Starting phenix.real_space_refine on Wed Jul 30 14:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrr_36603/07_2025/8jrr_36603.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrr_36603/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jrr_36603/07_2025/8jrr_36603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrr_36603/07_2025/8jrr_36603.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrr_36603/07_2025/8jrr_36603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrr_36603/07_2025/8jrr_36603.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 70 5.16 5 C 7868 2.51 5 N 2108 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5087 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 27, 'TRANS': 617} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1096 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5263 SG CYS B 37 62.978 32.443 94.524 1.00178.25 S ATOM 5537 SG CYS B 70 60.683 35.235 93.633 1.00162.28 S ATOM 5560 SG CYS B 73 63.463 37.412 93.236 1.00146.37 S ATOM 5901 SG CYS B 113 59.383 34.814 78.871 1.00162.87 S ATOM 6163 SG CYS B 143 58.033 35.303 75.513 1.00192.52 S Restraints were copied for chains: D, C Time building chain proxies: 10.91, per 1000 atoms: 0.88 Number of scatterers: 12370 At special positions: 0 Unit cell: (138.159, 108.171, 111.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 70 16.00 O 2320 8.00 N 2108 7.00 C 7868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 73 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 73 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 10 sheets defined 50.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 146 through 152 removed outlier: 3.609A pdb=" N ILE A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.693A pdb=" N SER A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.246A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.254A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Proline residue: A 265 - end of helix removed outlier: 3.575A pdb=" N GLU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.974A pdb=" N ARG A 279 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 removed outlier: 3.568A pdb=" N LEU A 286 " --> pdb=" O TYR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.357A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.586A pdb=" N GLU A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix removed outlier: 3.624A pdb=" N LYS A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 removed outlier: 5.070A pdb=" N LEU A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 4.059A pdb=" N GLU A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.928A pdb=" N ILE A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.795A pdb=" N CYS A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.760A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.216A pdb=" N VAL A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 506 removed outlier: 5.158A pdb=" N LEU A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 4.351A pdb=" N SER A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 3.757A pdb=" N ASP A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.588A pdb=" N GLU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 611 through 623 removed outlier: 3.980A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 4.034A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 655 through 668 removed outlier: 3.895A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.888A pdb=" N PHE A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 742 removed outlier: 3.764A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 766 through 771 removed outlier: 4.333A pdb=" N LEU A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 766 through 771' Processing helix chain 'A' and resid 786 through 795 removed outlier: 3.914A pdb=" N TRP A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU A 792 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 removed outlier: 3.596A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 863 " --> pdb=" O LYS A 859 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 4.501A pdb=" N THR B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.566A pdb=" N TYR B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.651A pdb=" N SER B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 4.434A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 96' Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.749A pdb=" N LEU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.609A pdb=" N ILE C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.693A pdb=" N SER C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 246 removed outlier: 4.246A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 4.254A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 270 Proline residue: C 265 - end of helix removed outlier: 3.575A pdb=" N GLU C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.974A pdb=" N ARG C 279 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 286 removed outlier: 3.568A pdb=" N LEU C 286 " --> pdb=" O TYR C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.357A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 315 removed outlier: 3.586A pdb=" N GLU C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.624A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 5.070A pdb=" N LEU C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 4.059A pdb=" N GLU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.928A pdb=" N ILE C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 349 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.795A pdb=" N CYS C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 381 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.760A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 removed outlier: 4.216A pdb=" N VAL C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 506 removed outlier: 5.158A pdb=" N LEU C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 492 " --> pdb=" O THR C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 removed outlier: 4.351A pdb=" N SER C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 removed outlier: 3.757A pdb=" N ASP C 535 " --> pdb=" O HIS C 531 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 540 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 removed outlier: 3.588A pdb=" N GLU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 610 Processing helix chain 'C' and resid 611 through 623 removed outlier: 3.980A pdb=" N ILE C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 617 " --> pdb=" O THR C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 4.034A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 655 through 668 removed outlier: 3.895A pdb=" N SER C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 3.888A pdb=" N PHE C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 717 " --> pdb=" O PHE C 713 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 742 removed outlier: 3.764A pdb=" N GLY C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 766 through 771 removed outlier: 4.333A pdb=" N LEU C 770 " --> pdb=" O ASP C 766 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 771 " --> pdb=" O PHE C 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 766 through 771' Processing helix chain 'C' and resid 786 through 795 removed outlier: 3.914A pdb=" N TRP C 791 " --> pdb=" O ILE C 787 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C 792 " --> pdb=" O ARG C 788 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 868 removed outlier: 3.596A pdb=" N LEU C 858 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 861 " --> pdb=" O LYS C 857 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU C 863 " --> pdb=" O LYS C 859 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 865 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 removed outlier: 4.501A pdb=" N THR D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.566A pdb=" N TYR D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 51' Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.651A pdb=" N SER D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 4.434A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.749A pdb=" N LEU D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 526 removed outlier: 5.513A pdb=" N LEU A 523 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A 558 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU A 525 " --> pdb=" O GLU A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 590 through 593 removed outlier: 4.044A pdb=" N TRP A 600 " --> pdb=" O THR A 591 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 682 through 684 removed outlier: 3.834A pdb=" N ILE A 682 " --> pdb=" O TYR A 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 694 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 91 removed outlier: 7.279A pdb=" N ASN B 134 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B 89 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE B 132 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 135 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 523 through 526 removed outlier: 5.513A pdb=" N LEU C 523 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C 558 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 525 " --> pdb=" O GLU C 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 590 through 593 removed outlier: 4.044A pdb=" N TRP C 600 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 682 through 684 removed outlier: 3.834A pdb=" N ILE C 682 " --> pdb=" O TYR C 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR C 694 " --> pdb=" O ILE C 682 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 91 removed outlier: 7.279A pdb=" N ASN D 134 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER D 89 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE D 132 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 135 " --> pdb=" O ARG D 138 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 3.35 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.850 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- 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 : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 1.66 % Allowed : 16.64 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.20), residues: 1496 helix: -4.04 (0.13), residues: 594 sheet: -1.99 (1.12), residues: 16 loop : -2.03 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 791 HIS 0.011 0.002 HIS A 655 PHE 0.027 0.004 PHE C 633 TYR 0.024 0.003 TYR C 592 ARG 0.009 0.001 ARG A 649 Details of bonding type rmsd hydrogen bonds : bond 0.33405 ( 334) hydrogen bonds : angle 11.53968 ( 960) metal coordination : bond 0.35722 ( 10) covalent geometry : bond 0.00833 (12580) covalent geometry : angle 1.08160 (16980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 453 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7993 (mmp80) REVERT: A 287 PHE cc_start: 0.7461 (m-80) cc_final: 0.6954 (m-80) REVERT: A 313 MET cc_start: 0.7854 (tpp) cc_final: 0.7621 (tpp) REVERT: A 323 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8225 (mmtm) REVERT: A 328 TRP cc_start: 0.8479 (m-10) cc_final: 0.8012 (m-10) REVERT: A 339 MET cc_start: 0.8832 (ptp) cc_final: 0.8141 (ptp) REVERT: A 340 MET cc_start: 0.7518 (ptm) cc_final: 0.7150 (ptt) REVERT: A 345 GLN cc_start: 0.7717 (mt0) cc_final: 0.7082 (mt0) REVERT: A 354 ASN cc_start: 0.8127 (m-40) cc_final: 0.7868 (p0) REVERT: A 373 LYS cc_start: 0.8605 (tttp) cc_final: 0.8110 (mmmm) REVERT: A 397 ASP cc_start: 0.7125 (m-30) cc_final: 0.6845 (m-30) REVERT: A 403 GLU cc_start: 0.7481 (tp30) cc_final: 0.7213 (tm-30) REVERT: A 454 LEU cc_start: 0.8640 (tp) cc_final: 0.8404 (tt) REVERT: A 472 GLU cc_start: 0.8469 (pt0) cc_final: 0.8205 (pm20) REVERT: A 477 PHE cc_start: 0.8128 (m-80) cc_final: 0.7808 (m-80) REVERT: A 478 MET cc_start: 0.7861 (tpp) cc_final: 0.7486 (tpp) REVERT: A 507 ILE cc_start: 0.7956 (tp) cc_final: 0.7673 (tp) REVERT: A 510 LEU cc_start: 0.8252 (mp) cc_final: 0.7893 (mt) REVERT: A 515 GLN cc_start: 0.7559 (mp10) cc_final: 0.7300 (mp10) REVERT: A 537 LEU cc_start: 0.8320 (tp) cc_final: 0.7957 (tp) REVERT: A 539 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7505 (tpp80) REVERT: A 558 GLU cc_start: 0.8029 (pt0) cc_final: 0.7695 (pm20) REVERT: A 578 VAL cc_start: 0.8078 (t) cc_final: 0.7528 (t) REVERT: A 580 GLU cc_start: 0.7595 (tp30) cc_final: 0.7187 (tp30) REVERT: A 593 ASP cc_start: 0.8209 (t0) cc_final: 0.7873 (t0) REVERT: A 597 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8696 (mtpp) REVERT: A 621 LEU cc_start: 0.8694 (mm) cc_final: 0.8454 (mm) REVERT: A 625 ASN cc_start: 0.6998 (p0) cc_final: 0.6712 (p0) REVERT: A 635 MET cc_start: 0.7679 (mpp) cc_final: 0.7035 (mmp) REVERT: A 639 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7005 (mmm-85) REVERT: A 640 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7947 (mtmt) REVERT: A 649 ARG cc_start: 0.7660 (ppt170) cc_final: 0.7349 (ptt90) REVERT: A 663 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8093 (ptpp) REVERT: A 684 GLN cc_start: 0.7349 (tp40) cc_final: 0.5893 (tm-30) REVERT: A 694 TYR cc_start: 0.6839 (t80) cc_final: 0.6627 (t80) REVERT: A 730 PHE cc_start: 0.7215 (t80) cc_final: 0.6672 (t80) REVERT: A 739 MET cc_start: 0.7858 (ttm) cc_final: 0.7624 (ttm) REVERT: A 754 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 822 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8114 (mmtm) REVERT: B 25 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7754 (mp0) REVERT: B 38 VAL cc_start: 0.7628 (p) cc_final: 0.7228 (m) REVERT: B 58 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7112 (t) REVERT: B 59 ILE cc_start: 0.7017 (mm) cc_final: 0.5625 (mm) REVERT: B 107 LEU cc_start: 0.8132 (tp) cc_final: 0.7919 (mm) REVERT: B 121 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6576 (mm-30) REVERT: B 122 LYS cc_start: 0.7817 (mttp) cc_final: 0.7520 (mttp) REVERT: B 124 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6296 (mmm160) REVERT: C 146 TYR cc_start: 0.7902 (p90) cc_final: 0.6944 (p90) REVERT: C 235 ASP cc_start: 0.7024 (m-30) cc_final: 0.6819 (m-30) REVERT: C 241 ARG cc_start: 0.8400 (mmp80) cc_final: 0.7981 (mmp80) REVERT: C 287 PHE cc_start: 0.7626 (m-80) cc_final: 0.7086 (m-80) REVERT: C 323 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8294 (mmtm) REVERT: C 324 LEU cc_start: 0.8693 (mt) cc_final: 0.8318 (mt) REVERT: C 328 TRP cc_start: 0.8504 (m-10) cc_final: 0.8135 (m-10) REVERT: C 335 GLN cc_start: 0.8328 (mm110) cc_final: 0.8072 (mm110) REVERT: C 336 ILE cc_start: 0.8683 (mt) cc_final: 0.8201 (mt) REVERT: C 340 MET cc_start: 0.7315 (ptm) cc_final: 0.7002 (ptt) REVERT: C 345 GLN cc_start: 0.7773 (mt0) cc_final: 0.7166 (mt0) REVERT: C 394 GLU cc_start: 0.7176 (tt0) cc_final: 0.5602 (tt0) REVERT: C 397 ASP cc_start: 0.7808 (m-30) cc_final: 0.7602 (m-30) REVERT: C 450 ILE cc_start: 0.8325 (mt) cc_final: 0.8046 (mt) REVERT: C 478 MET cc_start: 0.7851 (tpp) cc_final: 0.7407 (tpp) REVERT: C 507 ILE cc_start: 0.8079 (tp) cc_final: 0.7831 (tp) REVERT: C 511 TYR cc_start: 0.7259 (m-80) cc_final: 0.7013 (m-80) REVERT: C 531 HIS cc_start: 0.7443 (m90) cc_final: 0.7093 (m90) REVERT: C 537 LEU cc_start: 0.8393 (tp) cc_final: 0.8058 (tp) REVERT: C 539 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7605 (tpp80) REVERT: C 545 MET cc_start: 0.7485 (ptt) cc_final: 0.7281 (ptt) REVERT: C 558 GLU cc_start: 0.8015 (pt0) cc_final: 0.7723 (pm20) REVERT: C 580 GLU cc_start: 0.7685 (tp30) cc_final: 0.7032 (tp30) REVERT: C 597 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8726 (mtpp) REVERT: C 639 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7096 (mmm-85) REVERT: C 648 PHE cc_start: 0.7629 (t80) cc_final: 0.7299 (t80) REVERT: C 649 ARG cc_start: 0.7374 (ppt170) cc_final: 0.6910 (tmm160) REVERT: C 651 LEU cc_start: 0.8484 (tp) cc_final: 0.8275 (tp) REVERT: C 663 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8362 (ptpp) REVERT: C 684 GLN cc_start: 0.7845 (tp40) cc_final: 0.7079 (tm-30) REVERT: C 712 GLU cc_start: 0.8486 (tt0) cc_final: 0.7343 (tp30) REVERT: C 731 LYS cc_start: 0.7706 (tptt) cc_final: 0.7407 (tptt) REVERT: C 734 ARG cc_start: 0.6790 (ttt180) cc_final: 0.6283 (ttt90) REVERT: C 739 MET cc_start: 0.7974 (ttm) cc_final: 0.7646 (ttm) REVERT: C 751 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7139 (tpt170) REVERT: C 801 GLN cc_start: 0.7911 (mt0) cc_final: 0.7702 (mt0) REVERT: C 822 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7971 (tptp) REVERT: D 38 VAL cc_start: 0.7675 (p) cc_final: 0.7293 (m) REVERT: D 55 ARG cc_start: 0.8223 (mpt-90) cc_final: 0.7937 (mmt-90) REVERT: D 58 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7482 (t) REVERT: D 121 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 122 LYS cc_start: 0.7846 (mttp) cc_final: 0.7534 (mttp) REVERT: D 124 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6351 (tpt90) outliers start: 22 outliers final: 10 residues processed: 465 average time/residue: 0.3313 time to fit residues: 202.8125 Evaluate side-chains 405 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 393 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 0.0170 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 515 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS ** B 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 114 GLN C 517 GLN C 681 GLN C 738 HIS D 85 HIS D 98 GLN D 114 GLN D 125 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.154862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.125853 restraints weight = 28570.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.130847 restraints weight = 19106.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.134594 restraints weight = 13834.499| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12590 Z= 0.161 Angle : 0.723 11.862 16980 Z= 0.375 Chirality : 0.046 0.226 1912 Planarity : 0.006 0.058 2186 Dihedral : 6.634 23.712 1688 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.30 % Allowed : 5.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.21), residues: 1496 helix: -3.19 (0.16), residues: 636 sheet: -2.19 (0.82), residues: 40 loop : -1.56 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 328 HIS 0.005 0.001 HIS C 531 PHE 0.031 0.002 PHE A 343 TYR 0.027 0.002 TYR C 464 ARG 0.007 0.001 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 334) hydrogen bonds : angle 7.60028 ( 960) metal coordination : bond 0.00677 ( 10) covalent geometry : bond 0.00346 (12580) covalent geometry : angle 0.72287 (16980) *********************** 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 438 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 434 time to evaluate : 1.449 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 138 GLU cc_start: 0.8066 (tp30) cc_final: 0.7537 (tp30) REVERT: A 241 ARG cc_start: 0.8623 (mmp80) cc_final: 0.8046 (mmp80) REVERT: A 245 ARG cc_start: 0.6991 (mtt90) cc_final: 0.6701 (mtt-85) REVERT: A 282 ASN cc_start: 0.7915 (t0) cc_final: 0.7620 (t0) REVERT: A 313 MET cc_start: 0.7440 (tpp) cc_final: 0.6794 (tpp) REVERT: A 323 LYS cc_start: 0.8413 (mmmt) cc_final: 0.7665 (tptt) REVERT: A 324 LEU cc_start: 0.8544 (mt) cc_final: 0.8102 (mt) REVERT: A 328 TRP cc_start: 0.8545 (m-10) cc_final: 0.8283 (m-10) REVERT: A 336 ILE cc_start: 0.9042 (mt) cc_final: 0.8487 (mt) REVERT: A 339 MET cc_start: 0.8972 (ptp) cc_final: 0.8527 (ptp) REVERT: A 344 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7857 (tp-100) REVERT: A 354 ASN cc_start: 0.8300 (m-40) cc_final: 0.7894 (p0) REVERT: A 394 GLU cc_start: 0.7678 (tt0) cc_final: 0.7354 (tm-30) REVERT: A 410 GLN cc_start: 0.8640 (pt0) cc_final: 0.8301 (pt0) REVERT: A 424 ARG cc_start: 0.7819 (ttt-90) cc_final: 0.7556 (tpt-90) REVERT: A 472 GLU cc_start: 0.8421 (pt0) cc_final: 0.8177 (pp20) REVERT: A 477 PHE cc_start: 0.8354 (m-80) cc_final: 0.7618 (m-80) REVERT: A 478 MET cc_start: 0.8137 (tpp) cc_final: 0.7681 (tpp) REVERT: A 482 PHE cc_start: 0.7544 (p90) cc_final: 0.7091 (p90) REVERT: A 491 LEU cc_start: 0.8539 (tp) cc_final: 0.8319 (tp) REVERT: A 507 ILE cc_start: 0.8503 (tp) cc_final: 0.8283 (tp) REVERT: A 510 LEU cc_start: 0.8561 (mp) cc_final: 0.8124 (mm) REVERT: A 531 HIS cc_start: 0.8071 (m90) cc_final: 0.7797 (m90) REVERT: A 533 ILE cc_start: 0.8707 (mp) cc_final: 0.8375 (tp) REVERT: A 539 ARG cc_start: 0.8705 (tpp80) cc_final: 0.7811 (tpp80) REVERT: A 542 MET cc_start: 0.7887 (mmp) cc_final: 0.7434 (mmp) REVERT: A 558 GLU cc_start: 0.8198 (pt0) cc_final: 0.7689 (pm20) REVERT: A 576 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 580 GLU cc_start: 0.8303 (tp30) cc_final: 0.8070 (mm-30) REVERT: A 597 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8855 (mtpp) REVERT: A 635 MET cc_start: 0.7960 (mpp) cc_final: 0.7002 (mpp) REVERT: A 639 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7345 (mmm-85) REVERT: A 640 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7762 (mtmt) REVERT: A 648 PHE cc_start: 0.7632 (t80) cc_final: 0.7333 (t80) REVERT: A 651 LEU cc_start: 0.8084 (tp) cc_final: 0.7858 (tp) REVERT: A 663 LYS cc_start: 0.8448 (ptmm) cc_final: 0.7988 (ptpp) REVERT: A 684 GLN cc_start: 0.6945 (tp40) cc_final: 0.6228 (tm-30) REVERT: A 694 TYR cc_start: 0.6973 (t80) cc_final: 0.6609 (t80) REVERT: A 730 PHE cc_start: 0.7751 (t80) cc_final: 0.7290 (t80) REVERT: A 739 MET cc_start: 0.8333 (ttm) cc_final: 0.8045 (ttm) REVERT: A 742 ASN cc_start: 0.8543 (p0) cc_final: 0.8251 (p0) REVERT: A 754 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8486 (mt-10) REVERT: A 801 GLN cc_start: 0.8131 (mt0) cc_final: 0.7892 (mt0) REVERT: A 822 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8091 (mmtm) REVERT: B 47 ARG cc_start: 0.6141 (tmt-80) cc_final: 0.5929 (tmt-80) REVERT: B 55 ARG cc_start: 0.8137 (mpt-90) cc_final: 0.7810 (mmt-90) REVERT: B 74 LEU cc_start: 0.8396 (tp) cc_final: 0.8193 (tp) REVERT: B 79 LYS cc_start: 0.8614 (tptt) cc_final: 0.8163 (tptt) REVERT: B 81 SER cc_start: 0.8523 (p) cc_final: 0.8319 (t) REVERT: B 82 GLU cc_start: 0.7608 (pp20) cc_final: 0.7097 (pp20) REVERT: B 121 GLU cc_start: 0.7812 (mm-30) cc_final: 0.6894 (tp30) REVERT: B 124 ARG cc_start: 0.7906 (tpt170) cc_final: 0.6868 (mmm160) REVERT: B 131 ARG cc_start: 0.5495 (mtm180) cc_final: 0.5053 (mtm-85) REVERT: B 133 HIS cc_start: 0.7339 (m-70) cc_final: 0.6899 (m-70) REVERT: C 146 TYR cc_start: 0.8061 (p90) cc_final: 0.7814 (p90) REVERT: C 240 ARG cc_start: 0.9000 (mtt180) cc_final: 0.8697 (mtt180) REVERT: C 241 ARG cc_start: 0.8514 (mmp80) cc_final: 0.8182 (mmp80) REVERT: C 287 PHE cc_start: 0.7400 (m-80) cc_final: 0.6799 (m-80) REVERT: C 290 VAL cc_start: 0.7430 (m) cc_final: 0.6997 (t) REVERT: C 323 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7715 (tptt) REVERT: C 328 TRP cc_start: 0.8612 (m-10) cc_final: 0.8351 (m-10) REVERT: C 335 GLN cc_start: 0.8020 (mm110) cc_final: 0.7433 (mm110) REVERT: C 336 ILE cc_start: 0.8835 (mt) cc_final: 0.8312 (mt) REVERT: C 345 GLN cc_start: 0.7573 (mt0) cc_final: 0.6803 (mt0) REVERT: C 373 LYS cc_start: 0.8545 (tttp) cc_final: 0.7964 (tptp) REVERT: C 395 GLU cc_start: 0.7680 (pm20) cc_final: 0.7423 (pp20) REVERT: C 411 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7938 (tp30) REVERT: C 429 GLU cc_start: 0.8166 (mp0) cc_final: 0.7618 (pm20) REVERT: C 446 PHE cc_start: 0.8714 (m-80) cc_final: 0.8462 (m-10) REVERT: C 449 PHE cc_start: 0.8085 (m-80) cc_final: 0.7633 (m-80) REVERT: C 454 LEU cc_start: 0.8741 (tt) cc_final: 0.8514 (tp) REVERT: C 472 GLU cc_start: 0.8155 (pm20) cc_final: 0.7938 (pm20) REVERT: C 478 MET cc_start: 0.8104 (tpp) cc_final: 0.7701 (tpp) REVERT: C 491 LEU cc_start: 0.8615 (tp) cc_final: 0.8409 (tp) REVERT: C 511 TYR cc_start: 0.8098 (m-80) cc_final: 0.7668 (m-80) REVERT: C 533 ILE cc_start: 0.8411 (tp) cc_final: 0.8162 (tp) REVERT: C 539 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8049 (tpt-90) REVERT: C 542 MET cc_start: 0.7971 (mmp) cc_final: 0.7578 (mmp) REVERT: C 545 MET cc_start: 0.7896 (ptt) cc_final: 0.7692 (ptt) REVERT: C 576 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7458 (tp40) REVERT: C 580 GLU cc_start: 0.8428 (tp30) cc_final: 0.8082 (mm-30) REVERT: C 589 MET cc_start: 0.5983 (mtt) cc_final: 0.5761 (mtt) REVERT: C 594 GLU cc_start: 0.8162 (pm20) cc_final: 0.7757 (pm20) REVERT: C 597 LYS cc_start: 0.9163 (mtpp) cc_final: 0.8945 (mtpp) REVERT: C 631 VAL cc_start: 0.8460 (t) cc_final: 0.8215 (p) REVERT: C 635 MET cc_start: 0.8048 (mpp) cc_final: 0.7133 (mpp) REVERT: C 639 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.7377 (mmm-85) REVERT: C 640 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8027 (mtmt) REVERT: C 648 PHE cc_start: 0.7699 (t80) cc_final: 0.7335 (t80) REVERT: C 651 LEU cc_start: 0.8226 (tp) cc_final: 0.7981 (tp) REVERT: C 663 LYS cc_start: 0.8722 (ptmm) cc_final: 0.8173 (ptpp) REVERT: C 684 GLN cc_start: 0.7915 (tp40) cc_final: 0.7223 (tm-30) REVERT: C 694 TYR cc_start: 0.7777 (t80) cc_final: 0.7488 (t80) REVERT: C 739 MET cc_start: 0.8413 (ttm) cc_final: 0.8070 (ttm) REVERT: C 742 ASN cc_start: 0.8536 (p0) cc_final: 0.8269 (p0) REVERT: C 751 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7889 (tpp-160) REVERT: C 754 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8246 (mt-10) REVERT: C 784 SER cc_start: 0.7490 (t) cc_final: 0.6862 (m) REVERT: C 801 GLN cc_start: 0.7997 (mt0) cc_final: 0.7643 (mt0) REVERT: C 822 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7836 (tptp) REVERT: C 861 ARG cc_start: 0.6991 (ttp-110) cc_final: 0.6363 (mtp85) REVERT: D 47 ARG cc_start: 0.6163 (tmt-80) cc_final: 0.5892 (tpt170) REVERT: D 55 ARG cc_start: 0.8092 (mpt-90) cc_final: 0.7752 (mmt-90) REVERT: D 58 CYS cc_start: 0.6709 (t) cc_final: 0.5719 (t) REVERT: D 59 ILE cc_start: 0.6323 (mm) cc_final: 0.4697 (mm) REVERT: D 79 LYS cc_start: 0.8620 (tptt) cc_final: 0.8084 (tptt) REVERT: D 82 GLU cc_start: 0.7672 (pp20) cc_final: 0.7096 (pp20) REVERT: D 121 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6865 (mm-30) REVERT: D 124 ARG cc_start: 0.7803 (tpt170) cc_final: 0.6875 (mmm160) REVERT: D 133 HIS cc_start: 0.7179 (m-70) cc_final: 0.6740 (m-70) outliers start: 4 outliers final: 1 residues processed: 437 average time/residue: 0.3438 time to fit residues: 199.1614 Evaluate side-chains 392 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 611 GLN C 497 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.155411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.125245 restraints weight = 28979.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.130012 restraints weight = 19862.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.133840 restraints weight = 14754.260| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4201 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= 0.147 Angle : 0.652 12.527 16980 Z= 0.335 Chirality : 0.045 0.187 1912 Planarity : 0.005 0.054 2186 Dihedral : 5.831 22.888 1688 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.08 % Allowed : 5.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.21), residues: 1496 helix: -2.75 (0.16), residues: 664 sheet: -0.80 (1.11), residues: 16 loop : -1.47 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 791 HIS 0.004 0.000 HIS B 85 PHE 0.024 0.002 PHE A 633 TYR 0.030 0.001 TYR C 464 ARG 0.010 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 334) hydrogen bonds : angle 6.93653 ( 960) metal coordination : bond 0.00332 ( 10) covalent geometry : bond 0.00297 (12580) covalent geometry : angle 0.65221 (16980) *********************** 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 432 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 1.406 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: 0.7961 (p0) cc_final: 0.7625 (m-30) REVERT: A 241 ARG cc_start: 0.8593 (mmp80) cc_final: 0.8175 (mmp80) REVERT: A 245 ARG cc_start: 0.7014 (mtt90) cc_final: 0.6801 (mtt-85) REVERT: A 282 ASN cc_start: 0.7849 (t0) cc_final: 0.7451 (t0) REVERT: A 287 PHE cc_start: 0.7322 (m-80) cc_final: 0.6805 (m-80) REVERT: A 290 VAL cc_start: 0.7287 (m) cc_final: 0.6709 (t) REVERT: A 323 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8140 (tttp) REVERT: A 324 LEU cc_start: 0.8744 (mt) cc_final: 0.7831 (mt) REVERT: A 328 TRP cc_start: 0.8510 (m-10) cc_final: 0.8273 (m-10) REVERT: A 335 GLN cc_start: 0.7641 (mp10) cc_final: 0.7120 (mp10) REVERT: A 336 ILE cc_start: 0.8650 (mt) cc_final: 0.8069 (mm) REVERT: A 337 ARG cc_start: 0.7886 (mmp80) cc_final: 0.7006 (mmm160) REVERT: A 340 MET cc_start: 0.7896 (ptm) cc_final: 0.7123 (ptm) REVERT: A 344 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7713 (tp-100) REVERT: A 354 ASN cc_start: 0.8230 (m-40) cc_final: 0.7892 (p0) REVERT: A 410 GLN cc_start: 0.8449 (pt0) cc_final: 0.7986 (pt0) REVERT: A 424 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7267 (ttm-80) REVERT: A 459 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 464 TYR cc_start: 0.7119 (t80) cc_final: 0.6787 (t80) REVERT: A 472 GLU cc_start: 0.8458 (pt0) cc_final: 0.8122 (pp20) REVERT: A 473 ASN cc_start: 0.8811 (m110) cc_final: 0.8432 (m110) REVERT: A 477 PHE cc_start: 0.8354 (m-80) cc_final: 0.7513 (m-80) REVERT: A 478 MET cc_start: 0.8042 (tpp) cc_final: 0.7624 (tpp) REVERT: A 491 LEU cc_start: 0.8588 (tp) cc_final: 0.8380 (tp) REVERT: A 531 HIS cc_start: 0.8091 (m90) cc_final: 0.7841 (m90) REVERT: A 541 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7505 (mm-30) REVERT: A 542 MET cc_start: 0.7898 (mmp) cc_final: 0.7663 (mmt) REVERT: A 558 GLU cc_start: 0.8165 (pt0) cc_final: 0.7950 (pm20) REVERT: A 597 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8915 (mtpp) REVERT: A 611 GLN cc_start: 0.8198 (mp10) cc_final: 0.7944 (mp10) REVERT: A 635 MET cc_start: 0.7980 (mpp) cc_final: 0.7046 (mpp) REVERT: A 639 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7360 (mmm-85) REVERT: A 651 LEU cc_start: 0.8108 (tp) cc_final: 0.7883 (tp) REVERT: A 663 LYS cc_start: 0.8336 (ptmm) cc_final: 0.7679 (ptpp) REVERT: A 694 TYR cc_start: 0.7073 (t80) cc_final: 0.6692 (t80) REVERT: A 711 LYS cc_start: 0.8678 (mptt) cc_final: 0.8461 (mptt) REVERT: A 739 MET cc_start: 0.8386 (ttm) cc_final: 0.8123 (ttm) REVERT: A 742 ASN cc_start: 0.8483 (p0) cc_final: 0.8269 (p0) REVERT: A 751 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7656 (tpp-160) REVERT: A 754 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 822 LYS cc_start: 0.8373 (mmtm) cc_final: 0.8023 (mmtm) REVERT: B 25 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7625 (mp0) REVERT: B 52 PHE cc_start: 0.7174 (t80) cc_final: 0.6950 (t80) REVERT: B 79 LYS cc_start: 0.8626 (tptt) cc_final: 0.8118 (tptt) REVERT: B 82 GLU cc_start: 0.7748 (pp20) cc_final: 0.7074 (pp20) REVERT: B 105 ASP cc_start: 0.7941 (t70) cc_final: 0.7727 (p0) REVERT: B 121 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6737 (tp30) REVERT: B 124 ARG cc_start: 0.7903 (tpt170) cc_final: 0.7017 (mmm160) REVERT: B 131 ARG cc_start: 0.5483 (mtm180) cc_final: 0.5107 (mtt90) REVERT: B 133 HIS cc_start: 0.7211 (m-70) cc_final: 0.6951 (m-70) REVERT: C 240 ARG cc_start: 0.8915 (mtt180) cc_final: 0.7739 (tpp80) REVERT: C 241 ARG cc_start: 0.8423 (mmp80) cc_final: 0.7718 (mmp80) REVERT: C 287 PHE cc_start: 0.7325 (m-80) cc_final: 0.6949 (m-80) REVERT: C 290 VAL cc_start: 0.7256 (m) cc_final: 0.6951 (t) REVERT: C 323 LYS cc_start: 0.8535 (mmmt) cc_final: 0.7976 (mmtt) REVERT: C 324 LEU cc_start: 0.8599 (mt) cc_final: 0.7620 (mt) REVERT: C 328 TRP cc_start: 0.8474 (m-10) cc_final: 0.8274 (m-10) REVERT: C 334 ASP cc_start: 0.7936 (p0) cc_final: 0.6810 (p0) REVERT: C 335 GLN cc_start: 0.8053 (mm110) cc_final: 0.7383 (mm110) REVERT: C 340 MET cc_start: 0.7857 (ptp) cc_final: 0.7484 (ptt) REVERT: C 344 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7513 (tp40) REVERT: C 354 ASN cc_start: 0.8340 (m-40) cc_final: 0.8039 (p0) REVERT: C 373 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7880 (tptp) REVERT: C 398 GLU cc_start: 0.8149 (mp0) cc_final: 0.7026 (mp0) REVERT: C 441 LYS cc_start: 0.8030 (mptt) cc_final: 0.7770 (mmtm) REVERT: C 472 GLU cc_start: 0.8318 (pm20) cc_final: 0.7837 (pm20) REVERT: C 478 MET cc_start: 0.7985 (tpp) cc_final: 0.7392 (tpp) REVERT: C 511 TYR cc_start: 0.8078 (m-80) cc_final: 0.7840 (m-80) REVERT: C 524 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7060 (ttp-110) REVERT: C 537 LEU cc_start: 0.8337 (tp) cc_final: 0.7279 (tp) REVERT: C 539 ARG cc_start: 0.8635 (tpp80) cc_final: 0.7713 (tpp80) REVERT: C 542 MET cc_start: 0.7782 (mmp) cc_final: 0.7572 (mmt) REVERT: C 547 ASN cc_start: 0.7801 (t0) cc_final: 0.7587 (t0) REVERT: C 576 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7483 (tm-30) REVERT: C 580 GLU cc_start: 0.8325 (tp30) cc_final: 0.7907 (mm-30) REVERT: C 593 ASP cc_start: 0.8493 (t0) cc_final: 0.8173 (t0) REVERT: C 594 GLU cc_start: 0.8074 (pm20) cc_final: 0.7729 (pm20) REVERT: C 597 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8988 (mtpp) REVERT: C 625 ASN cc_start: 0.7400 (p0) cc_final: 0.6810 (p0) REVERT: C 635 MET cc_start: 0.8050 (mpp) cc_final: 0.7340 (mpp) REVERT: C 639 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: C 640 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8086 (mtmt) REVERT: C 648 PHE cc_start: 0.7828 (t80) cc_final: 0.7585 (t80) REVERT: C 651 LEU cc_start: 0.8275 (tp) cc_final: 0.8005 (tp) REVERT: C 663 LYS cc_start: 0.8501 (ptmm) cc_final: 0.8086 (ptpp) REVERT: C 684 GLN cc_start: 0.7949 (tp40) cc_final: 0.7205 (tm-30) REVERT: C 739 MET cc_start: 0.8481 (ttm) cc_final: 0.8211 (ttm) REVERT: C 742 ASN cc_start: 0.8497 (p0) cc_final: 0.8280 (p0) REVERT: C 751 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7840 (tpp-160) REVERT: C 754 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8151 (mt-10) REVERT: C 801 GLN cc_start: 0.8017 (mt0) cc_final: 0.7698 (mt0) REVERT: C 822 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7842 (tptp) REVERT: C 861 ARG cc_start: 0.7397 (ptp-110) cc_final: 0.6785 (mtp85) REVERT: D 25 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7488 (mp0) REVERT: D 47 ARG cc_start: 0.6032 (tmt-80) cc_final: 0.5755 (tpt170) REVERT: D 79 LYS cc_start: 0.8638 (tptt) cc_final: 0.8058 (mmmt) REVERT: D 82 GLU cc_start: 0.7737 (pp20) cc_final: 0.7226 (pp20) REVERT: D 101 LYS cc_start: 0.6360 (tptp) cc_final: 0.6155 (tptp) REVERT: D 121 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6950 (mm-30) REVERT: D 124 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7022 (mmm160) REVERT: D 133 HIS cc_start: 0.7287 (m-70) cc_final: 0.6776 (m-70) outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.3370 time to fit residues: 190.6104 Evaluate side-chains 389 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 9 optimal weight: 0.1980 chunk 103 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 124 optimal weight: 0.0060 chunk 115 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.157105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.127167 restraints weight = 28624.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.132107 restraints weight = 19648.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.135816 restraints weight = 14463.007| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4876 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= 0.120 Angle : 0.630 10.935 16980 Z= 0.320 Chirality : 0.043 0.151 1912 Planarity : 0.005 0.051 2186 Dihedral : 5.347 23.195 1688 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1496 helix: -2.37 (0.17), residues: 692 sheet: 0.15 (1.29), residues: 16 loop : -1.41 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 791 HIS 0.004 0.001 HIS B 85 PHE 0.022 0.002 PHE A 343 TYR 0.017 0.001 TYR C 146 ARG 0.010 0.001 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 334) hydrogen bonds : angle 6.34612 ( 960) metal coordination : bond 0.00422 ( 10) covalent geometry : bond 0.00264 (12580) covalent geometry : angle 0.63021 (16980) *********************** 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 404 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.459 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: 0.8690 (mmp80) cc_final: 0.8106 (mmp80) REVERT: A 287 PHE cc_start: 0.7241 (m-80) cc_final: 0.6942 (m-80) REVERT: A 290 VAL cc_start: 0.7163 (m) cc_final: 0.6589 (t) REVERT: A 309 PHE cc_start: 0.7950 (t80) cc_final: 0.7680 (t80) REVERT: A 313 MET cc_start: 0.7249 (tpp) cc_final: 0.6910 (tpp) REVERT: A 323 LYS cc_start: 0.8268 (mmmt) cc_final: 0.7912 (mmtt) REVERT: A 324 LEU cc_start: 0.8570 (mt) cc_final: 0.7597 (mt) REVERT: A 337 ARG cc_start: 0.7888 (mmp80) cc_final: 0.7370 (mmm160) REVERT: A 339 MET cc_start: 0.8920 (ptp) cc_final: 0.8389 (ptp) REVERT: A 340 MET cc_start: 0.7926 (ptm) cc_final: 0.7088 (ptm) REVERT: A 344 GLN cc_start: 0.8308 (tp-100) cc_final: 0.7660 (tp-100) REVERT: A 373 LYS cc_start: 0.8439 (mttm) cc_final: 0.7820 (mttm) REVERT: A 440 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7736 (ttt90) REVERT: A 459 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6994 (tm-30) REVERT: A 460 MET cc_start: 0.6282 (mpp) cc_final: 0.5588 (mpp) REVERT: A 466 PHE cc_start: 0.7815 (m-10) cc_final: 0.7605 (m-80) REVERT: A 472 GLU cc_start: 0.8470 (pt0) cc_final: 0.8159 (pp20) REVERT: A 473 ASN cc_start: 0.8841 (m110) cc_final: 0.8212 (m110) REVERT: A 477 PHE cc_start: 0.8233 (m-80) cc_final: 0.7569 (m-80) REVERT: A 478 MET cc_start: 0.7939 (tpp) cc_final: 0.7536 (tpp) REVERT: A 491 LEU cc_start: 0.8525 (tp) cc_final: 0.8268 (tp) REVERT: A 531 HIS cc_start: 0.8026 (m90) cc_final: 0.7801 (m90) REVERT: A 540 LEU cc_start: 0.8741 (pp) cc_final: 0.8212 (pp) REVERT: A 541 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 580 GLU cc_start: 0.8299 (tp30) cc_final: 0.8029 (mm-30) REVERT: A 597 LYS cc_start: 0.9171 (mtpp) cc_final: 0.8962 (mtpp) REVERT: A 611 GLN cc_start: 0.8221 (mp10) cc_final: 0.7986 (mp10) REVERT: A 635 MET cc_start: 0.7949 (mpp) cc_final: 0.7154 (mpp) REVERT: A 639 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7384 (mmm-85) REVERT: A 640 LYS cc_start: 0.8324 (mttt) cc_final: 0.7850 (mttt) REVERT: A 651 LEU cc_start: 0.8078 (tp) cc_final: 0.7844 (tp) REVERT: A 663 LYS cc_start: 0.8142 (ptmm) cc_final: 0.7703 (ptpp) REVERT: A 694 TYR cc_start: 0.7035 (t80) cc_final: 0.6764 (t80) REVERT: A 710 ARG cc_start: 0.7362 (ptt180) cc_final: 0.7090 (ptt180) REVERT: A 739 MET cc_start: 0.8323 (ttm) cc_final: 0.8104 (ttm) REVERT: A 742 ASN cc_start: 0.8452 (p0) cc_final: 0.7795 (p0) REVERT: A 751 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7556 (tpp-160) REVERT: A 754 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8402 (mt-10) REVERT: A 801 GLN cc_start: 0.8091 (mt0) cc_final: 0.7781 (mt0) REVERT: A 822 LYS cc_start: 0.8356 (mmtm) cc_final: 0.8063 (mmtm) REVERT: B 47 ARG cc_start: 0.6143 (tmt-80) cc_final: 0.5900 (tpt170) REVERT: B 58 CYS cc_start: 0.6426 (t) cc_final: 0.6152 (t) REVERT: B 74 LEU cc_start: 0.8158 (tp) cc_final: 0.7953 (tp) REVERT: B 79 LYS cc_start: 0.8546 (tptt) cc_final: 0.7967 (tptt) REVERT: B 82 GLU cc_start: 0.7853 (pp20) cc_final: 0.7245 (pp20) REVERT: B 114 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7485 (mm-40) REVERT: B 121 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7139 (tp30) REVERT: B 124 ARG cc_start: 0.8071 (tpt170) cc_final: 0.7154 (mmm160) REVERT: B 133 HIS cc_start: 0.7235 (m-70) cc_final: 0.6908 (m-70) REVERT: C 235 ASP cc_start: 0.7927 (p0) cc_final: 0.7712 (m-30) REVERT: C 240 ARG cc_start: 0.8907 (mtt180) cc_final: 0.7951 (tpp-160) REVERT: C 241 ARG cc_start: 0.8372 (mmp80) cc_final: 0.7734 (mmp80) REVERT: C 287 PHE cc_start: 0.7296 (m-80) cc_final: 0.6668 (m-80) REVERT: C 290 VAL cc_start: 0.7031 (m) cc_final: 0.6137 (t) REVERT: C 309 PHE cc_start: 0.7848 (t80) cc_final: 0.7563 (t80) REVERT: C 321 GLN cc_start: 0.8503 (mt0) cc_final: 0.8281 (mm-40) REVERT: C 324 LEU cc_start: 0.8523 (mt) cc_final: 0.7481 (mt) REVERT: C 339 MET cc_start: 0.8794 (ptp) cc_final: 0.8586 (ptt) REVERT: C 340 MET cc_start: 0.7867 (ptp) cc_final: 0.7558 (ptt) REVERT: C 344 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7547 (tp40) REVERT: C 373 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7730 (tptp) REVERT: C 395 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6761 (tm-30) REVERT: C 462 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7327 (mmmm) REVERT: C 472 GLU cc_start: 0.8461 (pm20) cc_final: 0.8113 (pm20) REVERT: C 478 MET cc_start: 0.7987 (tpp) cc_final: 0.7270 (tpp) REVERT: C 511 TYR cc_start: 0.8069 (m-80) cc_final: 0.7869 (m-80) REVERT: C 524 ARG cc_start: 0.7966 (mtt90) cc_final: 0.6565 (ttp-110) REVERT: C 539 ARG cc_start: 0.8493 (tpp80) cc_final: 0.7607 (ttt180) REVERT: C 542 MET cc_start: 0.7760 (mmp) cc_final: 0.7552 (mmt) REVERT: C 576 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7615 (tm-30) REVERT: C 580 GLU cc_start: 0.8320 (tp30) cc_final: 0.7815 (mm-30) REVERT: C 592 TYR cc_start: 0.7735 (t80) cc_final: 0.7320 (t80) REVERT: C 597 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8687 (mmmt) REVERT: C 607 GLU cc_start: 0.8297 (pm20) cc_final: 0.8018 (pm20) REVERT: C 635 MET cc_start: 0.8048 (mpp) cc_final: 0.7391 (mpp) REVERT: C 639 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.7684 (mmm-85) REVERT: C 640 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8045 (mtmt) REVERT: C 651 LEU cc_start: 0.8303 (tp) cc_final: 0.8013 (tp) REVERT: C 663 LYS cc_start: 0.8509 (ptmm) cc_final: 0.8074 (ptpp) REVERT: C 684 GLN cc_start: 0.7842 (tp40) cc_final: 0.7114 (tm-30) REVERT: C 731 LYS cc_start: 0.8308 (tptt) cc_final: 0.8030 (mptt) REVERT: C 739 MET cc_start: 0.8372 (ttm) cc_final: 0.8128 (ttm) REVERT: C 742 ASN cc_start: 0.8423 (p0) cc_final: 0.8167 (p0) REVERT: C 751 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7682 (tpt170) REVERT: C 754 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8091 (mt-10) REVERT: C 801 GLN cc_start: 0.7977 (mt0) cc_final: 0.7665 (mt0) REVERT: C 802 LYS cc_start: 0.7985 (mttp) cc_final: 0.7672 (mptt) REVERT: C 861 ARG cc_start: 0.7181 (ptp-110) cc_final: 0.6875 (ptm160) REVERT: D 25 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7462 (mp0) REVERT: D 47 ARG cc_start: 0.6025 (tmt-80) cc_final: 0.5749 (tpt170) REVERT: D 55 ARG cc_start: 0.8310 (mmt90) cc_final: 0.7961 (mmt90) REVERT: D 79 LYS cc_start: 0.8571 (tptt) cc_final: 0.7997 (tptt) REVERT: D 82 GLU cc_start: 0.7752 (pp20) cc_final: 0.7157 (pp20) REVERT: D 121 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7201 (tp30) REVERT: D 124 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7415 (mmm160) REVERT: D 133 HIS cc_start: 0.7283 (m-70) cc_final: 0.6873 (m-70) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.3355 time to fit residues: 177.9777 Evaluate side-chains 365 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 133 optimal weight: 8.9990 chunk 147 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 0.0570 chunk 11 optimal weight: 0.0980 chunk 115 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 60 optimal weight: 0.2980 chunk 88 optimal weight: 0.0870 chunk 141 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 655 HIS A 660 GLN A 715 ASN C 655 HIS C 660 GLN C 715 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.159781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.129387 restraints weight = 28422.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.134372 restraints weight = 19632.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.138168 restraints weight = 14522.897| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12590 Z= 0.111 Angle : 0.621 13.040 16980 Z= 0.309 Chirality : 0.043 0.155 1912 Planarity : 0.004 0.049 2186 Dihedral : 4.934 24.361 1688 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.21), residues: 1496 helix: -2.08 (0.18), residues: 696 sheet: -1.75 (0.78), residues: 40 loop : -1.30 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 328 HIS 0.004 0.001 HIS B 85 PHE 0.017 0.001 PHE C 343 TYR 0.012 0.001 TYR B 39 ARG 0.006 0.001 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 334) hydrogen bonds : angle 6.02596 ( 960) metal coordination : bond 0.00158 ( 10) covalent geometry : bond 0.00248 (12580) covalent geometry : angle 0.62058 (16980) *********************** 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 413 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.8442 (mmp80) cc_final: 0.8031 (mmp80) REVERT: A 287 PHE cc_start: 0.7306 (m-80) cc_final: 0.6736 (m-80) REVERT: A 290 VAL cc_start: 0.7123 (m) cc_final: 0.6500 (t) REVERT: A 309 PHE cc_start: 0.8102 (t80) cc_final: 0.7876 (t80) REVERT: A 324 LEU cc_start: 0.8469 (mt) cc_final: 0.7565 (mt) REVERT: A 335 GLN cc_start: 0.7471 (mp10) cc_final: 0.7199 (mp10) REVERT: A 337 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7505 (mmm160) REVERT: A 344 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7608 (tp-100) REVERT: A 373 LYS cc_start: 0.8257 (mttm) cc_final: 0.7848 (mttm) REVERT: A 424 ARG cc_start: 0.7666 (tpt-90) cc_final: 0.7144 (tpt-90) REVERT: A 473 ASN cc_start: 0.8763 (m110) cc_final: 0.8514 (p0) REVERT: A 477 PHE cc_start: 0.8317 (m-80) cc_final: 0.7515 (m-80) REVERT: A 478 MET cc_start: 0.7852 (tpp) cc_final: 0.7121 (tpp) REVERT: A 597 LYS cc_start: 0.9195 (mtpp) cc_final: 0.8983 (mtpp) REVERT: A 611 GLN cc_start: 0.8220 (mp10) cc_final: 0.7976 (mp10) REVERT: A 635 MET cc_start: 0.7896 (mpp) cc_final: 0.7205 (mpp) REVERT: A 639 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7463 (mmm-85) REVERT: A 640 LYS cc_start: 0.8145 (mttt) cc_final: 0.7693 (mttt) REVERT: A 651 LEU cc_start: 0.8130 (tp) cc_final: 0.7867 (tp) REVERT: A 663 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7723 (ptpp) REVERT: A 667 GLU cc_start: 0.8682 (mp0) cc_final: 0.8474 (mp0) REVERT: A 692 MET cc_start: 0.6413 (mpp) cc_final: 0.6043 (mpp) REVERT: A 693 MET cc_start: 0.7541 (tpt) cc_final: 0.7316 (tpt) REVERT: A 710 ARG cc_start: 0.7315 (ptt180) cc_final: 0.7035 (ptt180) REVERT: A 730 PHE cc_start: 0.8021 (t80) cc_final: 0.7667 (t80) REVERT: A 739 MET cc_start: 0.8180 (ttm) cc_final: 0.7922 (ttm) REVERT: A 742 ASN cc_start: 0.8309 (p0) cc_final: 0.8066 (p0) REVERT: A 751 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7705 (tpp-160) REVERT: A 754 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 801 GLN cc_start: 0.8068 (mt0) cc_final: 0.7737 (mt0) REVERT: A 807 GLN cc_start: 0.8459 (mt0) cc_final: 0.8255 (mm-40) REVERT: A 822 LYS cc_start: 0.8372 (mmtm) cc_final: 0.8155 (mmtm) REVERT: B 18 LYS cc_start: 0.8252 (mttt) cc_final: 0.7989 (mttt) REVERT: B 58 CYS cc_start: 0.6483 (t) cc_final: 0.6262 (t) REVERT: B 79 LYS cc_start: 0.8514 (tptt) cc_final: 0.7877 (tptt) REVERT: B 82 GLU cc_start: 0.7769 (pp20) cc_final: 0.7111 (pp20) REVERT: B 95 LEU cc_start: 0.8527 (pt) cc_final: 0.8313 (pt) REVERT: B 121 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7054 (tp30) REVERT: B 124 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7437 (mmm160) REVERT: B 133 HIS cc_start: 0.7190 (m-70) cc_final: 0.6912 (m-70) REVERT: C 241 ARG cc_start: 0.8393 (mmp80) cc_final: 0.7914 (mmp80) REVERT: C 242 VAL cc_start: 0.8678 (t) cc_final: 0.8368 (t) REVERT: C 287 PHE cc_start: 0.7315 (m-80) cc_final: 0.6973 (m-80) REVERT: C 323 LYS cc_start: 0.8208 (mttt) cc_final: 0.7917 (mmtt) REVERT: C 324 LEU cc_start: 0.8533 (mt) cc_final: 0.7498 (mt) REVERT: C 336 ILE cc_start: 0.8764 (mt) cc_final: 0.8440 (mt) REVERT: C 340 MET cc_start: 0.7804 (ptp) cc_final: 0.7537 (ptt) REVERT: C 344 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7397 (tp40) REVERT: C 345 GLN cc_start: 0.7511 (mt0) cc_final: 0.6797 (mt0) REVERT: C 373 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7589 (tptp) REVERT: C 376 LYS cc_start: 0.8494 (tttm) cc_final: 0.8252 (tttm) REVERT: C 380 TYR cc_start: 0.8028 (t80) cc_final: 0.7661 (t80) REVERT: C 392 HIS cc_start: 0.7714 (m-70) cc_final: 0.7487 (m-70) REVERT: C 398 GLU cc_start: 0.8008 (mp0) cc_final: 0.7767 (mp0) REVERT: C 406 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7160 (tm-30) REVERT: C 441 LYS cc_start: 0.7771 (mptt) cc_final: 0.7438 (mmtm) REVERT: C 472 GLU cc_start: 0.8381 (pm20) cc_final: 0.8028 (pm20) REVERT: C 478 MET cc_start: 0.7974 (tpp) cc_final: 0.7542 (tpp) REVERT: C 491 LEU cc_start: 0.8723 (mt) cc_final: 0.8391 (mt) REVERT: C 507 ILE cc_start: 0.8531 (tp) cc_final: 0.8248 (tp) REVERT: C 539 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7856 (ttt180) REVERT: C 542 MET cc_start: 0.7710 (mmp) cc_final: 0.7497 (mmt) REVERT: C 554 GLN cc_start: 0.7218 (tt0) cc_final: 0.6903 (tt0) REVERT: C 556 TYR cc_start: 0.6669 (t80) cc_final: 0.6468 (t80) REVERT: C 576 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 580 GLU cc_start: 0.8304 (tp30) cc_final: 0.7896 (mm-30) REVERT: C 594 GLU cc_start: 0.7829 (pm20) cc_final: 0.7621 (pm20) REVERT: C 597 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8872 (mtpp) REVERT: C 607 GLU cc_start: 0.8391 (pm20) cc_final: 0.8098 (pm20) REVERT: C 635 MET cc_start: 0.7961 (mpp) cc_final: 0.7299 (mpp) REVERT: C 640 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8102 (mtmt) REVERT: C 651 LEU cc_start: 0.8332 (tp) cc_final: 0.8023 (tp) REVERT: C 663 LYS cc_start: 0.8518 (ptmm) cc_final: 0.7964 (ptpp) REVERT: C 684 GLN cc_start: 0.7841 (tp40) cc_final: 0.6868 (tm-30) REVERT: C 739 MET cc_start: 0.8300 (ttm) cc_final: 0.8015 (ttm) REVERT: C 742 ASN cc_start: 0.8412 (p0) cc_final: 0.8198 (p0) REVERT: C 751 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7771 (tpp-160) REVERT: C 754 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 801 GLN cc_start: 0.7955 (mt0) cc_final: 0.7650 (mt0) REVERT: C 822 LYS cc_start: 0.8111 (mmmm) cc_final: 0.7883 (tptp) REVERT: C 861 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6716 (ptm160) REVERT: D 25 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7481 (mt-10) REVERT: D 95 LEU cc_start: 0.8442 (pt) cc_final: 0.8196 (pt) REVERT: D 121 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7477 (tp30) REVERT: D 124 ARG cc_start: 0.8326 (tpt170) cc_final: 0.7512 (mmm160) REVERT: D 133 HIS cc_start: 0.7215 (m-70) cc_final: 0.6833 (m-70) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.3310 time to fit residues: 180.5181 Evaluate side-chains 374 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 145 optimal weight: 0.0470 chunk 20 optimal weight: 0.0040 chunk 151 optimal weight: 4.9990 chunk 73 optimal weight: 0.0000 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS A 655 HIS ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.159944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.129817 restraints weight = 28492.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.134947 restraints weight = 19359.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.138810 restraints weight = 14143.034| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12590 Z= 0.111 Angle : 0.627 10.729 16980 Z= 0.312 Chirality : 0.043 0.169 1912 Planarity : 0.004 0.048 2186 Dihedral : 4.750 22.722 1688 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.21), residues: 1496 helix: -1.98 (0.18), residues: 704 sheet: -1.20 (0.79), residues: 40 loop : -1.19 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 791 HIS 0.003 0.000 HIS B 85 PHE 0.032 0.002 PHE C 309 TYR 0.017 0.001 TYR A 464 ARG 0.007 0.001 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 334) hydrogen bonds : angle 5.88867 ( 960) metal coordination : bond 0.00219 ( 10) covalent geometry : bond 0.00247 (12580) covalent geometry : angle 0.62662 (16980) *********************** 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 414 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.305 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: 0.8572 (mp0) cc_final: 0.7893 (mp0) REVERT: A 287 PHE cc_start: 0.7180 (m-80) cc_final: 0.6839 (m-80) REVERT: A 290 VAL cc_start: 0.7094 (m) cc_final: 0.6494 (t) REVERT: A 324 LEU cc_start: 0.8503 (mt) cc_final: 0.7522 (mt) REVERT: A 337 ARG cc_start: 0.7832 (mmp80) cc_final: 0.7104 (mmm160) REVERT: A 340 MET cc_start: 0.7846 (ptm) cc_final: 0.6748 (ptm) REVERT: A 344 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7569 (tp-100) REVERT: A 373 LYS cc_start: 0.8182 (mttm) cc_final: 0.7836 (mttm) REVERT: A 394 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 410 GLN cc_start: 0.8107 (pt0) cc_final: 0.7673 (pt0) REVERT: A 439 CYS cc_start: 0.7284 (m) cc_final: 0.6872 (m) REVERT: A 464 TYR cc_start: 0.7521 (t80) cc_final: 0.7315 (t80) REVERT: A 478 MET cc_start: 0.7731 (tpp) cc_final: 0.7323 (tpp) REVERT: A 491 LEU cc_start: 0.8650 (mt) cc_final: 0.8334 (mt) REVERT: A 543 ILE cc_start: 0.8081 (tp) cc_final: 0.7811 (pt) REVERT: A 576 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 580 GLU cc_start: 0.8303 (tp30) cc_final: 0.8017 (mm-30) REVERT: A 635 MET cc_start: 0.7843 (mpp) cc_final: 0.7268 (mpp) REVERT: A 640 LYS cc_start: 0.8174 (mttt) cc_final: 0.7902 (mttt) REVERT: A 642 MET cc_start: 0.8198 (mmp) cc_final: 0.7962 (mmp) REVERT: A 651 LEU cc_start: 0.8170 (tp) cc_final: 0.7889 (tp) REVERT: A 663 LYS cc_start: 0.8357 (ptmm) cc_final: 0.7841 (ptpp) REVERT: A 664 ASP cc_start: 0.8408 (p0) cc_final: 0.8166 (p0) REVERT: A 684 GLN cc_start: 0.6577 (tp40) cc_final: 0.5449 (tm-30) REVERT: A 692 MET cc_start: 0.6456 (mpp) cc_final: 0.6019 (mpp) REVERT: A 694 TYR cc_start: 0.6908 (t80) cc_final: 0.6706 (t80) REVERT: A 730 PHE cc_start: 0.7936 (t80) cc_final: 0.7603 (t80) REVERT: A 739 MET cc_start: 0.8060 (ttm) cc_final: 0.7774 (ttm) REVERT: A 754 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8306 (mt-10) REVERT: A 801 GLN cc_start: 0.8049 (mt0) cc_final: 0.7724 (mt0) REVERT: A 802 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7832 (mmtm) REVERT: A 822 LYS cc_start: 0.8187 (mmtm) cc_final: 0.7872 (mmtm) REVERT: B 18 LYS cc_start: 0.8248 (mttt) cc_final: 0.8012 (mttt) REVERT: B 25 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7458 (mt-10) REVERT: B 58 CYS cc_start: 0.6513 (t) cc_final: 0.5994 (t) REVERT: B 59 ILE cc_start: 0.6342 (mm) cc_final: 0.5984 (mm) REVERT: B 79 LYS cc_start: 0.8426 (tptt) cc_final: 0.7818 (tptt) REVERT: B 82 GLU cc_start: 0.7833 (pp20) cc_final: 0.7161 (pp20) REVERT: B 95 LEU cc_start: 0.8455 (pt) cc_final: 0.8232 (pt) REVERT: B 121 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7022 (tp30) REVERT: B 124 ARG cc_start: 0.8364 (tpt170) cc_final: 0.7445 (mmm160) REVERT: B 133 HIS cc_start: 0.7137 (m-70) cc_final: 0.6865 (m-70) REVERT: C 241 ARG cc_start: 0.8355 (mmp80) cc_final: 0.7841 (mmp80) REVERT: C 242 VAL cc_start: 0.8724 (t) cc_final: 0.8459 (t) REVERT: C 282 ASN cc_start: 0.7952 (t0) cc_final: 0.7665 (t0) REVERT: C 287 PHE cc_start: 0.7231 (m-80) cc_final: 0.6895 (m-80) REVERT: C 324 LEU cc_start: 0.8523 (mt) cc_final: 0.7458 (mt) REVERT: C 334 ASP cc_start: 0.7841 (p0) cc_final: 0.6572 (p0) REVERT: C 335 GLN cc_start: 0.8000 (mm110) cc_final: 0.7355 (mm110) REVERT: C 340 MET cc_start: 0.7803 (ptp) cc_final: 0.7577 (ptt) REVERT: C 344 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7394 (tp40) REVERT: C 345 GLN cc_start: 0.7574 (mt0) cc_final: 0.6890 (mt0) REVERT: C 373 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7795 (tptp) REVERT: C 406 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6820 (tm-30) REVERT: C 407 LEU cc_start: 0.8347 (mt) cc_final: 0.7996 (mt) REVERT: C 436 THR cc_start: 0.6784 (p) cc_final: 0.6549 (p) REVERT: C 464 TYR cc_start: 0.7097 (t80) cc_final: 0.6858 (t80) REVERT: C 472 GLU cc_start: 0.8376 (pm20) cc_final: 0.8021 (pm20) REVERT: C 478 MET cc_start: 0.7859 (tpp) cc_final: 0.7137 (tpp) REVERT: C 491 LEU cc_start: 0.8601 (mt) cc_final: 0.8294 (mt) REVERT: C 524 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7120 (ttp-110) REVERT: C 531 HIS cc_start: 0.7965 (m90) cc_final: 0.7212 (m90) REVERT: C 539 ARG cc_start: 0.8381 (tpp80) cc_final: 0.7665 (tpp80) REVERT: C 542 MET cc_start: 0.7693 (mmp) cc_final: 0.7473 (mmt) REVERT: C 576 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7613 (tm-30) REVERT: C 580 GLU cc_start: 0.8264 (tp30) cc_final: 0.7882 (mm-30) REVERT: C 589 MET cc_start: 0.5376 (ttm) cc_final: 0.4564 (tpp) REVERT: C 592 TYR cc_start: 0.7788 (t80) cc_final: 0.7441 (t80) REVERT: C 597 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8819 (tptp) REVERT: C 607 GLU cc_start: 0.8403 (pm20) cc_final: 0.8058 (pm20) REVERT: C 635 MET cc_start: 0.7964 (mpp) cc_final: 0.7278 (mpp) REVERT: C 639 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8142 (mmm-85) REVERT: C 640 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7943 (mtmt) REVERT: C 642 MET cc_start: 0.8068 (mmp) cc_final: 0.7773 (mmp) REVERT: C 649 ARG cc_start: 0.7335 (tmm-80) cc_final: 0.6776 (tmm-80) REVERT: C 651 LEU cc_start: 0.8347 (tp) cc_final: 0.8053 (tp) REVERT: C 663 LYS cc_start: 0.8434 (ptmm) cc_final: 0.8073 (ptpp) REVERT: C 684 GLN cc_start: 0.7794 (tp40) cc_final: 0.7083 (tm-30) REVERT: C 730 PHE cc_start: 0.8018 (t80) cc_final: 0.7545 (t80) REVERT: C 739 MET cc_start: 0.8220 (ttm) cc_final: 0.8009 (ttm) REVERT: C 751 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7708 (tpp-160) REVERT: C 754 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7989 (mt-10) REVERT: C 801 GLN cc_start: 0.7917 (mt0) cc_final: 0.7531 (mt0) REVERT: C 807 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7731 (mm-40) REVERT: C 822 LYS cc_start: 0.8015 (mmmm) cc_final: 0.7809 (tptp) REVERT: C 861 ARG cc_start: 0.6922 (ptp-110) cc_final: 0.6665 (ptm160) REVERT: D 25 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7421 (mt-10) REVERT: D 52 PHE cc_start: 0.7040 (t80) cc_final: 0.6771 (t80) REVERT: D 58 CYS cc_start: 0.6452 (t) cc_final: 0.5709 (t) REVERT: D 59 ILE cc_start: 0.5865 (mm) cc_final: 0.5605 (mm) REVERT: D 79 LYS cc_start: 0.8543 (tptt) cc_final: 0.7915 (tptt) REVERT: D 82 GLU cc_start: 0.7745 (pp20) cc_final: 0.7226 (pp20) REVERT: D 121 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7490 (tp30) REVERT: D 124 ARG cc_start: 0.8416 (tpt170) cc_final: 0.7614 (mmm160) REVERT: D 133 HIS cc_start: 0.7239 (m-70) cc_final: 0.6821 (m-70) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.3236 time to fit residues: 175.9599 Evaluate side-chains 382 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 0.0770 chunk 102 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 655 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.158879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.128587 restraints weight = 28584.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.133424 restraints weight = 19490.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.137396 restraints weight = 14403.583| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12590 Z= 0.128 Angle : 0.656 11.307 16980 Z= 0.327 Chirality : 0.044 0.177 1912 Planarity : 0.005 0.050 2186 Dihedral : 4.795 27.224 1688 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.08 % Allowed : 1.06 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.21), residues: 1496 helix: -1.91 (0.18), residues: 738 sheet: -1.42 (0.73), residues: 40 loop : -1.31 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 791 HIS 0.003 0.001 HIS B 85 PHE 0.043 0.002 PHE A 633 TYR 0.014 0.001 TYR A 464 ARG 0.008 0.001 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 334) hydrogen bonds : angle 5.86123 ( 960) metal coordination : bond 0.00358 ( 10) covalent geometry : bond 0.00280 (12580) covalent geometry : angle 0.65586 (16980) *********************** 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 410 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 1.285 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 135 GLU cc_start: 0.8565 (mp0) cc_final: 0.7970 (mp0) REVERT: A 309 PHE cc_start: 0.8215 (t80) cc_final: 0.7955 (t80) REVERT: A 324 LEU cc_start: 0.8479 (mt) cc_final: 0.7468 (mt) REVERT: A 337 ARG cc_start: 0.7830 (mmp80) cc_final: 0.7081 (mmm160) REVERT: A 340 MET cc_start: 0.7935 (ptm) cc_final: 0.6902 (ptm) REVERT: A 345 GLN cc_start: 0.7684 (mt0) cc_final: 0.6860 (mt0) REVERT: A 373 LYS cc_start: 0.8192 (mttm) cc_final: 0.7843 (mttm) REVERT: A 424 ARG cc_start: 0.7744 (tpt-90) cc_final: 0.7408 (tpt-90) REVERT: A 441 LYS cc_start: 0.8390 (ptmm) cc_final: 0.8156 (ptmm) REVERT: A 464 TYR cc_start: 0.7486 (t80) cc_final: 0.7178 (t80) REVERT: A 472 GLU cc_start: 0.8538 (pm20) cc_final: 0.8190 (pm20) REVERT: A 478 MET cc_start: 0.7696 (tpp) cc_final: 0.7329 (tpp) REVERT: A 491 LEU cc_start: 0.8633 (mt) cc_final: 0.8317 (mt) REVERT: A 541 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7406 (mm-30) REVERT: A 542 MET cc_start: 0.7486 (mmp) cc_final: 0.7149 (mmp) REVERT: A 597 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8551 (mmmt) REVERT: A 611 GLN cc_start: 0.8178 (mp10) cc_final: 0.7958 (mp10) REVERT: A 635 MET cc_start: 0.7918 (mpp) cc_final: 0.7276 (mpp) REVERT: A 640 LYS cc_start: 0.8263 (mttt) cc_final: 0.7833 (mttt) REVERT: A 651 LEU cc_start: 0.8186 (tp) cc_final: 0.7924 (tp) REVERT: A 663 LYS cc_start: 0.8283 (ptmm) cc_final: 0.7969 (ptpp) REVERT: A 694 TYR cc_start: 0.6245 (t80) cc_final: 0.5520 (t80) REVERT: A 720 TYR cc_start: 0.7753 (t80) cc_final: 0.6985 (t80) REVERT: A 730 PHE cc_start: 0.7955 (t80) cc_final: 0.7600 (t80) REVERT: A 739 MET cc_start: 0.8118 (ttm) cc_final: 0.7875 (ttm) REVERT: A 742 ASN cc_start: 0.8317 (p0) cc_final: 0.7684 (p0) REVERT: A 801 GLN cc_start: 0.8084 (mt0) cc_final: 0.7787 (mt0) REVERT: A 802 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7871 (mmtm) REVERT: A 807 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7632 (mm-40) REVERT: A 822 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7818 (mmtm) REVERT: A 857 LYS cc_start: 0.8545 (tttt) cc_final: 0.8285 (tttp) REVERT: B 18 LYS cc_start: 0.8282 (mttt) cc_final: 0.8021 (mttt) REVERT: B 25 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7553 (mt-10) REVERT: B 79 LYS cc_start: 0.8450 (tptt) cc_final: 0.7866 (tptt) REVERT: B 82 GLU cc_start: 0.7993 (pp20) cc_final: 0.7290 (pp20) REVERT: B 95 LEU cc_start: 0.8415 (pt) cc_final: 0.8155 (pt) REVERT: B 121 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7022 (tp30) REVERT: B 124 ARG cc_start: 0.8408 (tpt170) cc_final: 0.7426 (mmm160) REVERT: B 133 HIS cc_start: 0.7227 (m-70) cc_final: 0.6958 (m-70) REVERT: C 241 ARG cc_start: 0.8343 (mmp80) cc_final: 0.7925 (mmt-90) REVERT: C 242 VAL cc_start: 0.8751 (t) cc_final: 0.8503 (t) REVERT: C 324 LEU cc_start: 0.8536 (mt) cc_final: 0.7484 (mt) REVERT: C 340 MET cc_start: 0.7810 (ptp) cc_final: 0.7609 (ptt) REVERT: C 344 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7792 (tp-100) REVERT: C 345 GLN cc_start: 0.7734 (mt0) cc_final: 0.7008 (mt0) REVERT: C 373 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7676 (tptt) REVERT: C 406 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6952 (tm-30) REVERT: C 407 LEU cc_start: 0.8349 (mt) cc_final: 0.7999 (mt) REVERT: C 472 GLU cc_start: 0.8395 (pm20) cc_final: 0.8048 (pm20) REVERT: C 478 MET cc_start: 0.7744 (tpp) cc_final: 0.7172 (tpp) REVERT: C 491 LEU cc_start: 0.8560 (mt) cc_final: 0.8270 (mt) REVERT: C 507 ILE cc_start: 0.8583 (tp) cc_final: 0.8297 (tp) REVERT: C 528 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7397 (ttp-110) REVERT: C 531 HIS cc_start: 0.7895 (m90) cc_final: 0.7432 (m90) REVERT: C 539 ARG cc_start: 0.8435 (tpp80) cc_final: 0.7811 (ttt180) REVERT: C 542 MET cc_start: 0.7677 (mmp) cc_final: 0.7432 (mmt) REVERT: C 576 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 580 GLU cc_start: 0.8378 (tp30) cc_final: 0.7991 (mm-30) REVERT: C 597 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8962 (mtpp) REVERT: C 607 GLU cc_start: 0.8363 (pm20) cc_final: 0.8000 (pm20) REVERT: C 635 MET cc_start: 0.7994 (mpp) cc_final: 0.7316 (mpp) REVERT: C 640 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8092 (mtmt) REVERT: C 642 MET cc_start: 0.8095 (mmp) cc_final: 0.7834 (mmp) REVERT: C 651 LEU cc_start: 0.8331 (tp) cc_final: 0.8030 (tp) REVERT: C 663 LYS cc_start: 0.8491 (ptmm) cc_final: 0.8080 (ptpp) REVERT: C 684 GLN cc_start: 0.7881 (tp40) cc_final: 0.7177 (tm-30) REVERT: C 692 MET cc_start: 0.7607 (tmm) cc_final: 0.7193 (tmm) REVERT: C 693 MET cc_start: 0.8112 (tpt) cc_final: 0.7862 (mmm) REVERT: C 694 TYR cc_start: 0.5910 (t80) cc_final: 0.5487 (t80) REVERT: C 720 TYR cc_start: 0.7783 (t80) cc_final: 0.7258 (t80) REVERT: C 739 MET cc_start: 0.8212 (ttm) cc_final: 0.7976 (ttm) REVERT: C 751 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7653 (tpp-160) REVERT: C 754 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 801 GLN cc_start: 0.7969 (mt0) cc_final: 0.7563 (mt0) REVERT: C 807 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7746 (mm-40) REVERT: D 25 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7462 (mt-10) REVERT: D 52 PHE cc_start: 0.7183 (t80) cc_final: 0.6822 (t80) REVERT: D 57 LEU cc_start: 0.7446 (mt) cc_final: 0.7175 (mm) REVERT: D 58 CYS cc_start: 0.6567 (t) cc_final: 0.5861 (t) REVERT: D 59 ILE cc_start: 0.6355 (mm) cc_final: 0.6145 (mm) REVERT: D 133 HIS cc_start: 0.7186 (m-70) cc_final: 0.6925 (m-70) outliers start: 1 outliers final: 0 residues processed: 409 average time/residue: 0.3287 time to fit residues: 176.3694 Evaluate side-chains 383 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 0.0270 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN C 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.158883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.127998 restraints weight = 28907.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.132875 restraints weight = 19945.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.136813 restraints weight = 14855.053| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12590 Z= 0.125 Angle : 0.657 9.731 16980 Z= 0.329 Chirality : 0.044 0.217 1912 Planarity : 0.005 0.052 2186 Dihedral : 4.773 25.736 1688 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.21), residues: 1496 helix: -1.77 (0.18), residues: 738 sheet: -1.20 (0.67), residues: 36 loop : -1.23 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 791 HIS 0.002 0.001 HIS B 85 PHE 0.037 0.002 PHE A 633 TYR 0.023 0.001 TYR C 464 ARG 0.006 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 334) hydrogen bonds : angle 5.91312 ( 960) metal coordination : bond 0.00325 ( 10) covalent geometry : bond 0.00279 (12580) covalent geometry : angle 0.65734 (16980) *********************** 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 414 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.311 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 135 GLU cc_start: 0.8601 (mp0) cc_final: 0.8053 (mp0) REVERT: A 241 ARG cc_start: 0.8459 (mmp80) cc_final: 0.7988 (mmp80) REVERT: A 324 LEU cc_start: 0.8480 (mt) cc_final: 0.7391 (mt) REVERT: A 335 GLN cc_start: 0.7641 (mp10) cc_final: 0.7281 (mp10) REVERT: A 337 ARG cc_start: 0.7850 (mmp80) cc_final: 0.7148 (mmm160) REVERT: A 340 MET cc_start: 0.7941 (ptm) cc_final: 0.7203 (ptm) REVERT: A 373 LYS cc_start: 0.8226 (mttm) cc_final: 0.7860 (mttm) REVERT: A 412 LEU cc_start: 0.8488 (tt) cc_final: 0.8210 (tt) REVERT: A 424 ARG cc_start: 0.7826 (tpt-90) cc_final: 0.7522 (tpt-90) REVERT: A 441 LYS cc_start: 0.8364 (ptmm) cc_final: 0.8104 (ptmm) REVERT: A 460 MET cc_start: 0.6451 (mmp) cc_final: 0.5998 (mmt) REVERT: A 464 TYR cc_start: 0.7412 (t80) cc_final: 0.7041 (t80) REVERT: A 472 GLU cc_start: 0.8504 (pm20) cc_final: 0.8199 (pm20) REVERT: A 477 PHE cc_start: 0.8358 (m-80) cc_final: 0.7719 (m-80) REVERT: A 478 MET cc_start: 0.7770 (tpp) cc_final: 0.7570 (tpp) REVERT: A 491 LEU cc_start: 0.8422 (mt) cc_final: 0.7857 (mt) REVERT: A 528 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7338 (ttp-110) REVERT: A 531 HIS cc_start: 0.7973 (m90) cc_final: 0.7520 (m90) REVERT: A 537 LEU cc_start: 0.7845 (tp) cc_final: 0.6713 (tp) REVERT: A 541 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 542 MET cc_start: 0.7415 (mmp) cc_final: 0.7111 (mmp) REVERT: A 576 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 580 GLU cc_start: 0.8466 (tp30) cc_final: 0.8203 (mm-30) REVERT: A 597 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8544 (mmmt) REVERT: A 611 GLN cc_start: 0.8134 (mp10) cc_final: 0.7805 (mp10) REVERT: A 619 LEU cc_start: 0.8916 (tp) cc_final: 0.8590 (tp) REVERT: A 635 MET cc_start: 0.7844 (mpp) cc_final: 0.7270 (mpp) REVERT: A 639 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.7945 (mmm-85) REVERT: A 640 LYS cc_start: 0.8280 (mttt) cc_final: 0.7892 (mttt) REVERT: A 651 LEU cc_start: 0.8284 (tp) cc_final: 0.7947 (tp) REVERT: A 659 TYR cc_start: 0.8020 (t80) cc_final: 0.7548 (t80) REVERT: A 663 LYS cc_start: 0.8460 (ptmm) cc_final: 0.7949 (ptpp) REVERT: A 694 TYR cc_start: 0.5948 (t80) cc_final: 0.4847 (t80) REVERT: A 711 LYS cc_start: 0.8705 (mptt) cc_final: 0.8358 (mptt) REVERT: A 720 TYR cc_start: 0.7772 (t80) cc_final: 0.6801 (t80) REVERT: A 730 PHE cc_start: 0.7975 (t80) cc_final: 0.7649 (t80) REVERT: A 739 MET cc_start: 0.8034 (ttm) cc_final: 0.7768 (ttm) REVERT: A 742 ASN cc_start: 0.8254 (p0) cc_final: 0.7797 (p0) REVERT: A 754 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 801 GLN cc_start: 0.8057 (mt0) cc_final: 0.7761 (mt0) REVERT: A 807 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7561 (mm-40) REVERT: B 18 LYS cc_start: 0.8246 (mttt) cc_final: 0.7930 (mttt) REVERT: B 25 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7534 (mt-10) REVERT: B 52 PHE cc_start: 0.6677 (t80) cc_final: 0.6276 (t80) REVERT: B 58 CYS cc_start: 0.6675 (t) cc_final: 0.5998 (t) REVERT: B 59 ILE cc_start: 0.6674 (mm) cc_final: 0.6109 (mm) REVERT: B 121 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7086 (tp30) REVERT: B 124 ARG cc_start: 0.8300 (tpt170) cc_final: 0.7304 (mmm160) REVERT: B 133 HIS cc_start: 0.7246 (m-70) cc_final: 0.6928 (m-70) REVERT: C 241 ARG cc_start: 0.8313 (mmp80) cc_final: 0.7703 (mmp80) REVERT: C 242 VAL cc_start: 0.8751 (t) cc_final: 0.8533 (t) REVERT: C 309 PHE cc_start: 0.8048 (t80) cc_final: 0.7843 (t80) REVERT: C 324 LEU cc_start: 0.8581 (mt) cc_final: 0.7459 (mt) REVERT: C 334 ASP cc_start: 0.7897 (p0) cc_final: 0.6735 (p0) REVERT: C 335 GLN cc_start: 0.8184 (mm110) cc_final: 0.7374 (mm110) REVERT: C 344 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7770 (tp-100) REVERT: C 345 GLN cc_start: 0.7717 (mt0) cc_final: 0.7001 (mt0) REVERT: C 373 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7741 (tptp) REVERT: C 389 ASP cc_start: 0.7009 (p0) cc_final: 0.6561 (p0) REVERT: C 392 HIS cc_start: 0.7668 (m-70) cc_final: 0.7108 (m-70) REVERT: C 406 GLU cc_start: 0.7676 (tm-30) cc_final: 0.6984 (tm-30) REVERT: C 407 LEU cc_start: 0.8352 (mt) cc_final: 0.7997 (mt) REVERT: C 464 TYR cc_start: 0.7333 (t80) cc_final: 0.6798 (t80) REVERT: C 472 GLU cc_start: 0.8375 (pm20) cc_final: 0.8006 (pm20) REVERT: C 478 MET cc_start: 0.7780 (tpp) cc_final: 0.7182 (tpp) REVERT: C 491 LEU cc_start: 0.8534 (mt) cc_final: 0.8298 (mt) REVERT: C 507 ILE cc_start: 0.8614 (tp) cc_final: 0.8313 (tp) REVERT: C 522 TYR cc_start: 0.7401 (m-10) cc_final: 0.7106 (m-10) REVERT: C 531 HIS cc_start: 0.7182 (m90) cc_final: 0.6529 (m90) REVERT: C 539 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7836 (ttm170) REVERT: C 542 MET cc_start: 0.7643 (mmp) cc_final: 0.7371 (mmt) REVERT: C 556 TYR cc_start: 0.6795 (t80) cc_final: 0.6583 (t80) REVERT: C 576 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 580 GLU cc_start: 0.8437 (tp30) cc_final: 0.8058 (mm-30) REVERT: C 597 LYS cc_start: 0.9233 (mtpp) cc_final: 0.8811 (mtpp) REVERT: C 607 GLU cc_start: 0.8378 (pm20) cc_final: 0.7990 (pm20) REVERT: C 635 MET cc_start: 0.8013 (mpp) cc_final: 0.7360 (mpp) REVERT: C 639 ARG cc_start: 0.8423 (tpt-90) cc_final: 0.7698 (tpt-90) REVERT: C 640 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8015 (mtmt) REVERT: C 642 MET cc_start: 0.8047 (mmp) cc_final: 0.7807 (mmp) REVERT: C 651 LEU cc_start: 0.8343 (tp) cc_final: 0.8039 (tp) REVERT: C 663 LYS cc_start: 0.8554 (ptmm) cc_final: 0.8167 (mtmm) REVERT: C 684 GLN cc_start: 0.7884 (tp40) cc_final: 0.6839 (tm-30) REVERT: C 692 MET cc_start: 0.7659 (tmm) cc_final: 0.7426 (tmm) REVERT: C 693 MET cc_start: 0.8330 (tpt) cc_final: 0.7771 (tpt) REVERT: C 694 TYR cc_start: 0.6182 (t80) cc_final: 0.5343 (t80) REVERT: C 720 TYR cc_start: 0.7855 (t80) cc_final: 0.7400 (t80) REVERT: C 739 MET cc_start: 0.8247 (ttm) cc_final: 0.7984 (ttm) REVERT: C 751 ARG cc_start: 0.8098 (mmm160) cc_final: 0.7608 (tpp-160) REVERT: C 754 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7983 (mt-10) REVERT: C 801 GLN cc_start: 0.7671 (mt0) cc_final: 0.7282 (mt0) REVERT: C 861 ARG cc_start: 0.6884 (ptp-110) cc_final: 0.6417 (mtp85) REVERT: D 25 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7459 (mt-10) REVERT: D 52 PHE cc_start: 0.7335 (t80) cc_final: 0.6930 (t80) REVERT: D 58 CYS cc_start: 0.6648 (t) cc_final: 0.5967 (t) REVERT: D 59 ILE cc_start: 0.6479 (mm) cc_final: 0.6153 (mm) REVERT: D 124 ARG cc_start: 0.8197 (tpt170) cc_final: 0.7758 (mmm160) REVERT: D 133 HIS cc_start: 0.7333 (m-70) cc_final: 0.6949 (m-70) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.3248 time to fit residues: 177.3791 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 : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 chunk 25 optimal weight: 0.0870 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 485 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.160339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.129443 restraints weight = 28647.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.134494 restraints weight = 19720.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.138429 restraints weight = 14598.197| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12590 Z= 0.120 Angle : 0.674 10.721 16980 Z= 0.335 Chirality : 0.045 0.212 1912 Planarity : 0.005 0.057 2186 Dihedral : 4.746 25.420 1688 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.21), residues: 1496 helix: -1.73 (0.18), residues: 734 sheet: -1.00 (0.69), residues: 40 loop : -1.22 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP C 791 HIS 0.003 0.001 HIS A 632 PHE 0.032 0.002 PHE A 633 TYR 0.018 0.001 TYR B 91 ARG 0.013 0.001 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 334) hydrogen bonds : angle 5.86185 ( 960) metal coordination : bond 0.00219 ( 10) covalent geometry : bond 0.00267 (12580) covalent geometry : angle 0.67427 (16980) *********************** 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 409 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 1.432 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: 0.8528 (mp0) cc_final: 0.7894 (mp0) REVERT: A 241 ARG cc_start: 0.8416 (mmp80) cc_final: 0.8067 (mtm-85) REVERT: A 313 MET cc_start: 0.7555 (mmm) cc_final: 0.7225 (mmm) REVERT: A 321 GLN cc_start: 0.8355 (mp10) cc_final: 0.7810 (mp10) REVERT: A 324 LEU cc_start: 0.8478 (mt) cc_final: 0.7392 (mt) REVERT: A 335 GLN cc_start: 0.7583 (mp10) cc_final: 0.7218 (mp10) REVERT: A 337 ARG cc_start: 0.7831 (mmp80) cc_final: 0.7126 (mmm160) REVERT: A 340 MET cc_start: 0.7969 (ptm) cc_final: 0.7213 (ptm) REVERT: A 373 LYS cc_start: 0.8215 (mttm) cc_final: 0.7886 (mttm) REVERT: A 424 ARG cc_start: 0.7881 (tpt-90) cc_final: 0.7592 (tpt-90) REVERT: A 441 LYS cc_start: 0.8293 (ptmm) cc_final: 0.8064 (ptmm) REVERT: A 460 MET cc_start: 0.6369 (mmp) cc_final: 0.5907 (mmt) REVERT: A 464 TYR cc_start: 0.7249 (t80) cc_final: 0.6881 (t80) REVERT: A 472 GLU cc_start: 0.8424 (pm20) cc_final: 0.8058 (pm20) REVERT: A 477 PHE cc_start: 0.8343 (m-80) cc_final: 0.7699 (m-80) REVERT: A 478 MET cc_start: 0.7643 (tpp) cc_final: 0.7409 (tpp) REVERT: A 491 LEU cc_start: 0.8349 (mt) cc_final: 0.7819 (mt) REVERT: A 537 LEU cc_start: 0.7870 (tp) cc_final: 0.6793 (tp) REVERT: A 539 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7767 (tpp80) REVERT: A 541 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 542 MET cc_start: 0.7441 (mmp) cc_final: 0.7084 (mmp) REVERT: A 576 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 580 GLU cc_start: 0.8360 (tp30) cc_final: 0.8123 (mm-30) REVERT: A 597 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8446 (mmmt) REVERT: A 611 GLN cc_start: 0.8140 (mp10) cc_final: 0.7773 (mp10) REVERT: A 619 LEU cc_start: 0.8834 (tp) cc_final: 0.8491 (tp) REVERT: A 635 MET cc_start: 0.7810 (mpp) cc_final: 0.7207 (mpp) REVERT: A 639 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.7933 (mmm-85) REVERT: A 640 LYS cc_start: 0.8288 (mttt) cc_final: 0.7868 (mttt) REVERT: A 648 PHE cc_start: 0.6914 (t80) cc_final: 0.6573 (t80) REVERT: A 651 LEU cc_start: 0.8283 (tp) cc_final: 0.7969 (tp) REVERT: A 659 TYR cc_start: 0.8010 (t80) cc_final: 0.7533 (t80) REVERT: A 663 LYS cc_start: 0.8255 (ptmm) cc_final: 0.8045 (mtmm) REVERT: A 711 LYS cc_start: 0.8702 (mptt) cc_final: 0.8309 (mptt) REVERT: A 730 PHE cc_start: 0.7944 (t80) cc_final: 0.7648 (t80) REVERT: A 739 MET cc_start: 0.8019 (ttm) cc_final: 0.7737 (ttm) REVERT: A 742 ASN cc_start: 0.8211 (p0) cc_final: 0.7756 (p0) REVERT: A 801 GLN cc_start: 0.8035 (mt0) cc_final: 0.7788 (mt0) REVERT: A 807 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7612 (mm-40) REVERT: A 822 LYS cc_start: 0.7929 (tptp) cc_final: 0.7627 (tptp) REVERT: B 18 LYS cc_start: 0.8256 (mttt) cc_final: 0.7946 (mttt) REVERT: B 25 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 52 PHE cc_start: 0.6628 (t80) cc_final: 0.6298 (t80) REVERT: B 55 ARG cc_start: 0.7776 (mmt90) cc_final: 0.7431 (mmt90) REVERT: B 58 CYS cc_start: 0.6575 (t) cc_final: 0.5847 (t) REVERT: B 59 ILE cc_start: 0.6469 (mm) cc_final: 0.5962 (mm) REVERT: B 124 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7460 (mmm160) REVERT: B 131 ARG cc_start: 0.5162 (mtt90) cc_final: 0.4804 (mtt90) REVERT: B 133 HIS cc_start: 0.7228 (m-70) cc_final: 0.6942 (m-70) REVERT: C 138 GLU cc_start: 0.7859 (tp30) cc_final: 0.7380 (mp0) REVERT: C 241 ARG cc_start: 0.8238 (mmp80) cc_final: 0.7976 (mmp80) REVERT: C 324 LEU cc_start: 0.8553 (mt) cc_final: 0.7479 (mt) REVERT: C 334 ASP cc_start: 0.7814 (p0) cc_final: 0.6658 (p0) REVERT: C 335 GLN cc_start: 0.8127 (mm110) cc_final: 0.7313 (mm110) REVERT: C 344 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7708 (tp-100) REVERT: C 345 GLN cc_start: 0.7734 (mt0) cc_final: 0.6989 (mt0) REVERT: C 373 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7654 (tptp) REVERT: C 389 ASP cc_start: 0.7937 (p0) cc_final: 0.7492 (p0) REVERT: C 392 HIS cc_start: 0.7578 (m-70) cc_final: 0.7204 (m-70) REVERT: C 406 GLU cc_start: 0.7602 (tm-30) cc_final: 0.6894 (tm-30) REVERT: C 407 LEU cc_start: 0.8362 (mt) cc_final: 0.8028 (mt) REVERT: C 464 TYR cc_start: 0.7318 (t80) cc_final: 0.6718 (t80) REVERT: C 472 GLU cc_start: 0.8325 (pm20) cc_final: 0.7958 (pm20) REVERT: C 478 MET cc_start: 0.7716 (tpp) cc_final: 0.7048 (tpp) REVERT: C 491 LEU cc_start: 0.8504 (mt) cc_final: 0.8300 (mt) REVERT: C 494 TYR cc_start: 0.7701 (t80) cc_final: 0.7445 (t80) REVERT: C 507 ILE cc_start: 0.8607 (tp) cc_final: 0.8323 (tp) REVERT: C 539 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7788 (ttm170) REVERT: C 576 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 580 GLU cc_start: 0.8445 (tp30) cc_final: 0.8016 (mm-30) REVERT: C 592 TYR cc_start: 0.7650 (t80) cc_final: 0.7319 (t80) REVERT: C 597 LYS cc_start: 0.9149 (mtpp) cc_final: 0.8834 (mtpp) REVERT: C 607 GLU cc_start: 0.8348 (pm20) cc_final: 0.7952 (pm20) REVERT: C 635 MET cc_start: 0.7944 (mpp) cc_final: 0.7293 (mpp) REVERT: C 639 ARG cc_start: 0.8554 (tpt-90) cc_final: 0.7778 (tpt-90) REVERT: C 640 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7981 (mtmt) REVERT: C 642 MET cc_start: 0.8008 (mmp) cc_final: 0.7778 (mmp) REVERT: C 651 LEU cc_start: 0.8389 (tp) cc_final: 0.8117 (tp) REVERT: C 663 LYS cc_start: 0.8644 (ptmm) cc_final: 0.8142 (mtmm) REVERT: C 684 GLN cc_start: 0.7898 (tp40) cc_final: 0.6857 (tm-30) REVERT: C 692 MET cc_start: 0.7605 (tmm) cc_final: 0.7195 (tmm) REVERT: C 694 TYR cc_start: 0.6090 (t80) cc_final: 0.5532 (t80) REVERT: C 720 TYR cc_start: 0.7768 (t80) cc_final: 0.7340 (t80) REVERT: C 730 PHE cc_start: 0.8044 (t80) cc_final: 0.7561 (t80) REVERT: C 739 MET cc_start: 0.8158 (ttm) cc_final: 0.7814 (ttm) REVERT: C 742 ASN cc_start: 0.8376 (p0) cc_final: 0.7909 (p0) REVERT: C 751 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7764 (tpp-160) REVERT: C 754 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 801 GLN cc_start: 0.7630 (mt0) cc_final: 0.7238 (mt0) REVERT: C 807 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7582 (mm110) REVERT: C 861 ARG cc_start: 0.6811 (ptp-110) cc_final: 0.6433 (mtp85) REVERT: D 25 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7435 (mt-10) REVERT: D 52 PHE cc_start: 0.7298 (t80) cc_final: 0.6907 (t80) REVERT: D 58 CYS cc_start: 0.6487 (t) cc_final: 0.5629 (t) REVERT: D 124 ARG cc_start: 0.8365 (tpt170) cc_final: 0.7898 (tpt90) REVERT: D 133 HIS cc_start: 0.7254 (m-70) cc_final: 0.6904 (m-70) outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.3367 time to fit residues: 181.4252 Evaluate side-chains 367 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 9 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 148 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 0.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.160672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.130179 restraints weight = 27856.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.135101 restraints weight = 19261.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.138907 restraints weight = 14334.476| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12590 Z= 0.124 Angle : 0.691 10.308 16980 Z= 0.345 Chirality : 0.045 0.200 1912 Planarity : 0.005 0.071 2186 Dihedral : 4.786 23.891 1688 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.21), residues: 1496 helix: -1.67 (0.18), residues: 736 sheet: -1.02 (0.71), residues: 40 loop : -1.19 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP A 791 HIS 0.003 0.001 HIS A 632 PHE 0.029 0.002 PHE A 633 TYR 0.016 0.001 TYR C 464 ARG 0.011 0.001 ARG C 528 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 334) hydrogen bonds : angle 5.94939 ( 960) metal coordination : bond 0.00279 ( 10) covalent geometry : bond 0.00280 (12580) covalent geometry : angle 0.69064 (16980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8513 (mp0) cc_final: 0.7875 (mp0) REVERT: A 237 ASP cc_start: 0.7772 (p0) cc_final: 0.7293 (p0) REVERT: A 240 ARG cc_start: 0.8732 (mtt180) cc_final: 0.8204 (mtt180) REVERT: A 241 ARG cc_start: 0.8481 (mmp80) cc_final: 0.8133 (mtm-85) REVERT: A 272 THR cc_start: 0.7112 (t) cc_final: 0.6664 (p) REVERT: A 321 GLN cc_start: 0.8250 (mp10) cc_final: 0.7951 (mp10) REVERT: A 324 LEU cc_start: 0.8503 (mt) cc_final: 0.7375 (mt) REVERT: A 335 GLN cc_start: 0.7591 (mp10) cc_final: 0.7188 (mp10) REVERT: A 337 ARG cc_start: 0.7879 (mmp80) cc_final: 0.7017 (mmm160) REVERT: A 340 MET cc_start: 0.7873 (ptm) cc_final: 0.7134 (ptm) REVERT: A 373 LYS cc_start: 0.8168 (mttm) cc_final: 0.7917 (mttm) REVERT: A 398 GLU cc_start: 0.7737 (mp0) cc_final: 0.7474 (mp0) REVERT: A 424 ARG cc_start: 0.7905 (tpt-90) cc_final: 0.7271 (tpt-90) REVERT: A 439 CYS cc_start: 0.6899 (m) cc_final: 0.6692 (m) REVERT: A 440 ARG cc_start: 0.7663 (ttt90) cc_final: 0.6975 (tpt170) REVERT: A 441 LYS cc_start: 0.8362 (ptmm) cc_final: 0.8151 (ptmm) REVERT: A 460 MET cc_start: 0.6300 (mmp) cc_final: 0.5824 (mmt) REVERT: A 464 TYR cc_start: 0.7145 (t80) cc_final: 0.6824 (t80) REVERT: A 491 LEU cc_start: 0.8356 (mt) cc_final: 0.7781 (mt) REVERT: A 537 LEU cc_start: 0.7813 (tp) cc_final: 0.6773 (tp) REVERT: A 541 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 542 MET cc_start: 0.7205 (mmp) cc_final: 0.6829 (mmp) REVERT: A 576 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 580 GLU cc_start: 0.8330 (tp30) cc_final: 0.8098 (mm-30) REVERT: A 597 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8448 (mmmt) REVERT: A 619 LEU cc_start: 0.8855 (tp) cc_final: 0.8481 (tp) REVERT: A 629 LEU cc_start: 0.7814 (mt) cc_final: 0.7611 (mp) REVERT: A 635 MET cc_start: 0.7791 (mpp) cc_final: 0.7207 (mpp) REVERT: A 640 LYS cc_start: 0.8278 (mttt) cc_final: 0.7968 (mttt) REVERT: A 651 LEU cc_start: 0.8287 (tp) cc_final: 0.7991 (tp) REVERT: A 659 TYR cc_start: 0.8023 (t80) cc_final: 0.7552 (t80) REVERT: A 663 LYS cc_start: 0.8425 (ptmm) cc_final: 0.7882 (mtmm) REVERT: A 694 TYR cc_start: 0.5611 (t80) cc_final: 0.4722 (t80) REVERT: A 720 TYR cc_start: 0.7614 (t80) cc_final: 0.6948 (t80) REVERT: A 730 PHE cc_start: 0.7986 (t80) cc_final: 0.7702 (t80) REVERT: A 742 ASN cc_start: 0.8174 (p0) cc_final: 0.7784 (p0) REVERT: A 756 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 801 GLN cc_start: 0.7959 (mt0) cc_final: 0.7682 (mt0) REVERT: A 807 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7515 (mm-40) REVERT: B 18 LYS cc_start: 0.8272 (mttt) cc_final: 0.7955 (mttt) REVERT: B 25 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7519 (mt-10) REVERT: B 52 PHE cc_start: 0.6620 (t80) cc_final: 0.6318 (t80) REVERT: B 55 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7458 (mmt90) REVERT: B 58 CYS cc_start: 0.6662 (t) cc_final: 0.5896 (t) REVERT: B 59 ILE cc_start: 0.6538 (mm) cc_final: 0.6001 (mm) REVERT: B 124 ARG cc_start: 0.8189 (tpt170) cc_final: 0.7631 (tpt170) REVERT: B 133 HIS cc_start: 0.7190 (m-70) cc_final: 0.6921 (m-70) REVERT: C 138 GLU cc_start: 0.7793 (tp30) cc_final: 0.7356 (mp0) REVERT: C 241 ARG cc_start: 0.8218 (mmp80) cc_final: 0.7978 (mmp80) REVERT: C 313 MET cc_start: 0.7530 (mmm) cc_final: 0.6907 (tpp) REVERT: C 324 LEU cc_start: 0.8557 (mt) cc_final: 0.7413 (mt) REVERT: C 334 ASP cc_start: 0.7789 (p0) cc_final: 0.6626 (p0) REVERT: C 335 GLN cc_start: 0.8123 (mm110) cc_final: 0.7352 (mm110) REVERT: C 344 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7671 (tp-100) REVERT: C 345 GLN cc_start: 0.7685 (mt0) cc_final: 0.6957 (mt0) REVERT: C 373 LYS cc_start: 0.7934 (ttmm) cc_final: 0.7604 (tptp) REVERT: C 389 ASP cc_start: 0.7706 (p0) cc_final: 0.7481 (p0) REVERT: C 392 HIS cc_start: 0.7680 (m-70) cc_final: 0.7364 (m-70) REVERT: C 406 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6914 (tm-30) REVERT: C 456 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7458 (pp20) REVERT: C 464 TYR cc_start: 0.7382 (t80) cc_final: 0.6762 (t80) REVERT: C 473 ASN cc_start: 0.8434 (m110) cc_final: 0.8016 (m110) REVERT: C 478 MET cc_start: 0.7696 (tpp) cc_final: 0.7032 (tpp) REVERT: C 491 LEU cc_start: 0.8546 (mt) cc_final: 0.8318 (mt) REVERT: C 494 TYR cc_start: 0.7687 (t80) cc_final: 0.7401 (t80) REVERT: C 507 ILE cc_start: 0.8596 (tp) cc_final: 0.8301 (tp) REVERT: C 539 ARG cc_start: 0.8403 (tpp80) cc_final: 0.7791 (ttm170) REVERT: C 542 MET cc_start: 0.7504 (mmt) cc_final: 0.7001 (mmt) REVERT: C 576 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7512 (tm-30) REVERT: C 580 GLU cc_start: 0.8462 (tp30) cc_final: 0.8018 (mm-30) REVERT: C 589 MET cc_start: 0.4290 (ttm) cc_final: 0.3868 (ttm) REVERT: C 597 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8886 (mtpp) REVERT: C 607 GLU cc_start: 0.8340 (pm20) cc_final: 0.7948 (pm20) REVERT: C 635 MET cc_start: 0.8004 (mpp) cc_final: 0.7357 (mpp) REVERT: C 639 ARG cc_start: 0.8623 (tpt-90) cc_final: 0.7859 (tpt-90) REVERT: C 640 LYS cc_start: 0.8485 (mtmt) cc_final: 0.7916 (mtmt) REVERT: C 644 LYS cc_start: 0.5684 (mmmt) cc_final: 0.4464 (mmmt) REVERT: C 648 PHE cc_start: 0.7223 (t80) cc_final: 0.6848 (t80) REVERT: C 651 LEU cc_start: 0.8343 (tp) cc_final: 0.7926 (tp) REVERT: C 659 TYR cc_start: 0.8215 (t80) cc_final: 0.7748 (t80) REVERT: C 663 LYS cc_start: 0.8681 (ptmm) cc_final: 0.8169 (ptpp) REVERT: C 684 GLN cc_start: 0.7932 (tp40) cc_final: 0.6872 (tm-30) REVERT: C 692 MET cc_start: 0.7546 (tmm) cc_final: 0.7046 (tmm) REVERT: C 694 TYR cc_start: 0.6213 (t80) cc_final: 0.5393 (t80) REVERT: C 720 TYR cc_start: 0.7789 (t80) cc_final: 0.7359 (t80) REVERT: C 730 PHE cc_start: 0.7962 (t80) cc_final: 0.7479 (t80) REVERT: C 739 MET cc_start: 0.8183 (ttm) cc_final: 0.7852 (ttm) REVERT: C 742 ASN cc_start: 0.8415 (p0) cc_final: 0.7924 (p0) REVERT: C 751 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7639 (tpp-160) REVERT: C 754 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 801 GLN cc_start: 0.7647 (mt0) cc_final: 0.7261 (mt0) REVERT: C 807 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7569 (mm110) REVERT: C 861 ARG cc_start: 0.6756 (ptp-110) cc_final: 0.6338 (mtp85) REVERT: D 25 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7417 (mt-10) REVERT: D 52 PHE cc_start: 0.7191 (t80) cc_final: 0.6930 (t80) REVERT: D 58 CYS cc_start: 0.6469 (t) cc_final: 0.5792 (t) REVERT: D 59 ILE cc_start: 0.6419 (mm) cc_final: 0.6058 (mm) REVERT: D 74 LEU cc_start: 0.7987 (tp) cc_final: 0.7779 (tp) REVERT: D 124 ARG cc_start: 0.8582 (tpt170) cc_final: 0.7838 (tpt90) REVERT: D 133 HIS cc_start: 0.7261 (m-70) cc_final: 0.6939 (m-70) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3218 time to fit residues: 170.7893 Evaluate side-chains 363 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 118 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.160265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.129450 restraints weight = 28030.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.134495 restraints weight = 19356.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.138357 restraints weight = 14317.470| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12590 Z= 0.124 Angle : 0.679 9.794 16980 Z= 0.339 Chirality : 0.045 0.239 1912 Planarity : 0.005 0.049 2186 Dihedral : 4.745 25.845 1688 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.21), residues: 1496 helix: -1.48 (0.18), residues: 728 sheet: -1.09 (0.71), residues: 40 loop : -1.23 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 791 HIS 0.003 0.001 HIS A 632 PHE 0.029 0.002 PHE A 633 TYR 0.015 0.001 TYR A 495 ARG 0.008 0.001 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 334) hydrogen bonds : angle 5.92640 ( 960) metal coordination : bond 0.00312 ( 10) covalent geometry : bond 0.00280 (12580) covalent geometry : angle 0.67903 (16980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.05 seconds wall clock time: 89 minutes 24.19 seconds (5364.19 seconds total)