0.7038 (mp0) REVERT: C 428 LEU cc_start: 0.8461 (tp) cc_final: 0.8208 (tp) REVERT: C 441 LYS cc_start: 0.8142 (mptt) cc_final: 0.7846 (mmtm) REVERT: C 472 GLU cc_start: 0.8291 (pm20) cc_final: 0.7823 (pm20) REVERT: C 478 MET cc_start: 0.7918 (tpp) cc_final: 0.7507 (tpp) REVERT: C 524 ARG cc_start: 0.7936 (mtt90) cc_final: 0.6712 (ttp-110) REVERT: C 537 LEU cc_start: 0.8343 (tp) cc_final: 0.8136 (tp) REVERT: C 539 ARG cc_start: 0.8614 (tpp80) cc_final: 0.7636 (ttt180) REVERT: C 542 MET cc_start: 0.7757 (mmp) cc_final: 0.7514 (mmt) REVERT: C 576 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7504 (tm-30) REVERT: C 580 GLU cc_start: 0.8256 (tp30) cc_final: 0.7866 (mm-30) REVERT: C 592 TYR cc_start: 0.7350 (t80) cc_final: 0.6370 (t80) REVERT: C 597 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8750 (mtpp) REVERT: C 625 ASN cc_start: 0.7377 (p0) cc_final: 0.6785 (p0) REVERT: C 635 MET cc_start: 0.8015 (mpp) cc_final: 0.7316 (mpp) REVERT: C 639 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: C 640 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8099 (mtmt) REVERT: C 648 PHE cc_start: 0.7840 (t80) cc_final: 0.7558 (t80) REVERT: C 651 LEU cc_start: 0.8270 (tp) cc_final: 0.8004 (tp) REVERT: C 663 LYS cc_start: 0.8489 (ptmm) cc_final: 0.8017 (ptpp) REVERT: C 684 GLN cc_start: 0.7863 (tp40) cc_final: 0.7178 (tm-30) REVERT: C 694 TYR cc_start: 0.7916 (t80) cc_final: 0.7703 (t80) REVERT: C 711 LYS cc_start: 0.8661 (mptt) cc_final: 0.8458 (mptt) REVERT: C 739 MET cc_start: 0.8426 (ttm) cc_final: 0.8144 (ttm) REVERT: C 742 ASN cc_start: 0.8488 (p0) cc_final: 0.8256 (p0) REVERT: C 751 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7864 (tpp-160) REVERT: C 754 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8100 (mt-10) REVERT: C 801 GLN cc_start: 0.8015 (mt0) cc_final: 0.7684 (mt0) REVERT: C 822 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7821 (tptp) REVERT: D 25 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7462 (mp0) REVERT: D 47 ARG cc_start: 0.6050 (tmt-80) cc_final: 0.5762 (tpt170) REVERT: D 79 LYS cc_start: 0.8616 (tptt) cc_final: 0.8044 (mmmt) REVERT: D 82 GLU cc_start: 0.7734 (pp20) cc_final: 0.7233 (pp20) REVERT: D 121 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 124 ARG cc_start: 0.7938 (tpt170) cc_final: 0.7110 (mmm160) REVERT: D 133 HIS cc_start: 0.7250 (m-70) cc_final: 0.6764 (m-70) outliers start: 2 outliers final: 1 residues processed: 417 average time/residue: 0.1537 time to fit residues: 85.0589 Evaluate side-chains 374 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 73 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 93 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 282 ASN A 410 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 ASN C 382 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.151137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.122430 restraints weight = 28770.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.127270 restraints weight = 19433.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.131023 restraints weight = 14185.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.133871 restraints weight = 10827.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.136045 restraints weight = 8555.108| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12590 Z= 0.200 Angle : 0.698 12.936 16980 Z= 0.365 Chirality : 0.045 0.165 1912 Planarity : 0.005 0.050 2186 Dihedral : 5.791 21.286 1688 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.21), residues: 1496 helix: -2.31 (0.17), residues: 686 sheet: -2.11 (0.78), residues: 40 loop : -1.28 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 15 TYR 0.036 0.002 TYR C 146 PHE 0.038 0.002 PHE D 52 TRP 0.006 0.001 TRP A 791 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00400 (12580) covalent geometry : angle 0.69814 (16980) hydrogen bonds : bond 0.04713 ( 334) hydrogen bonds : angle 6.79122 ( 960) metal coordination : bond 0.00731 ( 10) *********************** 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 407 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.516 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 163 LEU cc_start: 0.8329 (tt) cc_final: 0.8090 (tt) REVERT: A 235 ASP cc_start: 0.8039 (p0) cc_final: 0.7572 (m-30) REVERT: A 282 ASN cc_start: 0.8187 (t160) cc_final: 0.7901 (t0) REVERT: A 287 PHE cc_start: 0.7321 (m-80) cc_final: 0.7010 (m-80) REVERT: A 309 PHE cc_start: 0.7996 (t80) cc_final: 0.7738 (t80) REVERT: A 324 LEU cc_start: 0.8586 (mt) cc_final: 0.7593 (mt) REVERT: A 328 TRP cc_start: 0.8505 (m-10) cc_final: 0.8189 (m-10) REVERT: A 335 GLN cc_start: 0.7651 (mp10) cc_final: 0.7112 (mp10) REVERT: A 336 ILE cc_start: 0.8592 (mm) cc_final: 0.8092 (mm) REVERT: A 337 ARG cc_start: 0.7879 (mmp80) cc_final: 0.7108 (mmm160) REVERT: A 340 MET cc_start: 0.8145 (ptm) cc_final: 0.7119 (ptm) REVERT: A 354 ASN cc_start: 0.8224 (m-40) cc_final: 0.7995 (p0) REVERT: A 373 LYS cc_start: 0.8422 (mttm) cc_final: 0.8075 (mttm) REVERT: A 472 GLU cc_start: 0.8385 (pt0) cc_final: 0.8104 (pp20) REVERT: A 473 ASN cc_start: 0.8890 (m110) cc_final: 0.8229 (m110) REVERT: A 477 PHE cc_start: 0.8425 (m-80) cc_final: 0.7729 (m-80) REVERT: A 478 MET cc_start: 0.8049 (tpp) cc_final: 0.7605 (tpp) REVERT: A 491 LEU cc_start: 0.8554 (tp) cc_final: 0.8320 (tp) REVERT: A 531 HIS cc_start: 0.8121 (m90) cc_final: 0.7732 (m90) REVERT: A 539 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8100 (tpp80) REVERT: A 542 MET cc_start: 0.7686 (mmp) cc_final: 0.7486 (mmt) REVERT: A 545 MET cc_start: 0.8051 (ptt) cc_final: 0.7716 (ptt) REVERT: A 558 GLU cc_start: 0.8191 (pt0) cc_final: 0.7870 (pp20) REVERT: A 576 GLN cc_start: 0.8302 (tp40) cc_final: 0.8095 (tm-30) REVERT: A 589 MET cc_start: 0.5161 (mtt) cc_final: 0.4909 (mtt) REVERT: A 597 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8548 (mmmt) REVERT: A 611 GLN cc_start: 0.8130 (mp10) cc_final: 0.7882 (mp10) REVERT: A 635 MET cc_start: 0.8010 (mpp) cc_final: 0.7338 (mpp) REVERT: A 640 LYS cc_start: 0.8395 (mttt) cc_final: 0.7813 (mttt) REVERT: A 651 LEU cc_start: 0.8129 (tp) cc_final: 0.7863 (tp) REVERT: A 663 LYS cc_start: 0.8251 (ptmm) cc_final: 0.7795 (ptpp) REVERT: A 684 GLN cc_start: 0.6833 (tp40) cc_final: 0.6177 (tm-30) REVERT: A 692 MET cc_start: 0.6708 (mpp) cc_final: 0.6304 (mpp) REVERT: A 694 TYR cc_start: 0.7614 (t80) cc_final: 0.7152 (t80) REVERT: A 739 MET cc_start: 0.8395 (ttm) cc_final: 0.8140 (ttm) REVERT: A 742 ASN cc_start: 0.8644 (p0) cc_final: 0.8410 (p0) REVERT: A 751 ARG cc_start: 0.8109 (mmm160) cc_final: 0.7386 (tpp-160) REVERT: A 754 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8488 (mt-10) REVERT: A 801 GLN cc_start: 0.8064 (mt0) cc_final: 0.7798 (mt0) REVERT: A 805 PHE cc_start: 0.7514 (t80) cc_final: 0.7249 (t80) REVERT: A 807 GLN cc_start: 0.8612 (mt0) cc_final: 0.8246 (mm110) REVERT: A 822 LYS cc_start: 0.8250 (mmtm) cc_final: 0.8050 (tptp) REVERT: B 79 LYS cc_start: 0.8556 (tptt) cc_final: 0.8065 (tptt) REVERT: B 82 GLU cc_start: 0.7630 (pp20) cc_final: 0.7056 (pp20) REVERT: B 114 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7627 (mm-40) REVERT: B 121 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7311 (tp30) REVERT: B 124 ARG cc_start: 0.7960 (tpt170) cc_final: 0.7016 (mmm160) REVERT: B 126 LEU cc_start: 0.8006 (mp) cc_final: 0.7468 (mp) REVERT: B 133 HIS cc_start: 0.7508 (m-70) cc_final: 0.7141 (m-70) REVERT: C 235 ASP cc_start: 0.8087 (p0) cc_final: 0.7720 (m-30) REVERT: C 241 ARG cc_start: 0.8439 (mmp80) cc_final: 0.7742 (mmp80) REVERT: C 287 PHE cc_start: 0.7476 (m-80) cc_final: 0.6907 (m-80) REVERT: C 309 PHE cc_start: 0.7765 (t80) cc_final: 0.7492 (t80) REVERT: C 324 LEU cc_start: 0.8542 (mt) cc_final: 0.7441 (mt) REVERT: C 328 TRP cc_start: 0.8452 (m-10) cc_final: 0.8219 (m-10) REVERT: C 339 MET cc_start: 0.8851 (ptp) cc_final: 0.8428 (ptp) REVERT: C 340 MET cc_start: 0.7973 (ptm) cc_final: 0.7483 (ptt) REVERT: C 344 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7369 (tp-100) REVERT: C 345 GLN cc_start: 0.7685 (mt0) cc_final: 0.6943 (mt0) REVERT: C 354 ASN cc_start: 0.8378 (m-40) cc_final: 0.8096 (p0) REVERT: C 373 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7629 (tptp) REVERT: C 376 LYS cc_start: 0.8539 (tttm) cc_final: 0.8307 (tttm) REVERT: C 391 ASN cc_start: 0.7727 (t0) cc_final: 0.7474 (t0) REVERT: C 395 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6881 (tm-30) REVERT: C 436 THR cc_start: 0.7331 (p) cc_final: 0.6726 (p) REVERT: C 441 LYS cc_start: 0.8463 (mptt) cc_final: 0.8070 (mmtm) REVERT: C 473 ASN cc_start: 0.8548 (m-40) cc_final: 0.8327 (m-40) REVERT: C 478 MET cc_start: 0.8043 (tpp) cc_final: 0.7671 (tpp) REVERT: C 482 PHE cc_start: 0.7363 (p90) cc_final: 0.7025 (p90) REVERT: C 491 LEU cc_start: 0.8554 (tp) cc_final: 0.8316 (tp) REVERT: C 511 TYR cc_start: 0.8302 (m-80) cc_final: 0.8017 (m-80) REVERT: C 539 ARG cc_start: 0.8643 (tpp80) cc_final: 0.7837 (ttt180) REVERT: C 541 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7626 (mm-30) REVERT: C 554 GLN cc_start: 0.7575 (tt0) cc_final: 0.7346 (tt0) REVERT: C 576 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 580 GLU cc_start: 0.8545 (tp30) cc_final: 0.8049 (mm-30) REVERT: C 592 TYR cc_start: 0.7613 (t80) cc_final: 0.6785 (t80) REVERT: C 597 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8787 (mtpp) REVERT: C 607 GLU cc_start: 0.8267 (pm20) cc_final: 0.7973 (pm20) REVERT: C 635 MET cc_start: 0.8103 (mpp) cc_final: 0.7352 (mpp) REVERT: C 639 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.7778 (mmm-85) REVERT: C 640 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8151 (mtmt) REVERT: C 648 PHE cc_start: 0.7902 (t80) cc_final: 0.7598 (t80) REVERT: C 651 LEU cc_start: 0.8281 (tp) cc_final: 0.7918 (tp) REVERT: C 659 TYR cc_start: 0.8155 (t80) cc_final: 0.7745 (t80) REVERT: C 663 LYS cc_start: 0.8625 (ptmm) cc_final: 0.8251 (ptpp) REVERT: C 684 GLN cc_start: 0.7878 (tp40) cc_final: 0.6938 (tm-30) REVERT: C 694 TYR cc_start: 0.7963 (t80) cc_final: 0.7748 (t80) REVERT: C 711 LYS cc_start: 0.8774 (mptt) cc_final: 0.8569 (mptt) REVERT: C 731 LYS cc_start: 0.8479 (tptt) cc_final: 0.8168 (mptt) REVERT: C 739 MET cc_start: 0.8383 (ttm) cc_final: 0.8172 (ttm) REVERT: C 751 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7589 (tpp-160) REVERT: C 754 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8252 (mt-10) REVERT: C 801 GLN cc_start: 0.8026 (mt0) cc_final: 0.7740 (mt0) REVERT: C 822 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7877 (tptp) REVERT: D 25 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7375 (mp0) REVERT: D 47 ARG cc_start: 0.6251 (tmt-80) cc_final: 0.5980 (tpt170) REVERT: D 54 PHE cc_start: 0.8028 (t80) cc_final: 0.7750 (t80) REVERT: D 79 LYS cc_start: 0.8577 (tptt) cc_final: 0.8039 (tptt) REVERT: D 82 GLU cc_start: 0.7762 (pp20) cc_final: 0.7227 (pp20) REVERT: D 121 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7070 (mm-30) REVERT: D 124 ARG cc_start: 0.8026 (tpt170) cc_final: 0.6962 (mmm160) REVERT: D 131 ARG cc_start: 0.6417 (mtt90) cc_final: 0.6134 (mtt90) REVERT: D 133 HIS cc_start: 0.7408 (m-70) cc_final: 0.7024 (m-70) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1430 time to fit residues: 77.4451 Evaluate side-chains 379 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.0370 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 410 GLN A 660 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN D 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.151641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.123125 restraints weight = 27974.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.127739 restraints weight = 18589.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.131375 restraints weight = 13502.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.134162 restraints weight = 10288.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.136318 restraints weight = 8134.817| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12590 Z= 0.188 Angle : 0.686 12.076 16980 Z= 0.354 Chirality : 0.045 0.174 1912 Planarity : 0.005 0.046 2186 Dihedral : 5.662 25.116 1688 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.21), residues: 1496 helix: -2.23 (0.17), residues: 696 sheet: -2.46 (0.73), residues: 40 loop : -1.12 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 15 TYR 0.022 0.001 TYR C 146 PHE 0.031 0.002 PHE C 466 TRP 0.007 0.001 TRP A 791 HIS 0.004 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00381 (12580) covalent geometry : angle 0.68650 (16980) hydrogen bonds : bond 0.04499 ( 334) hydrogen bonds : angle 6.63134 ( 960) metal coordination : bond 0.00793 ( 10) *********************** 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 : 0.446 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 163 LEU cc_start: 0.8351 (tt) cc_final: 0.8148 (tt) REVERT: A 266 ASN cc_start: 0.7255 (t0) cc_final: 0.6905 (m110) REVERT: A 287 PHE cc_start: 0.7557 (m-80) cc_final: 0.6993 (m-80) REVERT: A 313 MET cc_start: 0.7622 (mmm) cc_final: 0.7270 (mmm) REVERT: A 324 LEU cc_start: 0.8637 (mt) cc_final: 0.7641 (mt) REVERT: A 328 TRP cc_start: 0.8484 (m-10) cc_final: 0.8076 (m-10) REVERT: A 335 GLN cc_start: 0.7685 (mp10) cc_final: 0.7137 (mp10) REVERT: A 336 ILE cc_start: 0.8744 (mm) cc_final: 0.8244 (mm) REVERT: A 337 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7201 (mmm160) REVERT: A 340 MET cc_start: 0.8355 (ptm) cc_final: 0.7416 (ptm) REVERT: A 373 LYS cc_start: 0.8251 (mttm) cc_final: 0.7925 (mttm) REVERT: A 449 PHE cc_start: 0.7995 (m-80) cc_final: 0.7460 (m-80) REVERT: A 464 TYR cc_start: 0.7238 (t80) cc_final: 0.6550 (t80) REVERT: A 472 GLU cc_start: 0.8388 (pt0) cc_final: 0.8072 (pp20) REVERT: A 473 ASN cc_start: 0.8845 (m110) cc_final: 0.8469 (m110) REVERT: A 477 PHE cc_start: 0.8471 (m-80) cc_final: 0.7922 (m-80) REVERT: A 478 MET cc_start: 0.8034 (tpp) cc_final: 0.7626 (tpp) REVERT: A 515 GLN cc_start: 0.7612 (mp-120) cc_final: 0.7346 (mp-120) REVERT: A 524 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7368 (ttm110) REVERT: A 539 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8012 (tpp80) REVERT: A 553 LYS cc_start: 0.7631 (ttpt) cc_final: 0.7230 (ttpt) REVERT: A 576 GLN cc_start: 0.8260 (tp40) cc_final: 0.7580 (tp40) REVERT: A 580 GLU cc_start: 0.8669 (tp30) cc_final: 0.8233 (mt-10) REVERT: A 589 MET cc_start: 0.5326 (mtt) cc_final: 0.5047 (mtt) REVERT: A 597 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8607 (mmmt) REVERT: A 611 GLN cc_start: 0.7980 (mp10) cc_final: 0.7730 (mp10) REVERT: A 635 MET cc_start: 0.7948 (mpp) cc_final: 0.7175 (mpp) REVERT: A 639 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.7345 (mmm-85) REVERT: A 640 LYS cc_start: 0.8207 (mttt) cc_final: 0.7944 (mttt) REVERT: A 649 ARG cc_start: 0.7956 (tmm-80) cc_final: 0.7427 (ttp80) REVERT: A 651 LEU cc_start: 0.8220 (tp) cc_final: 0.7921 (tp) REVERT: A 663 LYS cc_start: 0.8357 (ptmm) cc_final: 0.7798 (ptpp) REVERT: A 667 GLU cc_start: 0.8718 (mp0) cc_final: 0.8513 (mp0) REVERT: A 692 MET cc_start: 0.6649 (mpp) cc_final: 0.6246 (mpp) REVERT: A 694 TYR cc_start: 0.7104 (t80) cc_final: 0.6380 (t80) REVERT: A 710 ARG cc_start: 0.7231 (ptt180) cc_final: 0.7016 (ptt180) REVERT: A 720 TYR cc_start: 0.7861 (t80) cc_final: 0.7113 (t80) REVERT: A 739 MET cc_start: 0.8351 (ttm) cc_final: 0.8112 (ttm) REVERT: A 742 ASN cc_start: 0.8576 (p0) cc_final: 0.8323 (p0) REVERT: A 751 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7657 (tpp-160) REVERT: A 754 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8545 (mt-10) REVERT: A 801 GLN cc_start: 0.8038 (mt0) cc_final: 0.7684 (mt0) REVERT: A 805 PHE cc_start: 0.7495 (t80) cc_final: 0.7208 (t80) REVERT: A 822 LYS cc_start: 0.8281 (mmtm) cc_final: 0.7817 (mmtm) REVERT: B 25 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7392 (mp0) REVERT: B 47 ARG cc_start: 0.6156 (tmt-80) cc_final: 0.5956 (tpt170) REVERT: B 79 LYS cc_start: 0.8519 (tptt) cc_final: 0.7966 (tptt) REVERT: B 82 GLU cc_start: 0.7637 (pp20) cc_final: 0.7198 (pp20) REVERT: B 114 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7447 (mm-40) REVERT: B 121 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7193 (tp30) REVERT: B 124 ARG cc_start: 0.7945 (tpt170) cc_final: 0.7024 (mmm160) REVERT: B 133 HIS cc_start: 0.7423 (m-70) cc_final: 0.7182 (m-70) REVERT: C 138 GLU cc_start: 0.8064 (tp30) cc_final: 0.7635 (tp30) REVERT: C 235 ASP cc_start: 0.8043 (p0) cc_final: 0.7638 (m-30) REVERT: C 241 ARG cc_start: 0.8421 (mmp80) cc_final: 0.7764 (mmp80) REVERT: C 287 PHE cc_start: 0.7506 (m-80) cc_final: 0.6988 (m-80) REVERT: C 290 VAL cc_start: 0.7196 (m) cc_final: 0.6340 (t) REVERT: C 324 LEU cc_start: 0.8520 (mt) cc_final: 0.7457 (mt) REVERT: C 328 TRP cc_start: 0.8341 (m-10) cc_final: 0.8097 (m-10) REVERT: C 340 MET cc_start: 0.8060 (ptm) cc_final: 0.7704 (ptt) REVERT: C 344 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7453 (tp-100) REVERT: C 345 GLN cc_start: 0.7462 (mt0) cc_final: 0.6984 (mt0) REVERT: C 354 ASN cc_start: 0.8407 (m-40) cc_final: 0.8109 (p0) REVERT: C 373 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7520 (tptp) REVERT: C 391 ASN cc_start: 0.7769 (t0) cc_final: 0.7565 (t0) REVERT: C 395 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6805 (tm-30) REVERT: C 406 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7034 (tm-30) REVERT: C 407 LEU cc_start: 0.8467 (mt) cc_final: 0.8202 (mt) REVERT: C 429 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7573 (mm-30) REVERT: C 441 LYS cc_start: 0.8552 (mptt) cc_final: 0.8227 (mppt) REVERT: C 472 GLU cc_start: 0.8227 (pm20) cc_final: 0.7775 (pm20) REVERT: C 478 MET cc_start: 0.8054 (tpp) cc_final: 0.7575 (tpp) REVERT: C 482 PHE cc_start: 0.7352 (p90) cc_final: 0.6965 (p90) REVERT: C 531 HIS cc_start: 0.8456 (m90) cc_final: 0.8178 (m90) REVERT: C 539 ARG cc_start: 0.8692 (tpp80) cc_final: 0.7923 (ttt180) REVERT: C 540 LEU cc_start: 0.8965 (tp) cc_final: 0.8703 (tt) REVERT: C 541 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7505 (mm-30) REVERT: C 542 MET cc_start: 0.7797 (mmt) cc_final: 0.7447 (mmt) REVERT: C 580 GLU cc_start: 0.8660 (tp30) cc_final: 0.8450 (tp30) REVERT: C 597 LYS cc_start: 0.9233 (mtpp) cc_final: 0.9032 (mtpp) REVERT: C 605 SER cc_start: 0.7953 (p) cc_final: 0.7625 (t) REVERT: C 607 GLU cc_start: 0.8293 (pm20) cc_final: 0.8008 (pm20) REVERT: C 633 PHE cc_start: 0.8484 (m-80) cc_final: 0.7976 (m-80) REVERT: C 635 MET cc_start: 0.8068 (mpp) cc_final: 0.7382 (mpp) REVERT: C 639 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.7324 (mmm-85) REVERT: C 640 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8080 (mtmt) REVERT: C 642 MET cc_start: 0.7958 (mmp) cc_final: 0.7614 (mmt) REVERT: C 649 ARG cc_start: 0.7618 (ptt90) cc_final: 0.6742 (ptt90) REVERT: C 651 LEU cc_start: 0.8335 (tp) cc_final: 0.7994 (tp) REVERT: C 663 LYS cc_start: 0.8569 (ptmm) cc_final: 0.8129 (ptpp) REVERT: C 684 GLN cc_start: 0.7949 (tp40) cc_final: 0.6166 (tm-30) REVERT: C 693 MET cc_start: 0.8548 (tpt) cc_final: 0.8319 (tpt) REVERT: C 694 TYR cc_start: 0.7857 (t80) cc_final: 0.7540 (t80) REVERT: C 728 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7850 (mtmm) REVERT: C 739 MET cc_start: 0.8429 (ttm) cc_final: 0.8190 (ttm) REVERT: C 751 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7431 (tpp-160) REVERT: C 754 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8077 (mt-10) REVERT: C 801 GLN cc_start: 0.7955 (mt0) cc_final: 0.7534 (mt0) REVERT: C 805 PHE cc_start: 0.7526 (t80) cc_final: 0.7259 (t80) REVERT: C 807 GLN cc_start: 0.8049 (mm110) cc_final: 0.7730 (mm110) REVERT: C 822 LYS cc_start: 0.8283 (mmtm) cc_final: 0.8030 (tptp) REVERT: D 25 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7548 (mt-10) REVERT: D 47 ARG cc_start: 0.6292 (tmt-80) cc_final: 0.6041 (tpt170) REVERT: D 58 CYS cc_start: 0.6652 (t) cc_final: 0.6318 (t) REVERT: D 79 LYS cc_start: 0.8551 (tptt) cc_final: 0.7937 (tptt) REVERT: D 82 GLU cc_start: 0.7804 (pp20) cc_final: 0.7259 (pp20) REVERT: D 121 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7479 (tp30) REVERT: D 124 ARG cc_start: 0.8165 (tpt170) cc_final: 0.7156 (tpt90) REVERT: D 131 ARG cc_start: 0.6385 (mtt90) cc_final: 0.6086 (mtt90) REVERT: D 133 HIS cc_start: 0.7531 (m-70) cc_final: 0.7126 (m-70) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1376 time to fit residues: 75.5806 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 : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 105 optimal weight: 0.0370 chunk 41 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 131 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 142 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.155709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.125963 restraints weight = 28173.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.130796 restraints weight = 19048.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.134652 restraints weight = 13954.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.137580 restraints weight = 10688.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.139570 restraints weight = 8475.179| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12590 Z= 0.120 Angle : 0.647 14.483 16980 Z= 0.323 Chirality : 0.044 0.181 1912 Planarity : 0.004 0.047 2186 Dihedral : 5.160 23.345 1688 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.21), residues: 1496 helix: -2.06 (0.17), residues: 712 sheet: -2.33 (0.71), residues: 40 loop : -1.13 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 131 TYR 0.016 0.001 TYR C 146 PHE 0.024 0.002 PHE A 466 TRP 0.012 0.002 TRP C 328 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00269 (12580) covalent geometry : angle 0.64676 (16980) hydrogen bonds : bond 0.03699 ( 334) hydrogen bonds : angle 6.18853 ( 960) metal coordination : bond 0.00403 ( 10) *********************** 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 407 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.498 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 163 LEU cc_start: 0.8251 (tt) cc_final: 0.8051 (tt) REVERT: A 241 ARG cc_start: 0.8536 (mmp80) cc_final: 0.7884 (mmp80) REVERT: A 266 ASN cc_start: 0.6905 (t0) cc_final: 0.6679 (m110) REVERT: A 282 ASN cc_start: 0.8305 (t0) cc_final: 0.8035 (t0) REVERT: A 287 PHE cc_start: 0.7504 (m-80) cc_final: 0.7056 (m-80) REVERT: A 324 LEU cc_start: 0.8528 (mt) cc_final: 0.7574 (mt) REVERT: A 328 TRP cc_start: 0.8324 (m-10) cc_final: 0.7962 (m-10) REVERT: A 335 GLN cc_start: 0.7613 (mp10) cc_final: 0.7333 (mp10) REVERT: A 337 ARG cc_start: 0.8050 (mmp80) cc_final: 0.7324 (mmm160) REVERT: A 339 MET cc_start: 0.8682 (ptp) cc_final: 0.8375 (ptp) REVERT: A 340 MET cc_start: 0.8254 (ptm) cc_final: 0.7217 (ptm) REVERT: A 373 LYS cc_start: 0.8166 (mttm) cc_final: 0.7844 (mttm) REVERT: A 439 CYS cc_start: 0.7475 (m) cc_final: 0.7272 (m) REVERT: A 464 TYR cc_start: 0.7005 (t80) cc_final: 0.6789 (t80) REVERT: A 472 GLU cc_start: 0.8263 (pt0) cc_final: 0.7987 (pp20) REVERT: A 473 ASN cc_start: 0.8866 (m110) cc_final: 0.8456 (m110) REVERT: A 477 PHE cc_start: 0.8324 (m-80) cc_final: 0.7859 (m-80) REVERT: A 478 MET cc_start: 0.7931 (tpp) cc_final: 0.7417 (tpp) REVERT: A 491 LEU cc_start: 0.8456 (tp) cc_final: 0.8241 (tp) REVERT: A 539 ARG cc_start: 0.8739 (tpp80) cc_final: 0.7908 (tpp80) REVERT: A 558 GLU cc_start: 0.8057 (pt0) cc_final: 0.7704 (pm20) REVERT: A 597 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8684 (mmmt) REVERT: A 611 GLN cc_start: 0.7921 (mp10) cc_final: 0.7711 (mp10) REVERT: A 635 MET cc_start: 0.7908 (mpp) cc_final: 0.7330 (mpp) REVERT: A 640 LYS cc_start: 0.8373 (mttt) cc_final: 0.7972 (mttt) REVERT: A 651 LEU cc_start: 0.8233 (tp) cc_final: 0.7951 (tp) REVERT: A 663 LYS cc_start: 0.8409 (ptmm) cc_final: 0.7702 (mtmm) REVERT: A 692 MET cc_start: 0.6573 (mpp) cc_final: 0.6298 (mpp) REVERT: A 739 MET cc_start: 0.8312 (ttm) cc_final: 0.8081 (ttm) REVERT: A 742 ASN cc_start: 0.8513 (p0) cc_final: 0.7867 (p0) REVERT: A 751 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7215 (tpp-160) REVERT: A 754 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 801 GLN cc_start: 0.7963 (mt0) cc_final: 0.7614 (mt0) REVERT: A 822 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7902 (mmtm) REVERT: A 861 ARG cc_start: 0.7488 (ptp-170) cc_final: 0.6884 (mtm110) REVERT: B 18 LYS cc_start: 0.8297 (mttt) cc_final: 0.8036 (mttt) REVERT: B 47 ARG cc_start: 0.5973 (tmt-80) cc_final: 0.5746 (tpt170) REVERT: B 58 CYS cc_start: 0.6621 (t) cc_final: 0.6292 (t) REVERT: B 79 LYS cc_start: 0.8444 (tptt) cc_final: 0.7842 (tptt) REVERT: B 82 GLU cc_start: 0.7483 (pp20) cc_final: 0.6839 (pp20) REVERT: B 114 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7531 (mm-40) REVERT: B 121 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7103 (tp30) REVERT: B 124 ARG cc_start: 0.8029 (tpt170) cc_final: 0.7058 (mmm160) REVERT: B 133 HIS cc_start: 0.7263 (m-70) cc_final: 0.6986 (m-70) REVERT: C 138 GLU cc_start: 0.7984 (tp30) cc_final: 0.7367 (tp30) REVERT: C 241 ARG cc_start: 0.8354 (mmp80) cc_final: 0.7831 (mmp80) REVERT: C 242 VAL cc_start: 0.8595 (t) cc_final: 0.8369 (t) REVERT: C 303 GLU cc_start: 0.7847 (mp0) cc_final: 0.7632 (mp0) REVERT: C 309 PHE cc_start: 0.7990 (t80) cc_final: 0.7686 (t80) REVERT: C 313 MET cc_start: 0.7502 (mmm) cc_final: 0.7291 (mmm) REVERT: C 324 LEU cc_start: 0.8407 (mt) cc_final: 0.8197 (mt) REVERT: C 335 GLN cc_start: 0.7504 (mp10) cc_final: 0.7218 (mp10) REVERT: C 340 MET cc_start: 0.7916 (ptm) cc_final: 0.7593 (ptt) REVERT: C 344 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7862 (tp-100) REVERT: C 345 GLN cc_start: 0.7499 (mt0) cc_final: 0.6798 (mt0) REVERT: C 373 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7378 (tptp) REVERT: C 376 LYS cc_start: 0.8461 (tttm) cc_final: 0.8105 (tttm) REVERT: C 392 HIS cc_start: 0.7806 (m90) cc_final: 0.7571 (m90) REVERT: C 395 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6727 (tm-30) REVERT: C 398 GLU cc_start: 0.8161 (mp0) cc_final: 0.7887 (mp0) REVERT: C 406 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7197 (tm-30) REVERT: C 407 LEU cc_start: 0.8501 (mt) cc_final: 0.8111 (mt) REVERT: C 441 LYS cc_start: 0.8526 (mptt) cc_final: 0.8124 (mptt) REVERT: C 472 GLU cc_start: 0.8251 (pm20) cc_final: 0.7931 (pm20) REVERT: C 478 MET cc_start: 0.8021 (tpp) cc_final: 0.7537 (tpp) REVERT: C 491 LEU cc_start: 0.8654 (mt) cc_final: 0.8323 (mt) REVERT: C 531 HIS cc_start: 0.8262 (m90) cc_final: 0.7993 (m90) REVERT: C 539 ARG cc_start: 0.8582 (tpp80) cc_final: 0.7830 (ttt180) REVERT: C 540 LEU cc_start: 0.8913 (tp) cc_final: 0.8653 (tt) REVERT: C 541 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7467 (mm-30) REVERT: C 542 MET cc_start: 0.7685 (mmt) cc_final: 0.7258 (mmt) REVERT: C 580 GLU cc_start: 0.8572 (tp30) cc_final: 0.8319 (tp30) REVERT: C 592 TYR cc_start: 0.7417 (t80) cc_final: 0.6804 (t80) REVERT: C 597 LYS cc_start: 0.9230 (mtpp) cc_final: 0.8684 (mtpp) REVERT: C 605 SER cc_start: 0.8090 (p) cc_final: 0.7702 (t) REVERT: C 607 GLU cc_start: 0.8392 (pm20) cc_final: 0.8058 (pm20) REVERT: C 635 MET cc_start: 0.8038 (mpp) cc_final: 0.7360 (mpp) REVERT: C 639 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7602 (mmm-85) REVERT: C 640 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8047 (mtmt) REVERT: C 642 MET cc_start: 0.7858 (mmp) cc_final: 0.7556 (mmt) REVERT: C 651 LEU cc_start: 0.8369 (tp) cc_final: 0.8052 (tp) REVERT: C 663 LYS cc_start: 0.8533 (ptmm) cc_final: 0.8099 (ptpp) REVERT: C 684 GLN cc_start: 0.7602 (tp40) cc_final: 0.6260 (tm-30) REVERT: C 694 TYR cc_start: 0.7698 (t80) cc_final: 0.7478 (t80) REVERT: C 739 MET cc_start: 0.8390 (ttm) cc_final: 0.8172 (ttm) REVERT: C 744 SER cc_start: 0.8442 (t) cc_final: 0.7791 (p) REVERT: C 751 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7222 (tpp-160) REVERT: C 754 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 801 GLN cc_start: 0.7943 (mt0) cc_final: 0.7569 (mt0) REVERT: C 802 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7684 (mmtt) REVERT: C 805 PHE cc_start: 0.7454 (t80) cc_final: 0.7252 (t80) REVERT: C 807 GLN cc_start: 0.7897 (mm110) cc_final: 0.7595 (mm110) REVERT: D 25 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7339 (mt-10) REVERT: D 36 GLU cc_start: 0.7572 (mp0) cc_final: 0.7234 (pm20) REVERT: D 58 CYS cc_start: 0.6453 (t) cc_final: 0.5809 (t) REVERT: D 59 ILE cc_start: 0.6433 (mm) cc_final: 0.6226 (mm) REVERT: D 79 LYS cc_start: 0.8505 (tptt) cc_final: 0.7863 (tptt) REVERT: D 82 GLU cc_start: 0.7788 (pp20) cc_final: 0.7161 (pp20) REVERT: D 114 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7657 (mm-40) REVERT: D 124 ARG cc_start: 0.8193 (tpt170) cc_final: 0.7382 (tpt90) REVERT: D 133 HIS cc_start: 0.7261 (m-70) cc_final: 0.6975 (m-70) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1510 time to fit residues: 81.7440 Evaluate side-chains 377 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 116 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 13 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 135 optimal weight: 0.0870 chunk 69 optimal weight: 0.2980 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS C 382 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.157673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.128857 restraints weight = 27260.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.133780 restraints weight = 18178.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.137488 restraints weight = 13126.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.140309 restraints weight = 10015.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.142547 restraints weight = 7898.585| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12590 Z= 0.119 Angle : 0.673 16.233 16980 Z= 0.328 Chirality : 0.044 0.181 1912 Planarity : 0.004 0.050 2186 Dihedral : 4.973 25.536 1688 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.22), residues: 1496 helix: -1.94 (0.18), residues: 720 sheet: -2.36 (0.67), residues: 40 loop : -1.00 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 649 TYR 0.016 0.001 TYR B 91 PHE 0.034 0.002 PHE A 633 TRP 0.050 0.004 TRP C 791 HIS 0.003 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00261 (12580) covalent geometry : angle 0.67312 (16980) hydrogen bonds : bond 0.03668 ( 334) hydrogen bonds : angle 6.06345 ( 960) metal coordination : bond 0.00229 ( 10) *********************** 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 414 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.505 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: 0.8434 (mmp80) cc_final: 0.7840 (mmp80) REVERT: A 242 VAL cc_start: 0.8691 (t) cc_final: 0.8469 (t) REVERT: A 266 ASN cc_start: 0.6970 (t0) cc_final: 0.6703 (m110) REVERT: A 287 PHE cc_start: 0.7374 (m-80) cc_final: 0.6854 (m-80) REVERT: A 324 LEU cc_start: 0.8513 (mt) cc_final: 0.7563 (mt) REVERT: A 328 TRP cc_start: 0.8312 (m-10) cc_final: 0.7942 (m-10) REVERT: A 335 GLN cc_start: 0.7581 (mp10) cc_final: 0.7286 (mp10) REVERT: A 337 ARG cc_start: 0.7993 (mmp80) cc_final: 0.7263 (mmm160) REVERT: A 339 MET cc_start: 0.8618 (ptp) cc_final: 0.8309 (ptp) REVERT: A 340 MET cc_start: 0.8144 (ptm) cc_final: 0.6946 (ptm) REVERT: A 373 LYS cc_start: 0.8150 (mttm) cc_final: 0.7867 (mttm) REVERT: A 376 LYS cc_start: 0.8301 (tttp) cc_final: 0.8075 (ttpp) REVERT: A 412 LEU cc_start: 0.8518 (tt) cc_final: 0.8235 (tt) REVERT: A 441 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8445 (ptmm) REVERT: A 464 TYR cc_start: 0.6894 (t80) cc_final: 0.6640 (t80) REVERT: A 472 GLU cc_start: 0.8215 (pt0) cc_final: 0.7860 (pp20) REVERT: A 473 ASN cc_start: 0.8855 (m110) cc_final: 0.8420 (m110) REVERT: A 477 PHE cc_start: 0.8236 (m-80) cc_final: 0.7759 (m-80) REVERT: A 478 MET cc_start: 0.7905 (tpp) cc_final: 0.7375 (tpp) REVERT: A 539 ARG cc_start: 0.8692 (tpp80) cc_final: 0.7977 (tpp80) REVERT: A 558 GLU cc_start: 0.8015 (pt0) cc_final: 0.7671 (pm20) REVERT: A 576 GLN cc_start: 0.8321 (tp40) cc_final: 0.7233 (tm-30) REVERT: A 580 GLU cc_start: 0.8363 (pt0) cc_final: 0.7976 (mm-30) REVERT: A 597 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8688 (mmmt) REVERT: A 611 GLN cc_start: 0.7997 (mp10) cc_final: 0.7786 (mp10) REVERT: A 635 MET cc_start: 0.7754 (mpp) cc_final: 0.7097 (mpp) REVERT: A 640 LYS cc_start: 0.8331 (mttt) cc_final: 0.7975 (mttt) REVERT: A 642 MET cc_start: 0.7931 (mmp) cc_final: 0.7591 (mmp) REVERT: A 648 PHE cc_start: 0.6702 (t80) cc_final: 0.6464 (t80) REVERT: A 651 LEU cc_start: 0.8170 (tp) cc_final: 0.7880 (tp) REVERT: A 663 LYS cc_start: 0.8322 (ptmm) cc_final: 0.7810 (mtmm) REVERT: A 694 TYR cc_start: 0.6918 (t80) cc_final: 0.6684 (t80) REVERT: A 711 LYS cc_start: 0.8716 (mptt) cc_final: 0.8359 (mptt) REVERT: A 730 PHE cc_start: 0.7958 (t80) cc_final: 0.7579 (t80) REVERT: A 739 MET cc_start: 0.8197 (ttm) cc_final: 0.7993 (ttm) REVERT: A 742 ASN cc_start: 0.8354 (p0) cc_final: 0.7988 (p0) REVERT: A 751 ARG cc_start: 0.7987 (mmm160) cc_final: 0.7055 (tpp-160) REVERT: A 754 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8438 (mt-10) REVERT: A 801 GLN cc_start: 0.7979 (mt0) cc_final: 0.7618 (mt0) REVERT: A 802 LYS cc_start: 0.8008 (mptt) cc_final: 0.7639 (mmtt) REVERT: A 822 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7855 (mmtm) REVERT: A 861 ARG cc_start: 0.7380 (ptp-170) cc_final: 0.6691 (mtm110) REVERT: B 18 LYS cc_start: 0.8283 (mttt) cc_final: 0.7934 (mttt) REVERT: B 47 ARG cc_start: 0.5928 (tmt-80) cc_final: 0.5709 (tpt170) REVERT: B 52 PHE cc_start: 0.6446 (t80) cc_final: 0.6222 (t80) REVERT: B 58 CYS cc_start: 0.6723 (t) cc_final: 0.6118 (t) REVERT: B 59 ILE cc_start: 0.6761 (mm) cc_final: 0.6290 (mm) REVERT: B 114 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7431 (mm-40) REVERT: B 121 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7286 (tp30) REVERT: B 133 HIS cc_start: 0.7226 (m-70) cc_final: 0.7018 (m-70) REVERT: C 138 GLU cc_start: 0.7851 (tp30) cc_final: 0.7173 (tp30) REVERT: C 241 ARG cc_start: 0.8322 (mmp80) cc_final: 0.7878 (mmp80) REVERT: C 242 VAL cc_start: 0.8663 (t) cc_final: 0.8449 (t) REVERT: C 282 ASN cc_start: 0.8066 (t0) cc_final: 0.7734 (t0) REVERT: C 309 PHE cc_start: 0.8027 (t80) cc_final: 0.7402 (t80) REVERT: C 313 MET cc_start: 0.7498 (mmm) cc_final: 0.7126 (mmm) REVERT: C 324 LEU cc_start: 0.8361 (mt) cc_final: 0.8160 (mt) REVERT: C 334 ASP cc_start: 0.7642 (p0) cc_final: 0.6990 (p0) REVERT: C 340 MET cc_start: 0.7764 (ptm) cc_final: 0.7474 (ptt) REVERT: C 344 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7818 (tp-100) REVERT: C 345 GLN cc_start: 0.7560 (mt0) cc_final: 0.7015 (mt0) REVERT: C 373 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7445 (tptp) REVERT: C 389 ASP cc_start: 0.7211 (t0) cc_final: 0.6863 (t70) REVERT: C 395 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6762 (tm-30) REVERT: C 398 GLU cc_start: 0.8099 (mp0) cc_final: 0.7859 (mp0) REVERT: C 406 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7110 (tm-30) REVERT: C 407 LEU cc_start: 0.8496 (mt) cc_final: 0.8100 (mt) REVERT: C 441 LYS cc_start: 0.8415 (mptt) cc_final: 0.7961 (mmtm) REVERT: C 472 GLU cc_start: 0.8208 (pm20) cc_final: 0.7909 (pm20) REVERT: C 478 MET cc_start: 0.7906 (tpp) cc_final: 0.7293 (tpp) REVERT: C 524 ARG cc_start: 0.8013 (mtt90) cc_final: 0.6858 (mtt90) REVERT: C 531 HIS cc_start: 0.8183 (m90) cc_final: 0.7924 (m90) REVERT: C 537 LEU cc_start: 0.8344 (tp) cc_final: 0.7251 (tp) REVERT: C 539 ARG cc_start: 0.8530 (tpp80) cc_final: 0.7854 (ttt180) REVERT: C 542 MET cc_start: 0.7374 (mmt) cc_final: 0.7056 (mmt) REVERT: C 554 GLN cc_start: 0.7830 (tt0) cc_final: 0.7482 (tt0) REVERT: C 558 GLU cc_start: 0.8048 (pt0) cc_final: 0.7738 (tm-30) REVERT: C 576 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7452 (tm-30) REVERT: C 580 GLU cc_start: 0.8445 (tp30) cc_final: 0.8030 (mm-30) REVERT: C 584 ASN cc_start: 0.8203 (m-40) cc_final: 0.8002 (m-40) REVERT: C 592 TYR cc_start: 0.7407 (t80) cc_final: 0.6880 (t80) REVERT: C 597 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8811 (mtpp) REVERT: C 605 SER cc_start: 0.7983 (p) cc_final: 0.7625 (t) REVERT: C 607 GLU cc_start: 0.8384 (pm20) cc_final: 0.8034 (pm20) REVERT: C 635 MET cc_start: 0.8071 (mpp) cc_final: 0.7352 (mpp) REVERT: C 639 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7541 (mmm-85) REVERT: C 640 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8125 (mtmt) REVERT: C 642 MET cc_start: 0.7745 (mmp) cc_final: 0.7469 (mmt) REVERT: C 651 LEU cc_start: 0.8409 (tp) cc_final: 0.8139 (tp) REVERT: C 684 GLN cc_start: 0.7599 (tp40) cc_final: 0.6183 (tm-30) REVERT: C 692 MET cc_start: 0.7492 (ppp) cc_final: 0.7013 (ppp) REVERT: C 694 TYR cc_start: 0.7505 (t80) cc_final: 0.6930 (t80) REVERT: C 739 MET cc_start: 0.8235 (ttm) cc_final: 0.7988 (ttm) REVERT: C 751 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7391 (tpp-160) REVERT: C 754 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 801 GLN cc_start: 0.7976 (mt0) cc_final: 0.7598 (mt0) REVERT: D 25 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7376 (mt-10) REVERT: D 36 GLU cc_start: 0.7601 (mp0) cc_final: 0.7294 (pm20) REVERT: D 52 PHE cc_start: 0.6890 (t80) cc_final: 0.6650 (t80) REVERT: D 58 CYS cc_start: 0.6510 (t) cc_final: 0.6100 (t) REVERT: D 114 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7690 (mm-40) REVERT: D 124 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7323 (tpt90) REVERT: D 133 HIS cc_start: 0.7121 (m-70) cc_final: 0.6847 (m-70) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1513 time to fit residues: 84.3096 Evaluate side-chains 372 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 101 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 393 ASN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.154132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.125659 restraints weight = 27630.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.130480 restraints weight = 18551.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.134063 restraints weight = 13481.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.136846 restraints weight = 10299.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.138923 restraints weight = 8123.472| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12590 Z= 0.159 Angle : 0.693 15.178 16980 Z= 0.348 Chirality : 0.046 0.193 1912 Planarity : 0.005 0.053 2186 Dihedral : 5.136 25.180 1688 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.21), residues: 1496 helix: -1.93 (0.17), residues: 726 sheet: -2.25 (0.69), residues: 40 loop : -1.03 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 440 TYR 0.017 0.001 TYR C 464 PHE 0.039 0.002 PHE A 633 TRP 0.028 0.002 TRP C 791 HIS 0.003 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00328 (12580) covalent geometry : angle 0.69283 (16980) hydrogen bonds : bond 0.03962 ( 334) hydrogen bonds : angle 6.22292 ( 960) metal coordination : bond 0.00551 ( 10) *********************** 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 401 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.513 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: 0.8504 (mmp80) cc_final: 0.7635 (mmp80) REVERT: A 266 ASN cc_start: 0.7144 (t0) cc_final: 0.6902 (m110) REVERT: A 282 ASN cc_start: 0.8309 (t0) cc_final: 0.8047 (t0) REVERT: A 309 PHE cc_start: 0.8216 (t80) cc_final: 0.7915 (t80) REVERT: A 324 LEU cc_start: 0.8598 (mt) cc_final: 0.8313 (mt) REVERT: A 335 GLN cc_start: 0.7823 (mp10) cc_final: 0.7580 (mp10) REVERT: A 336 ILE cc_start: 0.8783 (mm) cc_final: 0.8445 (mm) REVERT: A 337 ARG cc_start: 0.7999 (mmp80) cc_final: 0.7401 (mmm160) REVERT: A 339 MET cc_start: 0.8720 (ptp) cc_final: 0.8423 (ptp) REVERT: A 340 MET cc_start: 0.8420 (ptm) cc_final: 0.7384 (ptm) REVERT: A 373 LYS cc_start: 0.8172 (mttm) cc_final: 0.7864 (mttm) REVERT: A 412 LEU cc_start: 0.8547 (tt) cc_final: 0.8168 (tt) REVERT: A 441 LYS cc_start: 0.8916 (ptmm) cc_final: 0.8336 (ptmm) REVERT: A 449 PHE cc_start: 0.7970 (m-80) cc_final: 0.7535 (m-80) REVERT: A 464 TYR cc_start: 0.7118 (t80) cc_final: 0.6707 (t80) REVERT: A 472 GLU cc_start: 0.8228 (pt0) cc_final: 0.7846 (pp20) REVERT: A 473 ASN cc_start: 0.8876 (m110) cc_final: 0.8440 (m110) REVERT: A 477 PHE cc_start: 0.8432 (m-80) cc_final: 0.7909 (m-80) REVERT: A 478 MET cc_start: 0.8071 (tpp) cc_final: 0.7541 (tpp) REVERT: A 528 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7687 (ttm110) REVERT: A 531 HIS cc_start: 0.8081 (m90) cc_final: 0.7772 (m90) REVERT: A 539 ARG cc_start: 0.8704 (tpp80) cc_final: 0.8071 (tpp80) REVERT: A 542 MET cc_start: 0.7630 (mmt) cc_final: 0.7151 (mmt) REVERT: A 547 ASN cc_start: 0.8103 (t0) cc_final: 0.7867 (t0) REVERT: A 554 GLN cc_start: 0.7497 (tt0) cc_final: 0.7084 (tt0) REVERT: A 558 GLU cc_start: 0.8214 (pt0) cc_final: 0.7777 (pm20) REVERT: A 576 GLN cc_start: 0.8400 (tp40) cc_final: 0.8109 (tm-30) REVERT: A 580 GLU cc_start: 0.8407 (pt0) cc_final: 0.8017 (tp30) REVERT: A 597 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8684 (mmmt) REVERT: A 611 GLN cc_start: 0.8073 (mp10) cc_final: 0.7820 (mp10) REVERT: A 635 MET cc_start: 0.7949 (mpp) cc_final: 0.7263 (mpp) REVERT: A 642 MET cc_start: 0.7952 (mmp) cc_final: 0.7471 (mmt) REVERT: A 648 PHE cc_start: 0.7183 (t80) cc_final: 0.6921 (t80) REVERT: A 651 LEU cc_start: 0.8171 (tp) cc_final: 0.7914 (tp) REVERT: A 663 LYS cc_start: 0.8500 (ptmm) cc_final: 0.7855 (mtmm) REVERT: A 684 GLN cc_start: 0.6738 (tp40) cc_final: 0.5702 (tm-30) REVERT: A 694 TYR cc_start: 0.7039 (t80) cc_final: 0.5820 (t80) REVERT: A 720 TYR cc_start: 0.7644 (t80) cc_final: 0.7272 (t80) REVERT: A 751 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7197 (tpp-160) REVERT: A 754 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8454 (mt-10) REVERT: A 801 GLN cc_start: 0.8019 (mt0) cc_final: 0.7792 (mt0) REVERT: A 802 LYS cc_start: 0.8127 (mptt) cc_final: 0.7794 (mmtt) REVERT: A 807 GLN cc_start: 0.8473 (mt0) cc_final: 0.8234 (mm-40) REVERT: A 822 LYS cc_start: 0.8253 (mmtm) cc_final: 0.7819 (mmtm) REVERT: A 861 ARG cc_start: 0.7419 (ptp-170) cc_final: 0.6677 (mtm110) REVERT: B 18 LYS cc_start: 0.8303 (mttt) cc_final: 0.7932 (mttt) REVERT: B 47 ARG cc_start: 0.5940 (tmt-80) cc_final: 0.5704 (tmt-80) REVERT: B 52 PHE cc_start: 0.6615 (t80) cc_final: 0.6405 (t80) REVERT: B 58 CYS cc_start: 0.6782 (t) cc_final: 0.6269 (t) REVERT: B 59 ILE cc_start: 0.7033 (mm) cc_final: 0.6584 (mm) REVERT: B 107 LEU cc_start: 0.8304 (mm) cc_final: 0.8068 (mm) REVERT: B 114 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7748 (mm-40) REVERT: B 121 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6965 (tp30) REVERT: B 124 ARG cc_start: 0.8110 (tpt170) cc_final: 0.7237 (mmm160) REVERT: C 138 GLU cc_start: 0.7870 (tp30) cc_final: 0.7197 (tp30) REVERT: C 241 ARG cc_start: 0.8319 (mmp80) cc_final: 0.7873 (mmp80) REVERT: C 245 ARG cc_start: 0.5925 (mpp80) cc_final: 0.5692 (mpt-90) REVERT: C 246 LEU cc_start: 0.8488 (mm) cc_final: 0.7760 (tp) REVERT: C 323 LYS cc_start: 0.7224 (mmtt) cc_final: 0.6762 (mtpp) REVERT: C 344 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7555 (tp40) REVERT: C 345 GLN cc_start: 0.7551 (mt0) cc_final: 0.7137 (mt0) REVERT: C 373 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7417 (tptp) REVERT: C 395 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6826 (tm-30) REVERT: C 398 GLU cc_start: 0.8053 (mp0) cc_final: 0.7798 (mp0) REVERT: C 406 GLU cc_start: 0.7687 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 407 LEU cc_start: 0.8498 (mt) cc_final: 0.8145 (mt) REVERT: C 411 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8157 (tt0) REVERT: C 419 ASN cc_start: 0.7885 (m-40) cc_final: 0.7684 (m-40) REVERT: C 441 LYS cc_start: 0.8553 (mptt) cc_final: 0.8181 (mptt) REVERT: C 449 PHE cc_start: 0.7817 (m-80) cc_final: 0.7542 (m-80) REVERT: C 472 GLU cc_start: 0.8226 (pm20) cc_final: 0.7878 (pm20) REVERT: C 478 MET cc_start: 0.7941 (tpp) cc_final: 0.7371 (tpp) REVERT: C 491 LEU cc_start: 0.8732 (mt) cc_final: 0.8416 (mt) REVERT: C 531 HIS cc_start: 0.8342 (m90) cc_final: 0.8037 (m90) REVERT: C 539 ARG cc_start: 0.8533 (tpp80) cc_final: 0.7848 (ttt180) REVERT: C 542 MET cc_start: 0.7396 (mmt) cc_final: 0.7116 (mmt) REVERT: C 554 GLN cc_start: 0.7925 (tt0) cc_final: 0.7627 (tt0) REVERT: C 589 MET cc_start: 0.4958 (ttm) cc_final: 0.4439 (ttm) REVERT: C 592 TYR cc_start: 0.7451 (t80) cc_final: 0.7175 (t80) REVERT: C 597 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8894 (mtpp) REVERT: C 605 SER cc_start: 0.8032 (p) cc_final: 0.7738 (t) REVERT: C 607 GLU cc_start: 0.8331 (pm20) cc_final: 0.7939 (pm20) REVERT: C 627 CYS cc_start: 0.7176 (p) cc_final: 0.6865 (p) REVERT: C 629 LEU cc_start: 0.7750 (mp) cc_final: 0.7235 (mt) REVERT: C 635 MET cc_start: 0.8091 (mpp) cc_final: 0.7399 (mpp) REVERT: C 639 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7637 (mmm-85) REVERT: C 640 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8115 (mtmt) REVERT: C 642 MET cc_start: 0.7913 (mmp) cc_final: 0.7564 (mmt) REVERT: C 651 LEU cc_start: 0.8419 (tp) cc_final: 0.8112 (tp) REVERT: C 667 GLU cc_start: 0.8722 (mp0) cc_final: 0.8466 (mp0) REVERT: C 684 GLN cc_start: 0.7708 (tp40) cc_final: 0.6957 (tm-30) REVERT: C 694 TYR cc_start: 0.7127 (t80) cc_final: 0.6667 (t80) REVERT: C 715 ASN cc_start: 0.8808 (m110) cc_final: 0.8594 (m110) REVERT: C 720 TYR cc_start: 0.7921 (t80) cc_final: 0.7367 (t80) REVERT: C 739 MET cc_start: 0.8382 (ttm) cc_final: 0.8160 (ttm) REVERT: C 751 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7567 (tpp-160) REVERT: C 754 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8095 (mt-10) REVERT: C 766 ASP cc_start: 0.8161 (t0) cc_final: 0.7942 (t0) REVERT: C 801 GLN cc_start: 0.8038 (mt0) cc_final: 0.7700 (mt0) REVERT: C 807 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7560 (mm110) REVERT: D 25 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7418 (mt-10) REVERT: D 36 GLU cc_start: 0.7520 (mp0) cc_final: 0.7214 (pm20) REVERT: D 52 PHE cc_start: 0.6970 (t80) cc_final: 0.6631 (t80) REVERT: D 58 CYS cc_start: 0.6820 (t) cc_final: 0.6134 (t) REVERT: D 59 ILE cc_start: 0.7041 (mm) cc_final: 0.6633 (mm) REVERT: D 114 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7761 (mm-40) REVERT: D 121 GLU cc_start: 0.7472 (tp30) cc_final: 0.7134 (tt0) REVERT: D 123 GLN cc_start: 0.8378 (mp10) cc_final: 0.8164 (mp10) REVERT: D 124 ARG cc_start: 0.8108 (tpt170) cc_final: 0.7569 (tpt90) REVERT: D 133 HIS cc_start: 0.7308 (m-70) cc_final: 0.7078 (m-70) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1569 time to fit residues: 83.7660 Evaluate side-chains 366 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 55 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 21 GLN D 65 ASN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.152644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.124649 restraints weight = 27899.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.129357 restraints weight = 18629.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.132927 restraints weight = 13533.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.135656 restraints weight = 10325.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.137712 restraints weight = 8148.042| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 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 : 0.004 0.070 12590 Z= 0.179 Angle : 0.744 17.301 16980 Z= 0.371 Chirality : 0.047 0.249 1912 Planarity : 0.005 0.080 2186 Dihedral : 5.265 24.704 1688 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.21), residues: 1496 helix: -1.96 (0.17), residues: 752 sheet: -2.21 (0.70), residues: 40 loop : -1.16 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 710 TYR 0.028 0.002 TYR A 464 PHE 0.031 0.002 PHE A 633 TRP 0.019 0.002 TRP C 791 HIS 0.004 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00371 (12580) covalent geometry : angle 0.74438 (16980) hydrogen bonds : bond 0.04307 ( 334) hydrogen bonds : angle 6.43757 ( 960) metal coordination : bond 0.00738 ( 10) *********************** 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 414 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.493 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 135 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8133 (mp0) REVERT: A 240 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8506 (mtt180) REVERT: A 241 ARG cc_start: 0.8492 (mmp80) cc_final: 0.7580 (mmp80) REVERT: A 266 ASN cc_start: 0.7124 (t0) cc_final: 0.6923 (m110) REVERT: A 287 PHE cc_start: 0.7211 (m-10) cc_final: 0.6965 (m-10) REVERT: A 324 LEU cc_start: 0.8544 (mt) cc_final: 0.8287 (mt) REVERT: A 335 GLN cc_start: 0.7833 (mp10) cc_final: 0.7464 (mp10) REVERT: A 336 ILE cc_start: 0.8821 (mm) cc_final: 0.8460 (mm) REVERT: A 337 ARG cc_start: 0.8054 (mmp80) cc_final: 0.7428 (mmm160) REVERT: A 339 MET cc_start: 0.8631 (ptp) cc_final: 0.8320 (ptp) REVERT: A 340 MET cc_start: 0.8412 (ptm) cc_final: 0.7312 (ptm) REVERT: A 373 LYS cc_start: 0.8173 (mttm) cc_final: 0.7814 (mttm) REVERT: A 428 LEU cc_start: 0.8584 (tt) cc_final: 0.7883 (mp) REVERT: A 441 LYS cc_start: 0.8676 (ptmm) cc_final: 0.8260 (ptmm) REVERT: A 449 PHE cc_start: 0.7923 (m-80) cc_final: 0.7507 (m-80) REVERT: A 472 GLU cc_start: 0.8225 (pt0) cc_final: 0.7856 (pp20) REVERT: A 473 ASN cc_start: 0.8895 (m110) cc_final: 0.8387 (m110) REVERT: A 477 PHE cc_start: 0.8331 (m-80) cc_final: 0.7881 (m-80) REVERT: A 478 MET cc_start: 0.8071 (tpp) cc_final: 0.7612 (tpp) REVERT: A 531 HIS cc_start: 0.8121 (m90) cc_final: 0.7810 (m90) REVERT: A 539 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8263 (tpp80) REVERT: A 542 MET cc_start: 0.7652 (mmt) cc_final: 0.7187 (mmt) REVERT: A 558 GLU cc_start: 0.8162 (pt0) cc_final: 0.7765 (pm20) REVERT: A 576 GLN cc_start: 0.8350 (tp40) cc_final: 0.7952 (tm-30) REVERT: A 580 GLU cc_start: 0.8405 (pt0) cc_final: 0.8094 (tp30) REVERT: A 589 MET cc_start: 0.4530 (ttm) cc_final: 0.3640 (ttm) REVERT: A 597 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8606 (mmmt) REVERT: A 611 GLN cc_start: 0.8032 (mp10) cc_final: 0.7636 (mp10) REVERT: A 635 MET cc_start: 0.8033 (mpp) cc_final: 0.7227 (mmp) REVERT: A 639 ARG cc_start: 0.8690 (tpt-90) cc_final: 0.7516 (tpt-90) REVERT: A 642 MET cc_start: 0.7948 (mmp) cc_final: 0.7618 (mmt) REVERT: A 648 PHE cc_start: 0.7598 (t80) cc_final: 0.7295 (t80) REVERT: A 651 LEU cc_start: 0.8179 (tp) cc_final: 0.7864 (tp) REVERT: A 663 LYS cc_start: 0.8346 (ptmm) cc_final: 0.7815 (mtmm) REVERT: A 694 TYR cc_start: 0.7012 (t80) cc_final: 0.5784 (t80) REVERT: A 710 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7571 (mmp-170) REVERT: A 719 ASP cc_start: 0.8840 (m-30) cc_final: 0.8639 (m-30) REVERT: A 720 TYR cc_start: 0.7568 (t80) cc_final: 0.7205 (t80) REVERT: A 751 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7212 (tpp-160) REVERT: A 754 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8488 (mt-10) REVERT: A 801 GLN cc_start: 0.8015 (mt0) cc_final: 0.7758 (mt0) REVERT: A 802 LYS cc_start: 0.8131 (mptt) cc_final: 0.7761 (mmtt) REVERT: A 861 ARG cc_start: 0.7448 (ptp-170) cc_final: 0.6923 (mtt-85) REVERT: B 18 LYS cc_start: 0.8311 (mttt) cc_final: 0.7940 (mttt) REVERT: B 52 PHE cc_start: 0.6596 (t80) cc_final: 0.6358 (t80) REVERT: B 58 CYS cc_start: 0.6797 (t) cc_final: 0.6157 (t) REVERT: B 59 ILE cc_start: 0.7138 (mm) cc_final: 0.6398 (mm) REVERT: B 79 LYS cc_start: 0.8444 (tptt) cc_final: 0.7775 (tptt) REVERT: B 82 GLU cc_start: 0.7591 (pp20) cc_final: 0.6511 (pp20) REVERT: B 114 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7640 (mm-40) REVERT: B 121 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7014 (tp30) REVERT: B 124 ARG cc_start: 0.8089 (tpt170) cc_final: 0.7247 (mmm160) REVERT: C 138 GLU cc_start: 0.7842 (tp30) cc_final: 0.7598 (tp30) REVERT: C 241 ARG cc_start: 0.8333 (mmp80) cc_final: 0.7649 (mmp80) REVERT: C 245 ARG cc_start: 0.6043 (mpp80) cc_final: 0.5785 (mpt-90) REVERT: C 246 LEU cc_start: 0.8520 (mm) cc_final: 0.7762 (tp) REVERT: C 287 PHE cc_start: 0.7779 (m-10) cc_final: 0.7508 (m-10) REVERT: C 324 LEU cc_start: 0.8428 (mt) cc_final: 0.8190 (mt) REVERT: C 344 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7878 (tp-100) REVERT: C 345 GLN cc_start: 0.7486 (mt0) cc_final: 0.6818 (mt0) REVERT: C 373 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7323 (tptp) REVERT: C 376 LYS cc_start: 0.8435 (tttm) cc_final: 0.8069 (tttm) REVERT: C 389 ASP cc_start: 0.7321 (t70) cc_final: 0.7013 (t70) REVERT: C 395 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6874 (tm-30) REVERT: C 398 GLU cc_start: 0.7993 (mp0) cc_final: 0.7689 (mp0) REVERT: C 406 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7030 (tm-30) REVERT: C 407 LEU cc_start: 0.8568 (mt) cc_final: 0.8199 (mt) REVERT: C 411 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8255 (tt0) REVERT: C 419 ASN cc_start: 0.7858 (m-40) cc_final: 0.7650 (m-40) REVERT: C 441 LYS cc_start: 0.8593 (mptt) cc_final: 0.8239 (mptt) REVERT: C 449 PHE cc_start: 0.7686 (m-80) cc_final: 0.7383 (m-80) REVERT: C 472 GLU cc_start: 0.8166 (pm20) cc_final: 0.7825 (pm20) REVERT: C 478 MET cc_start: 0.7915 (tpp) cc_final: 0.7401 (tpp) REVERT: C 491 LEU cc_start: 0.8662 (mt) cc_final: 0.8361 (mt) REVERT: C 531 HIS cc_start: 0.8396 (m90) cc_final: 0.8082 (m90) REVERT: C 539 ARG cc_start: 0.8486 (tpp80) cc_final: 0.7844 (ttt180) REVERT: C 542 MET cc_start: 0.7425 (mmt) cc_final: 0.7088 (mmt) REVERT: C 554 GLN cc_start: 0.7944 (tt0) cc_final: 0.7628 (tt0) REVERT: C 555 LEU cc_start: 0.7604 (tp) cc_final: 0.7403 (tp) REVERT: C 580 GLU cc_start: 0.8751 (tp30) cc_final: 0.8352 (tp30) REVERT: C 592 TYR cc_start: 0.7401 (t80) cc_final: 0.7130 (t80) REVERT: C 597 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8877 (mtpp) REVERT: C 605 SER cc_start: 0.7973 (p) cc_final: 0.7698 (t) REVERT: C 607 GLU cc_start: 0.8251 (pm20) cc_final: 0.7868 (pm20) REVERT: C 627 CYS cc_start: 0.7259 (p) cc_final: 0.7025 (p) REVERT: C 629 LEU cc_start: 0.7717 (mp) cc_final: 0.7432 (mt) REVERT: C 635 MET cc_start: 0.8120 (mpp) cc_final: 0.7459 (mpp) REVERT: C 639 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7623 (mmm-85) REVERT: C 640 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8027 (mtmt) REVERT: C 642 MET cc_start: 0.7936 (mmp) cc_final: 0.7652 (mmt) REVERT: C 651 LEU cc_start: 0.8425 (tp) cc_final: 0.8115 (tp) REVERT: C 663 LYS cc_start: 0.8652 (ptmm) cc_final: 0.8257 (ptpp) REVERT: C 684 GLN cc_start: 0.8007 (tp40) cc_final: 0.6219 (tm-30) REVERT: C 694 TYR cc_start: 0.7333 (t80) cc_final: 0.6578 (t80) REVERT: C 720 TYR cc_start: 0.7797 (t80) cc_final: 0.7438 (t80) REVERT: C 739 MET cc_start: 0.8346 (ttm) cc_final: 0.8108 (ttm) REVERT: C 744 SER cc_start: 0.8195 (t) cc_final: 0.7708 (p) REVERT: C 751 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7538 (tpp-160) REVERT: C 754 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 801 GLN cc_start: 0.8067 (mt0) cc_final: 0.7732 (mt0) REVERT: C 802 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7874 (mmtt) REVERT: C 807 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7468 (mm110) REVERT: D 25 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7389 (mt-10) REVERT: D 52 PHE cc_start: 0.6984 (t80) cc_final: 0.6695 (t80) REVERT: D 58 CYS cc_start: 0.6717 (t) cc_final: 0.6243 (t) REVERT: D 59 ILE cc_start: 0.7245 (mm) cc_final: 0.6885 (mm) REVERT: D 79 LYS cc_start: 0.8487 (tptt) cc_final: 0.7867 (tptt) REVERT: D 82 GLU cc_start: 0.7695 (pp20) cc_final: 0.7123 (pp20) REVERT: D 114 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7731 (mm-40) REVERT: D 121 GLU cc_start: 0.7333 (tp30) cc_final: 0.7091 (tt0) REVERT: D 123 GLN cc_start: 0.8436 (mp10) cc_final: 0.8201 (mp10) REVERT: D 124 ARG cc_start: 0.8032 (tpt170) cc_final: 0.7425 (tpt90) REVERT: D 133 HIS cc_start: 0.7351 (m-70) cc_final: 0.7110 (m-70) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1542 time to fit residues: 85.5089 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 : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.0870 chunk 124 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 141 optimal weight: 0.3980 chunk 112 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 GLN B 133 HIS D 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.156723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.128050 restraints weight = 27453.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132943 restraints weight = 18430.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.136636 restraints weight = 13356.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.139468 restraints weight = 10175.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.141586 restraints weight = 8009.484| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.7044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12590 Z= 0.124 Angle : 0.722 18.320 16980 Z= 0.348 Chirality : 0.046 0.235 1912 Planarity : 0.005 0.090 2186 Dihedral : 4.979 23.798 1688 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.21), residues: 1496 helix: -1.79 (0.17), residues: 776 sheet: -2.35 (0.68), residues: 40 loop : -1.17 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 710 TYR 0.045 0.001 TYR C 464 PHE 0.017 0.002 PHE A 466 TRP 0.014 0.002 TRP C 791 HIS 0.003 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00276 (12580) covalent geometry : angle 0.72165 (16980) hydrogen bonds : bond 0.03804 ( 334) hydrogen bonds : angle 6.21790 ( 960) metal coordination : bond 0.00348 ( 10) ********************** 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 412 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.360 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 240 ARG cc_start: 0.8843 (mtt180) cc_final: 0.8419 (mtt180) REVERT: A 241 ARG cc_start: 0.8445 (mmp80) cc_final: 0.8007 (mmp80) REVERT: A 252 ILE cc_start: 0.8024 (tt) cc_final: 0.7822 (pt) REVERT: A 266 ASN cc_start: 0.7080 (t0) cc_final: 0.6841 (m110) REVERT: A 272 THR cc_start: 0.6923 (t) cc_final: 0.6391 (p) REVERT: A 287 PHE cc_start: 0.7458 (m-10) cc_final: 0.7008 (m-10) REVERT: A 324 LEU cc_start: 0.8513 (mt) cc_final: 0.7610 (mt) REVERT: A 328 TRP cc_start: 0.8331 (m-10) cc_final: 0.7893 (m-10) REVERT: A 335 GLN cc_start: 0.7774 (mp10) cc_final: 0.7379 (mp10) REVERT: A 336 ILE cc_start: 0.8855 (mm) cc_final: 0.8481 (mt) REVERT: A 337 ARG cc_start: 0.8089 (mmp80) cc_final: 0.7453 (mmm160) REVERT: A 339 MET cc_start: 0.8649 (ptp) cc_final: 0.8412 (ptp) REVERT: A 340 MET cc_start: 0.8356 (ptm) cc_final: 0.7308 (ptm) REVERT: A 373 LYS cc_start: 0.8082 (mttm) cc_final: 0.7658 (mttm) REVERT: A 412 LEU cc_start: 0.8657 (tt) cc_final: 0.8321 (tt) REVERT: A 441 LYS cc_start: 0.8663 (ptmm) cc_final: 0.8233 (ptmm) REVERT: A 449 PHE cc_start: 0.7934 (m-80) cc_final: 0.7523 (m-80) REVERT: A 472 GLU cc_start: 0.8232 (pt0) cc_final: 0.7754 (pp20) REVERT: A 473 ASN cc_start: 0.8849 (m110) cc_final: 0.8217 (m110) REVERT: A 477 PHE cc_start: 0.8300 (m-80) cc_final: 0.7405 (m-80) REVERT: A 478 MET cc_start: 0.8037 (tpp) cc_final: 0.7535 (tpp) REVERT: A 539 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8011 (tpp80) REVERT: A 542 MET cc_start: 0.7611 (mmt) cc_final: 0.7102 (mmt) REVERT: A 543 ILE cc_start: 0.8043 (tp) cc_final: 0.7277 (tp) REVERT: A 547 ASN cc_start: 0.8162 (t0) cc_final: 0.7836 (p0) REVERT: A 556 TYR cc_start: 0.6913 (t80) cc_final: 0.6600 (t80) REVERT: A 558 GLU cc_start: 0.7932 (pt0) cc_final: 0.7617 (pp20) REVERT: A 576 GLN cc_start: 0.8326 (tp40) cc_final: 0.7976 (tm-30) REVERT: A 580 GLU cc_start: 0.8257 (pt0) cc_final: 0.8011 (tp30) REVERT: A 582 ILE cc_start: 0.7931 (mt) cc_final: 0.7680 (mt) REVERT: A 589 MET cc_start: 0.4283 (ttm) cc_final: 0.3179 (ttm) REVERT: A 597 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8717 (mmmt) REVERT: A 611 GLN cc_start: 0.7992 (mp10) cc_final: 0.7603 (mp10) REVERT: A 635 MET cc_start: 0.7912 (mpp) cc_final: 0.7153 (mmp) REVERT: A 639 ARG cc_start: 0.8728 (tpt-90) cc_final: 0.7570 (tpt-90) REVERT: A 642 MET cc_start: 0.7880 (mmp) cc_final: 0.7577 (mmt) REVERT: A 649 ARG cc_start: 0.7842 (ppt170) cc_final: 0.7633 (ttp80) REVERT: A 651 LEU cc_start: 0.8139 (tp) cc_final: 0.7881 (tp) REVERT: A 659 TYR cc_start: 0.7886 (t80) cc_final: 0.7681 (t80) REVERT: A 663 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7843 (ptpp) REVERT: A 694 TYR cc_start: 0.6893 (t80) cc_final: 0.6622 (t80) REVERT: A 710 ARG cc_start: 0.8382 (mmm160) cc_final: 0.8114 (tpp-160) REVERT: A 730 PHE cc_start: 0.8185 (t80) cc_final: 0.7682 (t80) REVERT: A 751 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7544 (tpp-160) REVERT: A 754 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 791 TRP cc_start: 0.6047 (m-90) cc_final: 0.5450 (m-90) REVERT: A 801 GLN cc_start: 0.8035 (mt0) cc_final: 0.7767 (mt0) REVERT: A 807 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7311 (mm-40) REVERT: A 861 ARG cc_start: 0.7209 (ptp-170) cc_final: 0.6716 (mtt-85) REVERT: B 18 LYS cc_start: 0.8286 (mttt) cc_final: 0.7917 (mttt) REVERT: B 52 PHE cc_start: 0.6488 (t80) cc_final: 0.6251 (t80) REVERT: B 58 CYS cc_start: 0.6619 (t) cc_final: 0.6068 (t) REVERT: B 59 ILE cc_start: 0.6823 (mm) cc_final: 0.6273 (mm) REVERT: B 83 TYR cc_start: 0.7207 (m-10) cc_final: 0.6805 (m-80) REVERT: B 114 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7655 (mm-40) REVERT: B 121 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7351 (tp30) REVERT: B 123 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8069 (mp10) REVERT: B 124 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7343 (mmm160) REVERT: B 133 HIS cc_start: 0.7424 (m-70) cc_final: 0.7165 (m90) REVERT: C 138 GLU cc_start: 0.7772 (tp30) cc_final: 0.7118 (tp30) REVERT: C 241 ARG cc_start: 0.8310 (mmp80) cc_final: 0.7608 (mmp80) REVERT: C 284 LEU cc_start: 0.7951 (pp) cc_final: 0.7623 (pp) REVERT: C 287 PHE cc_start: 0.7770 (m-10) cc_final: 0.7347 (m-10) REVERT: C 313 MET cc_start: 0.7491 (mmm) cc_final: 0.7181 (mmm) REVERT: C 321 GLN cc_start: 0.8465 (mp10) cc_final: 0.8235 (mp10) REVERT: C 344 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7848 (tp-100) REVERT: C 345 GLN cc_start: 0.7477 (mt0) cc_final: 0.6792 (mt0) REVERT: C 373 LYS cc_start: 0.7858 (ttmm) cc_final: 0.7263 (tptp) REVERT: C 389 ASP cc_start: 0.7372 (t70) cc_final: 0.7031 (t70) REVERT: C 395 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6817 (tm-30) REVERT: C 398 GLU cc_start: 0.7958 (mp0) cc_final: 0.7725 (mp0) REVERT: C 406 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7051 (tm-30) REVERT: C 407 LEU cc_start: 0.8532 (mt) cc_final: 0.8143 (mt) REVERT: C 411 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8207 (tt0) REVERT: C 441 LYS cc_start: 0.8489 (mptt) cc_final: 0.8110 (mptt) REVERT: C 449 PHE cc_start: 0.7765 (m-80) cc_final: 0.7492 (m-80) REVERT: C 472 GLU cc_start: 0.8141 (pm20) cc_final: 0.7831 (pm20) REVERT: C 478 MET cc_start: 0.7663 (tpp) cc_final: 0.7297 (tpp) REVERT: C 491 LEU cc_start: 0.8623 (mt) cc_final: 0.8028 (mt) REVERT: C 494 TYR cc_start: 0.7692 (t80) cc_final: 0.7473 (t80) REVERT: C 531 HIS cc_start: 0.8304 (m90) cc_final: 0.8004 (m90) REVERT: C 542 MET cc_start: 0.7370 (mmt) cc_final: 0.6961 (mmt) REVERT: C 554 GLN cc_start: 0.7889 (tt0) cc_final: 0.7391 (tt0) REVERT: C 580 GLU cc_start: 0.8672 (tp30) cc_final: 0.8220 (tp30) REVERT: C 589 MET cc_start: 0.4466 (ttm) cc_final: 0.4132 (ttm) REVERT: C 592 TYR cc_start: 0.7303 (t80) cc_final: 0.6461 (t80) REVERT: C 597 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8642 (mmmm) REVERT: C 607 GLU cc_start: 0.8309 (pm20) cc_final: 0.7884 (pm20) REVERT: C 627 CYS cc_start: 0.7034 (p) cc_final: 0.6732 (p) REVERT: C 629 LEU cc_start: 0.7654 (mp) cc_final: 0.7396 (mt) REVERT: C 635 MET cc_start: 0.8010 (mpp) cc_final: 0.7265 (mpp) REVERT: C 639 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7662 (mmm-85) REVERT: C 640 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8034 (mtmt) REVERT: C 642 MET cc_start: 0.7826 (mmp) cc_final: 0.7505 (mmt) REVERT: C 648 PHE cc_start: 0.7827 (t80) cc_final: 0.7601 (t80) REVERT: C 651 LEU cc_start: 0.8445 (tp) cc_final: 0.8071 (tp) REVERT: C 659 TYR cc_start: 0.8177 (t80) cc_final: 0.7797 (t80) REVERT: C 684 GLN cc_start: 0.7710 (tp40) cc_final: 0.6014 (tm-30) REVERT: C 692 MET cc_start: 0.7373 (ppp) cc_final: 0.7027 (ppp) REVERT: C 693 MET cc_start: 0.7830 (tpt) cc_final: 0.7447 (tpt) REVERT: C 694 TYR cc_start: 0.7046 (t80) cc_final: 0.5960 (t80) REVERT: C 720 TYR cc_start: 0.7603 (t80) cc_final: 0.7115 (t80) REVERT: C 739 MET cc_start: 0.8183 (ttm) cc_final: 0.7918 (ttm) REVERT: C 742 ASN cc_start: 0.8545 (p0) cc_final: 0.7969 (p0) REVERT: C 744 SER cc_start: 0.8165 (t) cc_final: 0.7740 (p) REVERT: C 751 ARG cc_start: 0.8023 (mmm160) cc_final: 0.6925 (tpp-160) REVERT: C 754 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 801 GLN cc_start: 0.8059 (mt0) cc_final: 0.7721 (mt0) REVERT: C 807 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7595 (mm-40) REVERT: D 25 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7252 (mt-10) REVERT: D 36 GLU cc_start: 0.7428 (mp0) cc_final: 0.7092 (pm20) REVERT: D 58 CYS cc_start: 0.6743 (t) cc_final: 0.6117 (t) REVERT: D 59 ILE cc_start: 0.6998 (mm) cc_final: 0.6651 (mm) REVERT: D 79 LYS cc_start: 0.8423 (tptt) cc_final: 0.7820 (tptt) REVERT: D 82 GLU cc_start: 0.7661 (pp20) cc_final: 0.7032 (pp20) REVERT: D 114 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7715 (mm-40) REVERT: D 123 GLN cc_start: 0.8416 (mp10) cc_final: 0.8215 (mp10) REVERT: D 124 ARG cc_start: 0.8089 (tpt170) cc_final: 0.7440 (tpt170) REVERT: D 133 HIS cc_start: 0.7224 (m-70) cc_final: 0.6955 (m90) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1468 time to fit residues: 80.9403 Evaluate side-chains 370 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 102 optimal weight: 0.3980 chunk 143 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 632 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.153374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.125102 restraints weight = 27513.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.129877 restraints weight = 18351.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133465 restraints weight = 13311.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.136237 restraints weight = 10145.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.138411 restraints weight = 8007.462| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12590 Z= 0.155 Angle : 0.730 19.202 16980 Z= 0.358 Chirality : 0.046 0.242 1912 Planarity : 0.005 0.083 2186 Dihedral : 5.065 20.659 1688 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.21), residues: 1496 helix: -1.80 (0.17), residues: 778 sheet: -2.35 (0.69), residues: 40 loop : -1.23 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 710 TYR 0.035 0.001 TYR A 464 PHE 0.027 0.002 PHE A 633 TRP 0.011 0.001 TRP C 328 HIS 0.004 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00328 (12580) covalent geometry : angle 0.73009 (16980) hydrogen bonds : bond 0.03973 ( 334) hydrogen bonds : angle 6.34551 ( 960) metal coordination : bond 0.00556 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.48 seconds wall clock time: 42 minutes 15.67 seconds (2535.67 seconds total)