Starting phenix.real_space_refine on Fri Jun 27 12:40:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y13_38824/06_2025/8y13_38824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y13_38824/06_2025/8y13_38824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y13_38824/06_2025/8y13_38824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y13_38824/06_2025/8y13_38824.map" model { file = "/net/cci-nas-00/data/ceres_data/8y13_38824/06_2025/8y13_38824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y13_38824/06_2025/8y13_38824.cif" } resolution = 3.18 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= 0.010 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 20558 2.51 5 N 5114 2.21 5 O 5944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31740 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 946, 7893 Classifications: {'peptide': 946} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 926} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7978 Classifications: {'peptide': 956} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 936} Chain breaks: 4 Chain: "C" Number of atoms: 7893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 946, 7893 Classifications: {'peptide': 946} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 926} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 7976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 956, 7976 Classifications: {'peptide': 956} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 936} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 21.23, per 1000 atoms: 0.67 Number of scatterers: 31740 At special positions: 0 Unit cell: (103.96, 124.2, 275.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 5944 8.00 N 5114 7.00 C 20558 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: 8.54 Conformation dependent library (CDL) restraints added in 4.3 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7272 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 12 sheets defined 68.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.654A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.848A pdb=" N SER A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 4.002A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.712A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 removed outlier: 4.241A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 254 through 265 Processing helix chain 'A' and resid 281 through 298 Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.548A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.657A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 445 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 468 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 523 through 529 removed outlier: 3.641A pdb=" N LEU A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 529' Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.587A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.547A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 626 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.710A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 removed outlier: 3.721A pdb=" N LYS A 675 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 676 " --> pdb=" O ILE A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 676' Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.723A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 750 through 763 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.692A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 3.556A pdb=" N SER A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 878 through 898 Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 937 through 944 removed outlier: 3.904A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 removed outlier: 3.880A pdb=" N LEU A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 974 through 990 Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 7 through 21 Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.654A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.848A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 4.001A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.712A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 removed outlier: 4.241A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 281 through 298 Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.547A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.656A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 493 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 523 through 529 removed outlier: 3.641A pdb=" N LEU B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 529' Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.587A pdb=" N ASN B 598 " --> pdb=" O PHE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.546A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 629 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 removed outlier: 3.709A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.722A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.724A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 763 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.692A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.555A pdb=" N SER B 821 " --> pdb=" O SER B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 840 Processing helix chain 'B' and resid 846 through 855 Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 878 through 898 Processing helix chain 'B' and resid 913 through 922 Processing helix chain 'B' and resid 929 through 933 Processing helix chain 'B' and resid 937 through 944 removed outlier: 3.904A pdb=" N ASP B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 removed outlier: 3.879A pdb=" N LEU B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 971 Processing helix chain 'B' and resid 974 through 990 Processing helix chain 'B' and resid 994 through 1003 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 23 through 39 removed outlier: 3.654A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 54 removed outlier: 3.848A pdb=" N SER C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 4.002A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.712A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 122 removed outlier: 4.240A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 222 through 235 Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 304 through 317 removed outlier: 3.548A pdb=" N VAL C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 366 through 372 Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 417 through 426 removed outlier: 3.657A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 445 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 468 through 493 Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 523 through 529 removed outlier: 3.641A pdb=" N LEU C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 523 through 529' Processing helix chain 'C' and resid 540 through 546 Processing helix chain 'C' and resid 551 through 562 Processing helix chain 'C' and resid 579 through 598 removed outlier: 3.586A pdb=" N ASN C 598 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.546A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 626 Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 removed outlier: 3.710A pdb=" N ILE C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 676 removed outlier: 3.722A pdb=" N LYS C 675 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 676 " --> pdb=" O ILE C 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 672 through 676' Processing helix chain 'C' and resid 680 through 701 removed outlier: 3.724A pdb=" N ALA C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 723 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 743 Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 800 through 812 removed outlier: 3.691A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.557A pdb=" N SER C 821 " --> pdb=" O SER C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 840 Processing helix chain 'C' and resid 846 through 855 Processing helix chain 'C' and resid 863 through 868 Processing helix chain 'C' and resid 878 through 898 Processing helix chain 'C' and resid 912 through 922 Processing helix chain 'C' and resid 929 through 933 Processing helix chain 'C' and resid 937 through 944 removed outlier: 3.905A pdb=" N ASP C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 961 removed outlier: 3.879A pdb=" N LEU C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 971 Processing helix chain 'C' and resid 974 through 990 Processing helix chain 'C' and resid 994 through 1003 Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 23 through 39 removed outlier: 3.654A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 3.848A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 4.001A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.712A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 122 removed outlier: 4.241A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 281 through 298 Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.547A pdb=" N VAL D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 372 Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 417 through 426 removed outlier: 3.656A pdb=" N MET D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 468 through 493 Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 523 through 529 removed outlier: 3.642A pdb=" N LEU D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 529' Processing helix chain 'D' and resid 540 through 546 Processing helix chain 'D' and resid 551 through 562 Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.587A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 604 removed outlier: 3.546A pdb=" N VAL D 603 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 629 Processing helix chain 'D' and resid 648 through 659 Processing helix chain 'D' and resid 660 through 671 removed outlier: 3.710A pdb=" N ILE D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 676 removed outlier: 3.722A pdb=" N LYS D 675 " --> pdb=" O SER D 672 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 676 " --> pdb=" O ILE D 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 672 through 676' Processing helix chain 'D' and resid 680 through 701 removed outlier: 3.723A pdb=" N ALA D 701 " --> pdb=" O LYS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 723 Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 750 through 763 Processing helix chain 'D' and resid 768 through 786 Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.692A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 825 removed outlier: 3.555A pdb=" N SER D 821 " --> pdb=" O SER D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 840 Processing helix chain 'D' and resid 846 through 855 Processing helix chain 'D' and resid 863 through 868 Processing helix chain 'D' and resid 878 through 898 Processing helix chain 'D' and resid 913 through 922 Processing helix chain 'D' and resid 929 through 933 Processing helix chain 'D' and resid 937 through 944 removed outlier: 3.904A pdb=" N ASP D 941 " --> pdb=" O ASP D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 961 removed outlier: 3.880A pdb=" N LEU D 959 " --> pdb=" O ILE D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 971 Processing helix chain 'D' and resid 974 through 990 Processing helix chain 'D' and resid 994 through 1003 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.907A pdb=" N HIS A 128 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 44 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 341 Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.906A pdb=" N HIS B 128 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 44 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AA7, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.907A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 44 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 213 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 246 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE C 215 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 152 Processing sheet with id=AA9, first strand: chain 'C' and resid 338 through 341 Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.907A pdb=" N HIS D 128 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 44 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 150 through 152 Processing sheet with id=AB3, first strand: chain 'D' and resid 338 through 341 1697 hydrogen bonds defined for protein. 4971 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: 14.60 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7419 1.33 - 1.45: 7401 1.45 - 1.57: 17432 1.57 - 1.69: 4 1.69 - 1.81: 208 Bond restraints: 32464 Sorted by residual: bond pdb=" N VAL A 110 " pdb=" CA VAL A 110 " ideal model delta sigma weight residual 1.459 1.412 0.047 1.19e-02 7.06e+03 1.54e+01 bond pdb=" CA ASN B 563 " pdb=" CB ASN B 563 " ideal model delta sigma weight residual 1.524 1.573 -0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" CA ASN A 563 " pdb=" CB ASN A 563 " ideal model delta sigma weight residual 1.524 1.572 -0.049 1.30e-02 5.92e+03 1.41e+01 bond pdb=" CA ASN C 563 " pdb=" CB ASN C 563 " ideal model delta sigma weight residual 1.524 1.572 -0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" CA ASN D 563 " pdb=" CB ASN D 563 " ideal model delta sigma weight residual 1.524 1.572 -0.049 1.30e-02 5.92e+03 1.40e+01 ... (remaining 32459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 42839 3.24 - 6.48: 797 6.48 - 9.72: 66 9.72 - 12.95: 13 12.95 - 16.19: 20 Bond angle restraints: 43735 Sorted by residual: angle pdb=" CA ASN B 563 " pdb=" CB ASN B 563 " pdb=" CG ASN B 563 " ideal model delta sigma weight residual 112.60 118.73 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" CA ASN C 563 " pdb=" CB ASN C 563 " pdb=" CG ASN C 563 " ideal model delta sigma weight residual 112.60 118.72 -6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" CA ASN D 563 " pdb=" CB ASN D 563 " pdb=" CG ASN D 563 " ideal model delta sigma weight residual 112.60 118.67 -6.07 1.00e+00 1.00e+00 3.69e+01 angle pdb=" CA ASN A 563 " pdb=" CB ASN A 563 " pdb=" CG ASN A 563 " ideal model delta sigma weight residual 112.60 118.67 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" C VAL C 565 " pdb=" N ARG C 566 " pdb=" CA ARG C 566 " ideal model delta sigma weight residual 121.70 132.33 -10.63 1.80e+00 3.09e-01 3.49e+01 ... (remaining 43730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 17776 15.41 - 30.82: 1213 30.82 - 46.23: 355 46.23 - 61.64: 17 61.64 - 77.05: 8 Dihedral angle restraints: 19369 sinusoidal: 8063 harmonic: 11306 Sorted by residual: dihedral pdb=" CA ASN D 563 " pdb=" C ASN D 563 " pdb=" N LYS D 564 " pdb=" CA LYS D 564 " ideal model delta harmonic sigma weight residual -180.00 -127.22 -52.78 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ASN B 563 " pdb=" C ASN B 563 " pdb=" N LYS B 564 " pdb=" CA LYS B 564 " ideal model delta harmonic sigma weight residual -180.00 -127.24 -52.76 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ASN C 563 " pdb=" C ASN C 563 " pdb=" N LYS C 564 " pdb=" CA LYS C 564 " ideal model delta harmonic sigma weight residual -180.00 -127.27 -52.73 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 19366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4041 0.086 - 0.173: 553 0.173 - 0.259: 39 0.259 - 0.346: 12 0.346 - 0.432: 4 Chirality restraints: 4649 Sorted by residual: chirality pdb=" CB VAL B 980 " pdb=" CA VAL B 980 " pdb=" CG1 VAL B 980 " pdb=" CG2 VAL B 980 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CB VAL A 980 " pdb=" CA VAL A 980 " pdb=" CG1 VAL A 980 " pdb=" CG2 VAL A 980 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CB VAL D 980 " pdb=" CA VAL D 980 " pdb=" CG1 VAL D 980 " pdb=" CG2 VAL D 980 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 4646 not shown) Planarity restraints: 5576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 565 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C VAL C 565 " 0.079 2.00e-02 2.50e+03 pdb=" O VAL C 565 " -0.030 2.00e-02 2.50e+03 pdb=" N ARG C 566 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 565 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C VAL A 565 " -0.079 2.00e-02 2.50e+03 pdb=" O VAL A 565 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG A 566 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 222 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C ASP C 222 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP C 222 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR C 223 " -0.017 2.00e-02 2.50e+03 ... (remaining 5573 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2746 2.73 - 3.27: 32430 3.27 - 3.82: 53727 3.82 - 4.36: 67850 4.36 - 4.90: 110429 Nonbonded interactions: 267182 Sorted by model distance: nonbonded pdb=" OG1 THR A 257 " pdb=" OH TYR C 71 " model vdw 2.188 3.040 nonbonded pdb=" O MET C 930 " pdb=" OH TYR C 940 " model vdw 2.224 3.040 nonbonded pdb=" O MET D 930 " pdb=" OH TYR D 940 " model vdw 2.224 3.040 nonbonded pdb=" O MET B 930 " pdb=" OH TYR B 940 " model vdw 2.225 3.040 nonbonded pdb=" O MET A 930 " pdb=" OH TYR A 940 " model vdw 2.225 3.040 ... (remaining 267177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 109 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 111 through 493 or resid 504 through 565 or \ resid 578 through 898 or resid 912 through 1005)) selection = (chain 'B' and (resid 12 through 109 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 111 through 493 or resid 504 through 565 or \ resid 578 through 626 or resid 644 through 986 or (resid 987 and (name N or nam \ e CA or name C or name O or name CB )) or resid 988 through 1005)) selection = (chain 'C' and (resid 12 through 109 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 111 through 493 or resid 504 through 565 or \ resid 578 through 898 or resid 912 through 1005)) selection = (chain 'D' and (resid 12 through 493 or resid 504 through 565 or resid 578 throu \ gh 626 or resid 644 through 986 or (resid 987 and (name N or name CA or name C o \ r name O or name CB )) or resid 988 through 1005)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.450 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 77.920 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 32464 Z= 0.365 Angle : 1.132 16.192 43735 Z= 0.630 Chirality : 0.061 0.432 4649 Planarity : 0.007 0.056 5576 Dihedral : 11.389 77.047 12097 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.44 % Favored : 92.32 % Rotamer: Outliers : 0.34 % Allowed : 5.15 % Favored : 94.51 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.81 % 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: -4.66 (0.10), residues: 3764 helix: -2.95 (0.07), residues: 2434 sheet: -4.62 (0.55), residues: 20 loop : -2.99 (0.15), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP D 601 HIS 0.011 0.003 HIS A 128 PHE 0.040 0.004 PHE D 722 TYR 0.033 0.004 TYR B 197 ARG 0.017 0.001 ARG D 587 Details of bonding type rmsd hydrogen bonds : bond 0.14751 ( 1697) hydrogen bonds : angle 9.53277 ( 4971) covalent geometry : bond 0.00807 (32464) covalent geometry : angle 1.13236 (43735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 542 time to evaluate : 4.036 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: A 50 VAL cc_start: 0.4659 (t) cc_final: 0.4432 (p) REVERT: A 56 TYR cc_start: 0.2317 (t80) cc_final: -0.0584 (t80) REVERT: A 100 PHE cc_start: 0.4615 (t80) cc_final: 0.4328 (t80) REVERT: A 231 TRP cc_start: 0.1097 (t60) cc_final: 0.0848 (t-100) REVERT: A 557 LYS cc_start: 0.2927 (ttmt) cc_final: 0.2287 (mmtp) REVERT: A 704 MET cc_start: 0.0847 (mmt) cc_final: 0.0532 (mmt) REVERT: A 775 ILE cc_start: 0.5465 (mt) cc_final: 0.5211 (mt) REVERT: A 781 LEU cc_start: 0.6472 (mm) cc_final: 0.6043 (tp) REVERT: A 936 MET cc_start: -0.3593 (mpp) cc_final: -0.4243 (ttm) REVERT: A 965 LYS cc_start: 0.7134 (tppt) cc_final: 0.6865 (mtmm) REVERT: A 975 HIS cc_start: 0.6987 (m170) cc_final: 0.6164 (m-70) REVERT: A 976 MET cc_start: -0.1411 (mpt) cc_final: -0.1698 (mtt) REVERT: B 667 LEU cc_start: 0.8570 (mp) cc_final: 0.8342 (mp) REVERT: B 742 PHE cc_start: 0.8058 (m-80) cc_final: 0.7165 (m-80) REVERT: B 781 LEU cc_start: 0.8365 (mm) cc_final: 0.8136 (mm) REVERT: B 815 PHE cc_start: 0.8058 (t80) cc_final: 0.7722 (t80) REVERT: C 21 MET cc_start: 0.7061 (ttm) cc_final: 0.6771 (ttp) REVERT: C 117 ILE cc_start: 0.2776 (pp) cc_final: 0.2560 (pt) REVERT: C 585 LEU cc_start: 0.4040 (OUTLIER) cc_final: 0.3777 (pp) REVERT: C 647 MET cc_start: 0.0926 (mtp) cc_final: 0.0597 (ttm) REVERT: C 810 HIS cc_start: 0.6991 (t-90) cc_final: 0.6606 (t-90) REVERT: C 818 LYS cc_start: 0.7414 (mptm) cc_final: 0.7145 (tppt) REVERT: C 913 MET cc_start: -0.1505 (tpt) cc_final: -0.2336 (mtt) REVERT: C 1003 TYR cc_start: 0.3838 (m-80) cc_final: 0.3562 (m-80) REVERT: D 733 LEU cc_start: 0.8669 (tt) cc_final: 0.8456 (tp) REVERT: D 738 LYS cc_start: 0.8429 (tttt) cc_final: 0.7913 (ttpt) REVERT: D 781 LEU cc_start: 0.8430 (mm) cc_final: 0.8109 (tt) REVERT: D 870 ARG cc_start: 0.6390 (tpm170) cc_final: 0.5129 (mmm160) REVERT: D 913 MET cc_start: -0.2685 (tpt) cc_final: -0.3641 (mmm) REVERT: D 974 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7863 (mmtp) outliers start: 12 outliers final: 3 residues processed: 552 average time/residue: 0.5141 time to fit residues: 440.0797 Evaluate side-chains 314 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 310 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 741 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.9990 chunk 286 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 343 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 93 ASN A 226 ASN A 391 ASN A 475 GLN A 521 ASN A 536 GLN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN A 658 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 765 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 HIS A 910 ASN A 975 HIS A 979 HIS B 93 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 391 ASN B 475 GLN B 487 GLN B 536 GLN ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN B 698 GLN B 705 ASN B 765 ASN B 810 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN C 391 ASN C 467 ASN C 475 GLN C 536 GLN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN ** C 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN C 765 ASN C 975 HIS C 990 ASN D 226 ASN D 391 ASN D 475 GLN D 536 GLN ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN D 610 GLN D 614 ASN D 698 GLN D 705 ASN D 765 ASN D 789 GLN D 852 HIS ** D 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.162310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.142970 restraints weight = 125809.375| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 3.97 r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5780 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32464 Z= 0.157 Angle : 0.669 13.651 43735 Z= 0.358 Chirality : 0.044 0.262 4649 Planarity : 0.005 0.061 5576 Dihedral : 6.020 48.330 4192 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 1.77 % Allowed : 9.44 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.63 (0.12), residues: 3764 helix: -1.06 (0.09), residues: 2480 sheet: -4.06 (0.36), residues: 108 loop : -2.78 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 448 HIS 0.022 0.002 HIS D 852 PHE 0.025 0.002 PHE B 45 TYR 0.022 0.002 TYR A 755 ARG 0.005 0.001 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 1697) hydrogen bonds : angle 5.74500 ( 4971) covalent geometry : bond 0.00339 (32464) covalent geometry : angle 0.66890 (43735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 345 time to evaluate : 5.245 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: A 35 GLU cc_start: 0.6284 (tp30) cc_final: 0.5721 (tt0) REVERT: A 85 LEU cc_start: 0.6597 (tp) cc_final: 0.6384 (pp) REVERT: A 139 ASP cc_start: 0.1987 (OUTLIER) cc_final: 0.0539 (m-30) REVERT: A 231 TRP cc_start: 0.1764 (t60) cc_final: 0.0886 (m-10) REVERT: A 307 GLU cc_start: 0.5553 (tp30) cc_final: 0.5103 (pt0) REVERT: A 473 LEU cc_start: 0.4920 (mp) cc_final: 0.4283 (mt) REVERT: A 531 MET cc_start: -0.2578 (mmt) cc_final: -0.2796 (mmm) REVERT: A 694 GLU cc_start: 0.2211 (tp30) cc_final: 0.1628 (tp30) REVERT: A 825 LEU cc_start: 0.4675 (pp) cc_final: 0.4177 (tt) REVERT: A 936 MET cc_start: -0.3443 (mpp) cc_final: -0.5025 (ttm) REVERT: B 204 MET cc_start: 0.8260 (ttm) cc_final: 0.7854 (ttm) REVERT: B 781 LEU cc_start: 0.8370 (mm) cc_final: 0.8168 (mm) REVERT: B 804 TYR cc_start: 0.7174 (m-80) cc_final: 0.6713 (m-80) REVERT: B 842 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7727 (tt) REVERT: B 930 MET cc_start: 0.1228 (tpt) cc_final: 0.0797 (mtt) REVERT: B 936 MET cc_start: 0.3099 (OUTLIER) cc_final: 0.2501 (ptm) REVERT: C 21 MET cc_start: 0.7274 (ttm) cc_final: 0.6636 (ppp) REVERT: C 607 GLU cc_start: 0.5384 (tt0) cc_final: 0.5104 (mt-10) REVERT: C 612 ILE cc_start: 0.5702 (mm) cc_final: 0.5282 (mm) REVERT: C 658 HIS cc_start: 0.4246 (m-70) cc_final: 0.2840 (m-70) REVERT: C 711 GLN cc_start: 0.7358 (mt0) cc_final: 0.6758 (tm-30) REVERT: C 742 PHE cc_start: 0.4248 (OUTLIER) cc_final: 0.3284 (m-80) REVERT: C 774 ILE cc_start: 0.8633 (mm) cc_final: 0.8262 (tp) REVERT: C 913 MET cc_start: -0.1918 (tpt) cc_final: -0.2884 (mtt) REVERT: C 976 MET cc_start: 0.2702 (mpt) cc_final: 0.2355 (mpt) REVERT: C 1001 MET cc_start: 0.4548 (ttm) cc_final: 0.4304 (ttp) REVERT: D 60 TRP cc_start: 0.5762 (t60) cc_final: 0.5468 (t60) REVERT: D 227 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7170 (mmp) REVERT: D 755 TYR cc_start: 0.8373 (t80) cc_final: 0.8170 (t80) REVERT: D 781 LEU cc_start: 0.8438 (mm) cc_final: 0.8012 (tt) REVERT: D 870 ARG cc_start: 0.5708 (tpm170) cc_final: 0.5236 (tpt170) REVERT: D 913 MET cc_start: -0.3236 (tpt) cc_final: -0.3494 (ptt) outliers start: 62 outliers final: 25 residues processed: 393 average time/residue: 0.5287 time to fit residues: 329.2452 Evaluate side-chains 283 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 444 CYS Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 878 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 284 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 180 optimal weight: 0.0170 chunk 150 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 244 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 269 optimal weight: 8.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 343 ASN A 614 ASN A 698 GLN A 786 HIS A 810 HIS ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 ASN ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS D 563 ASN ** D 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.155551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.135828 restraints weight = 123068.282| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 3.74 r_work: 0.4296 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32464 Z= 0.143 Angle : 0.616 9.088 43735 Z= 0.327 Chirality : 0.043 0.218 4649 Planarity : 0.004 0.058 5576 Dihedral : 5.486 46.405 4188 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.86 % Allowed : 11.18 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3764 helix: -0.15 (0.10), residues: 2460 sheet: -3.69 (0.38), residues: 106 loop : -2.60 (0.16), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 448 HIS 0.010 0.001 HIS C 978 PHE 0.020 0.002 PHE B 559 TYR 0.032 0.002 TYR C1003 ARG 0.006 0.001 ARG D 10 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 1697) hydrogen bonds : angle 5.15775 ( 4971) covalent geometry : bond 0.00313 (32464) covalent geometry : angle 0.61628 (43735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 3.542 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: A 35 GLU cc_start: 0.6318 (tp30) cc_final: 0.5906 (tt0) REVERT: A 85 LEU cc_start: 0.6161 (tp) cc_final: 0.5757 (pp) REVERT: A 155 GLU cc_start: 0.0933 (OUTLIER) cc_final: -0.2978 (pm20) REVERT: A 204 MET cc_start: 0.2458 (mtp) cc_final: 0.1500 (ttt) REVERT: A 231 TRP cc_start: 0.2143 (t60) cc_final: 0.1644 (t-100) REVERT: A 307 GLU cc_start: 0.6308 (tp30) cc_final: 0.5849 (pt0) REVERT: A 578 MET cc_start: 0.1979 (ttt) cc_final: -0.0460 (mtt) REVERT: A 647 MET cc_start: -0.1369 (ttm) cc_final: -0.1579 (tmm) REVERT: A 694 GLU cc_start: 0.2394 (tp30) cc_final: 0.1862 (tp30) REVERT: A 825 LEU cc_start: 0.4587 (pp) cc_final: 0.3886 (tt) REVERT: A 870 ARG cc_start: 0.6484 (tpm170) cc_final: 0.6170 (tpm170) REVERT: A 936 MET cc_start: -0.3367 (mpp) cc_final: -0.3859 (ttm) REVERT: B 290 MET cc_start: 0.8285 (mmm) cc_final: 0.8002 (mmm) REVERT: B 822 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7130 (tm-30) REVERT: B 842 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7830 (tt) REVERT: B 866 MET cc_start: 0.2556 (mmt) cc_final: 0.2066 (mmt) REVERT: B 930 MET cc_start: 0.1403 (tpt) cc_final: 0.0847 (mtt) REVERT: B 936 MET cc_start: 0.2671 (ptp) cc_final: 0.2466 (ptm) REVERT: C 21 MET cc_start: 0.7144 (ttm) cc_final: 0.6921 (ttp) REVERT: C 119 ASP cc_start: 0.5566 (m-30) cc_final: 0.4525 (t70) REVERT: C 290 MET cc_start: 0.7471 (mmt) cc_final: 0.7132 (mmt) REVERT: C 612 ILE cc_start: 0.6145 (mm) cc_final: 0.5891 (mm) REVERT: C 655 ILE cc_start: 0.6129 (mt) cc_final: 0.5791 (mt) REVERT: C 711 GLN cc_start: 0.7745 (mt0) cc_final: 0.7482 (mm-40) REVERT: C 774 ILE cc_start: 0.8892 (mm) cc_final: 0.8582 (tp) REVERT: C 850 LYS cc_start: 0.6519 (mttt) cc_final: 0.6295 (tmtt) REVERT: C 866 MET cc_start: 0.3515 (tpt) cc_final: 0.2996 (mmt) REVERT: C 913 MET cc_start: -0.1858 (tpt) cc_final: -0.2754 (mtt) REVERT: C 976 MET cc_start: 0.2494 (mpt) cc_final: 0.2044 (mpt) REVERT: D 98 MET cc_start: 0.4157 (pmm) cc_final: 0.3281 (pmm) REVERT: D 563 ASN cc_start: 0.4144 (OUTLIER) cc_final: 0.3813 (m-40) REVERT: D 578 MET cc_start: 0.4096 (ppp) cc_final: 0.3864 (ppp) REVERT: D 585 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7328 (tp) REVERT: D 755 TYR cc_start: 0.8365 (t80) cc_final: 0.8108 (t80) REVERT: D 781 LEU cc_start: 0.8498 (mm) cc_final: 0.8216 (tt) REVERT: D 870 ARG cc_start: 0.6455 (tpm170) cc_final: 0.5542 (tpt170) REVERT: D 913 MET cc_start: -0.2827 (tpt) cc_final: -0.4073 (mmm) outliers start: 65 outliers final: 32 residues processed: 343 average time/residue: 0.4452 time to fit residues: 243.4290 Evaluate side-chains 277 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 241 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 444 CYS Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 563 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 603 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 312 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 289 optimal weight: 0.0980 chunk 144 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 521 ASN ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN C 591 ASN ** D 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 GLN D 810 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.159740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.137291 restraints weight = 113388.576| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 3.48 r_work: 0.4300 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32464 Z= 0.136 Angle : 0.588 12.126 43735 Z= 0.312 Chirality : 0.042 0.235 4649 Planarity : 0.004 0.064 5576 Dihedral : 5.194 43.681 4186 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.46 % Allowed : 11.70 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3764 helix: 0.23 (0.10), residues: 2516 sheet: -3.69 (0.33), residues: 150 loop : -2.52 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 60 HIS 0.009 0.001 HIS D 978 PHE 0.027 0.001 PHE C 778 TYR 0.022 0.002 TYR A1003 ARG 0.006 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 1697) hydrogen bonds : angle 4.79764 ( 4971) covalent geometry : bond 0.00299 (32464) covalent geometry : angle 0.58768 (43735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 276 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.6423 (tp30) cc_final: 0.5911 (tt0) REVERT: A 139 ASP cc_start: 0.2035 (OUTLIER) cc_final: -0.0143 (m-30) REVERT: A 158 VAL cc_start: -0.1489 (OUTLIER) cc_final: -0.1813 (t) REVERT: A 189 ASP cc_start: 0.1858 (OUTLIER) cc_final: 0.0345 (t0) REVERT: A 231 TRP cc_start: 0.2150 (t60) cc_final: 0.1734 (t-100) REVERT: A 578 MET cc_start: 0.2354 (ttt) cc_final: -0.0304 (mtt) REVERT: A 616 MET cc_start: -0.0448 (mtm) cc_final: -0.1587 (mmp) REVERT: A 647 MET cc_start: -0.0022 (ttm) cc_final: -0.0411 (ttp) REVERT: A 694 GLU cc_start: 0.2245 (tp30) cc_final: 0.1673 (tp30) REVERT: A 825 LEU cc_start: 0.4913 (pp) cc_final: 0.4396 (tt) REVERT: A 870 ARG cc_start: 0.6345 (tpm170) cc_final: 0.6009 (tpm170) REVERT: A 936 MET cc_start: -0.3676 (mpp) cc_final: -0.5118 (ttm) REVERT: A 1001 MET cc_start: 0.5027 (ptm) cc_final: 0.4285 (mtt) REVERT: A 1004 PHE cc_start: 0.3258 (OUTLIER) cc_final: 0.2808 (m-10) REVERT: B 143 TRP cc_start: 0.6762 (t60) cc_final: 0.6443 (t60) REVERT: B 290 MET cc_start: 0.8327 (mmm) cc_final: 0.7917 (mmm) REVERT: B 487 GLN cc_start: 0.7204 (pt0) cc_final: 0.6938 (mt0) REVERT: B 646 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7245 (t80) REVERT: B 822 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7182 (tm-30) REVERT: B 842 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7790 (mp) REVERT: B 930 MET cc_start: 0.1640 (tpt) cc_final: 0.1041 (mtt) REVERT: B 936 MET cc_start: 0.2898 (OUTLIER) cc_final: 0.2592 (ptm) REVERT: C 119 ASP cc_start: 0.5666 (m-30) cc_final: 0.4749 (t70) REVERT: C 290 MET cc_start: 0.7844 (mmt) cc_final: 0.7607 (mmt) REVERT: C 482 TYR cc_start: 0.8141 (t80) cc_final: 0.7800 (t80) REVERT: C 578 MET cc_start: 0.2620 (ttm) cc_final: 0.1467 (tpt) REVERT: C 599 CYS cc_start: 0.7352 (m) cc_final: 0.7085 (m) REVERT: C 655 ILE cc_start: 0.6375 (mt) cc_final: 0.6083 (mt) REVERT: C 711 GLN cc_start: 0.7840 (mt0) cc_final: 0.7589 (mm-40) REVERT: C 850 LYS cc_start: 0.6678 (mttt) cc_final: 0.6451 (tmtt) REVERT: C 866 MET cc_start: 0.3780 (tpt) cc_final: 0.3535 (tpt) REVERT: C 913 MET cc_start: -0.1675 (tpt) cc_final: -0.2377 (mmm) REVERT: C 976 MET cc_start: 0.2127 (mpt) cc_final: 0.1843 (mpt) REVERT: D 98 MET cc_start: 0.4102 (pmm) cc_final: 0.3508 (pmm) REVERT: D 423 LYS cc_start: 0.9153 (tppt) cc_final: 0.8883 (tmmt) REVERT: D 510 GLU cc_start: 0.8489 (tp30) cc_final: 0.8268 (mm-30) REVERT: D 564 LYS cc_start: 0.5414 (mptt) cc_final: 0.4850 (mtpt) REVERT: D 755 TYR cc_start: 0.8385 (t80) cc_final: 0.8144 (t80) REVERT: D 781 LEU cc_start: 0.8468 (mm) cc_final: 0.8163 (tt) REVERT: D 870 ARG cc_start: 0.6582 (tpm170) cc_final: 0.5495 (tpt170) REVERT: D 913 MET cc_start: -0.2394 (tpt) cc_final: -0.3777 (mmm) REVERT: D 936 MET cc_start: 0.2324 (mmp) cc_final: 0.1476 (mmm) REVERT: D 976 MET cc_start: 0.6298 (ttt) cc_final: 0.6072 (ttm) REVERT: D 1001 MET cc_start: 0.4864 (tmm) cc_final: 0.4319 (tmm) outliers start: 86 outliers final: 43 residues processed: 345 average time/residue: 0.4619 time to fit residues: 255.6078 Evaluate side-chains 291 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 487 GLN Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 487 GLN Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 810 HIS Chi-restraints excluded: chain D residue 842 LEU Chi-restraints excluded: chain D residue 878 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 347 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 240 optimal weight: 0.3980 chunk 185 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 365 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 147 optimal weight: 0.0030 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 782 GLN A 832 GLN B 475 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 609 HIS D 58 GLN D 136 ASN D 211 HIS D 789 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.150618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.130194 restraints weight = 118856.921| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 3.23 r_work: 0.4241 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32464 Z= 0.171 Angle : 0.630 10.381 43735 Z= 0.333 Chirality : 0.043 0.230 4649 Planarity : 0.004 0.062 5576 Dihedral : 5.214 44.491 4186 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 2.43 % Allowed : 12.30 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3764 helix: 0.32 (0.10), residues: 2482 sheet: -3.30 (0.48), residues: 70 loop : -2.53 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 448 HIS 0.042 0.001 HIS D 810 PHE 0.038 0.002 PHE C 778 TYR 0.038 0.002 TYR D 721 ARG 0.008 0.001 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 1697) hydrogen bonds : angle 4.82757 ( 4971) covalent geometry : bond 0.00393 (32464) covalent geometry : angle 0.62980 (43735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 289 time to evaluate : 3.553 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: A 56 TYR cc_start: 0.4778 (t80) cc_final: 0.0835 (t80) REVERT: A 68 GLU cc_start: 0.4414 (OUTLIER) cc_final: 0.3993 (tt0) REVERT: A 139 ASP cc_start: 0.1739 (OUTLIER) cc_final: 0.0190 (m-30) REVERT: A 155 GLU cc_start: 0.0877 (OUTLIER) cc_final: -0.3404 (pt0) REVERT: A 158 VAL cc_start: -0.1078 (OUTLIER) cc_final: -0.1585 (t) REVERT: A 189 ASP cc_start: 0.2183 (OUTLIER) cc_final: -0.0606 (t0) REVERT: A 190 TYR cc_start: 0.4998 (m-80) cc_final: 0.4388 (m-10) REVERT: A 245 PHE cc_start: 0.5489 (t80) cc_final: 0.5085 (t80) REVERT: A 261 TYR cc_start: 0.1794 (OUTLIER) cc_final: -0.0886 (m-80) REVERT: A 487 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.6330 (mp10) REVERT: A 531 MET cc_start: -0.1606 (mtt) cc_final: -0.3143 (ttm) REVERT: A 578 MET cc_start: 0.2616 (ttt) cc_final: -0.0111 (mtt) REVERT: A 611 TYR cc_start: 0.1491 (t80) cc_final: 0.0894 (m-80) REVERT: A 647 MET cc_start: 0.0154 (ttm) cc_final: -0.0432 (ttp) REVERT: A 694 GLU cc_start: 0.2270 (tp30) cc_final: 0.1659 (tp30) REVERT: A 749 LEU cc_start: 0.0430 (OUTLIER) cc_final: 0.0108 (tt) REVERT: A 825 LEU cc_start: 0.4909 (pp) cc_final: 0.4420 (tt) REVERT: A 870 ARG cc_start: 0.6066 (tpm170) cc_final: 0.5734 (tpm170) REVERT: A 936 MET cc_start: -0.4024 (mpp) cc_final: -0.5006 (ttm) REVERT: A 967 LEU cc_start: 0.4302 (mp) cc_final: 0.3878 (mp) REVERT: A 1001 MET cc_start: 0.4997 (ptm) cc_final: 0.4083 (mtt) REVERT: B 525 ASP cc_start: 0.7888 (t0) cc_final: 0.7577 (t0) REVERT: B 722 PHE cc_start: 0.8706 (t80) cc_final: 0.8503 (t80) REVERT: B 747 ARG cc_start: 0.7587 (ptt180) cc_final: 0.7338 (ptm160) REVERT: B 822 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7174 (tm-30) REVERT: B 842 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7944 (mp) REVERT: B 866 MET cc_start: 0.3492 (mtt) cc_final: 0.2987 (mmp) REVERT: B 930 MET cc_start: 0.1816 (tpt) cc_final: 0.1135 (mtt) REVERT: B 936 MET cc_start: 0.2863 (OUTLIER) cc_final: 0.1807 (ptm) REVERT: C 66 TYR cc_start: 0.2359 (m-10) cc_final: 0.1989 (m-10) REVERT: C 119 ASP cc_start: 0.6126 (m-30) cc_final: 0.5474 (t70) REVERT: C 222 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6908 (m-30) REVERT: C 482 TYR cc_start: 0.8342 (t80) cc_final: 0.7844 (t80) REVERT: C 578 MET cc_start: 0.2374 (ttm) cc_final: 0.1560 (tpt) REVERT: C 655 ILE cc_start: 0.7321 (mt) cc_final: 0.6768 (mt) REVERT: C 913 MET cc_start: -0.1615 (tpt) cc_final: -0.2405 (mmm) REVERT: D 60 TRP cc_start: 0.5133 (t60) cc_final: 0.4891 (t60) REVERT: D 423 LYS cc_start: 0.9262 (tppt) cc_final: 0.8906 (tmmt) REVERT: D 564 LYS cc_start: 0.5912 (mptt) cc_final: 0.5576 (mtpt) REVERT: D 578 MET cc_start: 0.4730 (ppp) cc_final: 0.3936 (ppp) REVERT: D 582 ILE cc_start: 0.7369 (mm) cc_final: 0.7107 (mt) REVERT: D 755 TYR cc_start: 0.8310 (t80) cc_final: 0.8088 (t80) REVERT: D 781 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8213 (tt) REVERT: D 913 MET cc_start: -0.2927 (tpt) cc_final: -0.4127 (mmp) REVERT: D 936 MET cc_start: 0.1745 (mmp) cc_final: 0.1096 (mmm) outliers start: 85 outliers final: 46 residues processed: 353 average time/residue: 0.4503 time to fit residues: 258.6370 Evaluate side-chains 305 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 487 GLN Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 487 GLN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 842 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 152 optimal weight: 0.5980 chunk 243 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 261 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 348 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.150935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.131046 restraints weight = 119701.991| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 3.31 r_work: 0.4269 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32464 Z= 0.126 Angle : 0.580 11.274 43735 Z= 0.305 Chirality : 0.042 0.202 4649 Planarity : 0.004 0.066 5576 Dihedral : 4.957 45.107 4186 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.23 % Allowed : 13.33 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3764 helix: 0.54 (0.10), residues: 2498 sheet: -3.20 (0.41), residues: 108 loop : -2.47 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 448 HIS 0.008 0.001 HIS D 810 PHE 0.034 0.001 PHE C 778 TYR 0.032 0.001 TYR A 313 ARG 0.009 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 1697) hydrogen bonds : angle 4.62064 ( 4971) covalent geometry : bond 0.00277 (32464) covalent geometry : angle 0.58032 (43735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 280 time to evaluate : 5.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.4526 (t80) cc_final: 0.0791 (t80) REVERT: A 60 TRP cc_start: 0.6356 (p-90) cc_final: 0.5843 (p90) REVERT: A 61 ARG cc_start: 0.6414 (ttp80) cc_final: 0.5804 (ppt170) REVERT: A 68 GLU cc_start: 0.4387 (OUTLIER) cc_final: 0.4132 (pp20) REVERT: A 100 PHE cc_start: 0.6651 (t80) cc_final: 0.4468 (t80) REVERT: A 158 VAL cc_start: -0.0573 (OUTLIER) cc_final: -0.0881 (t) REVERT: A 189 ASP cc_start: 0.2419 (OUTLIER) cc_final: -0.0318 (t0) REVERT: A 190 TYR cc_start: 0.4646 (m-80) cc_final: 0.4266 (m-10) REVERT: A 389 GLU cc_start: 0.4488 (mm-30) cc_final: 0.4100 (mp0) REVERT: A 519 MET cc_start: 0.0303 (mmp) cc_final: -0.0584 (mmp) REVERT: A 531 MET cc_start: -0.1626 (mtt) cc_final: -0.3295 (ttt) REVERT: A 578 MET cc_start: 0.1971 (ttt) cc_final: -0.0383 (mtt) REVERT: A 611 TYR cc_start: 0.1577 (t80) cc_final: 0.1084 (m-10) REVERT: A 616 MET cc_start: -0.0515 (mtm) cc_final: -0.0864 (mmm) REVERT: A 694 GLU cc_start: 0.2874 (tp30) cc_final: 0.2239 (tp30) REVERT: A 708 PHE cc_start: 0.1772 (t80) cc_final: 0.1527 (t80) REVERT: A 749 LEU cc_start: 0.0164 (OUTLIER) cc_final: -0.0094 (tt) REVERT: A 825 LEU cc_start: 0.4379 (pp) cc_final: 0.4008 (tt) REVERT: A 870 ARG cc_start: 0.5941 (tpm170) cc_final: 0.5455 (ptp-170) REVERT: A 936 MET cc_start: -0.3975 (mpp) cc_final: -0.4500 (mmm) REVERT: A 967 LEU cc_start: 0.3933 (mp) cc_final: 0.3633 (mp) REVERT: A 1001 MET cc_start: 0.5164 (ptm) cc_final: 0.4244 (mtt) REVERT: B 525 ASP cc_start: 0.7838 (t0) cc_final: 0.7503 (t0) REVERT: B 646 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7378 (t80) REVERT: B 747 ARG cc_start: 0.7517 (ptt180) cc_final: 0.7278 (ptm160) REVERT: B 804 TYR cc_start: 0.7086 (m-80) cc_final: 0.6704 (m-80) REVERT: B 822 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7115 (tm-30) REVERT: B 930 MET cc_start: 0.1662 (tpt) cc_final: 0.1051 (mtt) REVERT: C 119 ASP cc_start: 0.6292 (m-30) cc_final: 0.5534 (t70) REVERT: C 222 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6815 (m-30) REVERT: C 482 TYR cc_start: 0.8221 (t80) cc_final: 0.7748 (t80) REVERT: C 578 MET cc_start: 0.1467 (ttm) cc_final: 0.0754 (tpt) REVERT: C 647 MET cc_start: 0.6137 (tpp) cc_final: 0.5714 (tpp) REVERT: C 651 ASP cc_start: 0.7775 (m-30) cc_final: 0.7412 (m-30) REVERT: C 837 PHE cc_start: 0.4687 (t80) cc_final: 0.4410 (t80) REVERT: C 866 MET cc_start: 0.4205 (tpt) cc_final: 0.3076 (mtt) REVERT: C 913 MET cc_start: -0.1741 (tpt) cc_final: -0.2361 (mmm) REVERT: D 60 TRP cc_start: 0.4793 (t60) cc_final: 0.4558 (t60) REVERT: D 578 MET cc_start: 0.4422 (ppp) cc_final: 0.3637 (ppp) REVERT: D 582 ILE cc_start: 0.7331 (mm) cc_final: 0.7092 (mt) REVERT: D 761 LEU cc_start: 0.8124 (tt) cc_final: 0.7865 (tp) REVERT: D 781 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8175 (tt) REVERT: D 819 ARG cc_start: 0.8309 (tpp-160) cc_final: 0.7340 (tpt90) REVERT: D 913 MET cc_start: -0.3291 (tpt) cc_final: -0.3691 (pmm) REVERT: D 936 MET cc_start: 0.1664 (mmp) cc_final: 0.1094 (mmm) outliers start: 78 outliers final: 44 residues processed: 339 average time/residue: 0.6140 time to fit residues: 341.5740 Evaluate side-chains 297 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 646 PHE Chi-restraints excluded: chain B residue 666 ASN Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 487 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 878 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 274 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 170 optimal weight: 0.0570 chunk 88 optimal weight: 7.9990 chunk 215 optimal weight: 0.6980 chunk 231 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 356 optimal weight: 6.9990 chunk 359 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS A 483 GLN A 606 HIS A 765 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 349 HIS B 666 ASN B 881 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN C 339 HIS ** C 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN D 666 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.150347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.129372 restraints weight = 112957.897| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.20 r_work: 0.4174 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.8278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 32464 Z= 0.213 Angle : 0.700 11.094 43735 Z= 0.368 Chirality : 0.046 0.349 4649 Planarity : 0.004 0.071 5576 Dihedral : 5.409 49.611 4186 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.72 % Favored : 93.20 % Rotamer: Outliers : 2.37 % Allowed : 13.87 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3764 helix: 0.28 (0.10), residues: 2448 sheet: -4.14 (0.39), residues: 100 loop : -2.38 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 448 HIS 0.008 0.001 HIS A 975 PHE 0.030 0.002 PHE C 778 TYR 0.030 0.002 TYR C 223 ARG 0.005 0.001 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1697) hydrogen bonds : angle 4.95957 ( 4971) covalent geometry : bond 0.00494 (32464) covalent geometry : angle 0.69972 (43735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 291 time to evaluate : 3.926 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: A 155 GLU cc_start: 0.1092 (OUTLIER) cc_final: -0.3564 (pm20) REVERT: A 158 VAL cc_start: 0.0390 (OUTLIER) cc_final: -0.0265 (p) REVERT: A 186 LYS cc_start: 0.3363 (OUTLIER) cc_final: 0.2966 (mtmm) REVERT: A 189 ASP cc_start: 0.2160 (OUTLIER) cc_final: 0.0656 (m-30) REVERT: A 190 TYR cc_start: 0.5187 (m-80) cc_final: 0.4736 (m-10) REVERT: A 245 PHE cc_start: 0.5895 (t80) cc_final: 0.5300 (t80) REVERT: A 261 TYR cc_start: 0.2504 (OUTLIER) cc_final: -0.0938 (m-80) REVERT: A 359 ARG cc_start: 0.4475 (tpm170) cc_final: 0.4020 (tpm170) REVERT: A 389 GLU cc_start: 0.5064 (mm-30) cc_final: 0.4841 (mp0) REVERT: A 519 MET cc_start: -0.0811 (mmp) cc_final: -0.1597 (mmp) REVERT: A 531 MET cc_start: -0.1859 (mtt) cc_final: -0.3340 (ttt) REVERT: A 578 MET cc_start: 0.2508 (ttt) cc_final: -0.0050 (mtt) REVERT: A 611 TYR cc_start: 0.1938 (t80) cc_final: 0.1461 (m-80) REVERT: A 614 ASN cc_start: 0.0904 (m110) cc_final: 0.0429 (t0) REVERT: A 694 GLU cc_start: 0.2584 (tp30) cc_final: 0.1963 (tp30) REVERT: A 721 TYR cc_start: 0.3023 (OUTLIER) cc_final: 0.2614 (m-10) REVERT: A 756 VAL cc_start: 0.0817 (t) cc_final: 0.0610 (p) REVERT: A 825 LEU cc_start: 0.3455 (pp) cc_final: 0.3240 (tt) REVERT: A 866 MET cc_start: 0.2679 (OUTLIER) cc_final: 0.1694 (mpp) REVERT: A 870 ARG cc_start: 0.6214 (tpm170) cc_final: 0.5774 (ptp-170) REVERT: A 936 MET cc_start: -0.4197 (mpp) cc_final: -0.5234 (ttm) REVERT: A 1001 MET cc_start: 0.5321 (ptm) cc_final: 0.4285 (mtt) REVERT: B 525 ASP cc_start: 0.7871 (t0) cc_final: 0.7661 (t0) REVERT: B 531 MET cc_start: 0.8879 (mmt) cc_final: 0.8557 (mmt) REVERT: B 722 PHE cc_start: 0.8715 (t80) cc_final: 0.8501 (t80) REVERT: B 744 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8692 (t80) REVERT: B 842 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 866 MET cc_start: 0.4630 (mtp) cc_final: 0.4188 (mmm) REVERT: B 919 TRP cc_start: 0.5714 (m-10) cc_final: 0.4970 (m-10) REVERT: B 930 MET cc_start: 0.1360 (tpt) cc_final: 0.0657 (mtt) REVERT: C 119 ASP cc_start: 0.7500 (m-30) cc_final: 0.6677 (t70) REVERT: C 190 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.7032 (t80) REVERT: C 222 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: C 309 ILE cc_start: 0.6480 (mm) cc_final: 0.6044 (mt) REVERT: C 482 TYR cc_start: 0.8283 (t80) cc_final: 0.7649 (t80) REVERT: C 578 MET cc_start: 0.1751 (ttm) cc_final: 0.1148 (tpt) REVERT: C 837 PHE cc_start: 0.5386 (t80) cc_final: 0.5086 (t80) REVERT: C 913 MET cc_start: -0.1477 (tpt) cc_final: -0.2451 (mtt) REVERT: C 1004 PHE cc_start: 0.3204 (OUTLIER) cc_final: 0.2908 (m-80) REVERT: D 9 LYS cc_start: 0.8331 (tmtm) cc_final: 0.7397 (tptp) REVERT: D 60 TRP cc_start: 0.5423 (t60) cc_final: 0.4998 (t60) REVERT: D 165 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8501 (ptp-170) REVERT: D 578 MET cc_start: 0.4965 (ppp) cc_final: 0.4110 (ppp) REVERT: D 582 ILE cc_start: 0.7381 (mm) cc_final: 0.7164 (mt) REVERT: D 772 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7728 (tp) REVERT: D 781 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8270 (tt) outliers start: 83 outliers final: 42 residues processed: 351 average time/residue: 0.4541 time to fit residues: 256.7656 Evaluate side-chains 316 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 878 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 342 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 chunk 162 optimal weight: 0.4980 chunk 346 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 319 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN A 614 ASN A 786 HIS ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN C 658 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.150781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.128260 restraints weight = 111615.359| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 3.85 r_work: 0.4125 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.8581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32464 Z= 0.138 Angle : 0.607 10.406 43735 Z= 0.317 Chirality : 0.042 0.219 4649 Planarity : 0.004 0.072 5576 Dihedral : 5.010 45.796 4186 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.94 % Allowed : 14.73 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3764 helix: 0.54 (0.10), residues: 2478 sheet: -3.60 (0.36), residues: 132 loop : -2.30 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 143 HIS 0.007 0.001 HIS A 786 PHE 0.040 0.002 PHE C 778 TYR 0.019 0.001 TYR A 436 ARG 0.005 0.000 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 1697) hydrogen bonds : angle 4.65963 ( 4971) covalent geometry : bond 0.00311 (32464) covalent geometry : angle 0.60686 (43735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.6210 (ttp80) cc_final: 0.5674 (ppt170) REVERT: A 68 GLU cc_start: 0.5027 (pt0) cc_final: 0.4797 (mt-10) REVERT: A 158 VAL cc_start: -0.0625 (OUTLIER) cc_final: -0.0958 (t) REVERT: A 189 ASP cc_start: 0.2981 (OUTLIER) cc_final: -0.0007 (t0) REVERT: A 190 TYR cc_start: 0.5539 (m-80) cc_final: 0.4998 (m-10) REVERT: A 197 TYR cc_start: 0.0816 (m-10) cc_final: 0.0579 (m-80) REVERT: A 261 TYR cc_start: 0.1533 (OUTLIER) cc_final: -0.0371 (m-80) REVERT: A 306 ASP cc_start: 0.6521 (m-30) cc_final: 0.5990 (m-30) REVERT: A 310 ASP cc_start: 0.6276 (m-30) cc_final: 0.6018 (m-30) REVERT: A 369 GLU cc_start: 0.2082 (tp30) cc_final: 0.1778 (tt0) REVERT: A 519 MET cc_start: 0.0955 (mmp) cc_final: 0.0454 (mpp) REVERT: A 531 MET cc_start: -0.1898 (mtt) cc_final: -0.3480 (ttt) REVERT: A 578 MET cc_start: 0.2962 (ttt) cc_final: 0.0684 (mtt) REVERT: A 611 TYR cc_start: 0.2042 (t80) cc_final: 0.1492 (m-80) REVERT: A 616 MET cc_start: 0.1201 (tmm) cc_final: 0.0736 (tmm) REVERT: A 694 GLU cc_start: 0.2986 (tp30) cc_final: 0.2259 (tp30) REVERT: A 866 MET cc_start: 0.2866 (mmm) cc_final: 0.2275 (mmm) REVERT: A 870 ARG cc_start: 0.6302 (tpm170) cc_final: 0.5683 (ptp-170) REVERT: A 889 LEU cc_start: -0.2688 (OUTLIER) cc_final: -0.2909 (tt) REVERT: A 936 MET cc_start: -0.3880 (mpp) cc_final: -0.4315 (mmm) REVERT: A 1001 MET cc_start: 0.5218 (ptm) cc_final: 0.4445 (mtt) REVERT: B 492 PHE cc_start: 0.6064 (t80) cc_final: 0.5766 (t80) REVERT: B 525 ASP cc_start: 0.8271 (t0) cc_final: 0.7984 (t0) REVERT: B 559 PHE cc_start: 0.4346 (t80) cc_final: 0.3844 (t80) REVERT: B 722 PHE cc_start: 0.8719 (t80) cc_final: 0.8485 (t80) REVERT: B 842 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7770 (mp) REVERT: B 913 MET cc_start: 0.0735 (tpt) cc_final: -0.0382 (mmm) REVERT: B 919 TRP cc_start: 0.5992 (m-10) cc_final: 0.5366 (m-10) REVERT: B 930 MET cc_start: 0.1498 (tpt) cc_final: 0.0672 (mtt) REVERT: C 222 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: C 309 ILE cc_start: 0.6712 (mm) cc_final: 0.6407 (mt) REVERT: C 482 TYR cc_start: 0.8230 (t80) cc_final: 0.7865 (t80) REVERT: C 647 MET cc_start: 0.6280 (tpp) cc_final: 0.5776 (mmm) REVERT: C 866 MET cc_start: 0.3756 (tpt) cc_final: 0.3250 (mtt) REVERT: C 913 MET cc_start: -0.1000 (tpt) cc_final: -0.2042 (mtt) REVERT: C 1004 PHE cc_start: 0.4315 (OUTLIER) cc_final: 0.4078 (m-80) REVERT: D 138 ILE cc_start: 0.5587 (OUTLIER) cc_final: 0.5384 (tt) REVERT: D 578 MET cc_start: 0.4998 (ppp) cc_final: 0.4545 (ppp) REVERT: D 582 ILE cc_start: 0.7433 (mm) cc_final: 0.7219 (mt) REVERT: D 704 MET cc_start: 0.7260 (mmm) cc_final: 0.6920 (mmm) REVERT: D 781 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8230 (tt) REVERT: D 866 MET cc_start: 0.5145 (tmt) cc_final: 0.4511 (mtt) REVERT: D 913 MET cc_start: -0.0031 (tpp) cc_final: -0.2420 (mmp) outliers start: 68 outliers final: 41 residues processed: 321 average time/residue: 0.4582 time to fit residues: 235.5331 Evaluate side-chains 288 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 878 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 309 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 354 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 269 optimal weight: 0.0870 chunk 293 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN C 609 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.145940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.123965 restraints weight = 112000.535| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.64 r_work: 0.4099 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.8997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32464 Z= 0.152 Angle : 0.628 10.929 43735 Z= 0.328 Chirality : 0.043 0.200 4649 Planarity : 0.004 0.071 5576 Dihedral : 5.015 44.513 4186 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.86 % Allowed : 15.41 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3764 helix: 0.54 (0.10), residues: 2496 sheet: -3.48 (0.44), residues: 83 loop : -2.23 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 601 HIS 0.012 0.001 HIS A 786 PHE 0.037 0.002 PHE C 778 TYR 0.039 0.002 TYR A 721 ARG 0.009 0.001 ARG A 819 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1697) hydrogen bonds : angle 4.64460 ( 4971) covalent geometry : bond 0.00347 (32464) covalent geometry : angle 0.62806 (43735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 3.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.6008 (tp30) cc_final: 0.5751 (tp30) REVERT: A 68 GLU cc_start: 0.5369 (pt0) cc_final: 0.5164 (mt-10) REVERT: A 155 GLU cc_start: 0.0773 (OUTLIER) cc_final: -0.0693 (mm-30) REVERT: A 186 LYS cc_start: 0.3550 (OUTLIER) cc_final: 0.1551 (ptmt) REVERT: A 189 ASP cc_start: 0.2975 (OUTLIER) cc_final: -0.0221 (m-30) REVERT: A 190 TYR cc_start: 0.5503 (m-80) cc_final: 0.4994 (m-10) REVERT: A 197 TYR cc_start: 0.1157 (m-10) cc_final: 0.0842 (m-80) REVERT: A 245 PHE cc_start: 0.6084 (t80) cc_final: 0.5494 (t80) REVERT: A 261 TYR cc_start: 0.1812 (OUTLIER) cc_final: -0.1429 (m-80) REVERT: A 310 ASP cc_start: 0.6306 (m-30) cc_final: 0.5998 (m-30) REVERT: A 369 GLU cc_start: 0.1934 (tp30) cc_final: 0.1729 (tt0) REVERT: A 519 MET cc_start: 0.1074 (mmp) cc_final: 0.0539 (mmm) REVERT: A 531 MET cc_start: -0.1934 (mtt) cc_final: -0.3259 (ttt) REVERT: A 578 MET cc_start: 0.3060 (ttt) cc_final: 0.0957 (mtt) REVERT: A 611 TYR cc_start: 0.2206 (t80) cc_final: 0.1500 (m-80) REVERT: A 694 GLU cc_start: 0.2882 (tp30) cc_final: 0.2188 (tp30) REVERT: A 866 MET cc_start: 0.2858 (mmm) cc_final: 0.2010 (mmm) REVERT: A 870 ARG cc_start: 0.6131 (tpm170) cc_final: 0.5607 (ptp-170) REVERT: A 889 LEU cc_start: -0.2665 (OUTLIER) cc_final: -0.2884 (tt) REVERT: A 936 MET cc_start: -0.4018 (mpp) cc_final: -0.5172 (ttm) REVERT: A 1001 MET cc_start: 0.5189 (ptm) cc_final: 0.4476 (mtt) REVERT: B 98 MET cc_start: 0.8158 (mmm) cc_final: 0.7832 (mmt) REVERT: B 525 ASP cc_start: 0.8138 (t0) cc_final: 0.7862 (t0) REVERT: B 559 PHE cc_start: 0.5137 (t80) cc_final: 0.4528 (t80) REVERT: B 722 PHE cc_start: 0.8716 (t80) cc_final: 0.8483 (t80) REVERT: B 842 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 913 MET cc_start: 0.1353 (tpt) cc_final: 0.0491 (mmm) REVERT: B 930 MET cc_start: 0.1097 (tpt) cc_final: 0.0283 (mtt) REVERT: B 936 MET cc_start: 0.3503 (ptp) cc_final: 0.3245 (ptp) REVERT: C 222 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: C 309 ILE cc_start: 0.6825 (mm) cc_final: 0.6515 (mt) REVERT: C 482 TYR cc_start: 0.8201 (t80) cc_final: 0.7940 (t80) REVERT: C 487 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6787 (pp30) REVERT: C 578 MET cc_start: 0.2500 (tpt) cc_final: 0.1533 (mtt) REVERT: C 647 MET cc_start: 0.6594 (tpp) cc_final: 0.5888 (mmm) REVERT: C 782 GLN cc_start: 0.6449 (mt0) cc_final: 0.6072 (tt0) REVERT: C 866 MET cc_start: 0.3872 (tpt) cc_final: 0.3373 (mtt) REVERT: C 913 MET cc_start: -0.1011 (tpt) cc_final: -0.2059 (mtt) REVERT: C 1004 PHE cc_start: 0.4163 (OUTLIER) cc_final: 0.3934 (m-80) REVERT: D 362 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8058 (mm-30) REVERT: D 578 MET cc_start: 0.4996 (ppp) cc_final: 0.4542 (ppp) REVERT: D 704 MET cc_start: 0.7281 (mmm) cc_final: 0.6999 (mmm) REVERT: D 781 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (tt) REVERT: D 913 MET cc_start: 0.0550 (tpp) cc_final: -0.2139 (mmp) REVERT: D 936 MET cc_start: 0.2687 (mmp) cc_final: 0.1906 (mmm) outliers start: 65 outliers final: 41 residues processed: 303 average time/residue: 0.4459 time to fit residues: 215.6619 Evaluate side-chains 284 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 601 TRP Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 487 GLN Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 678 PHE Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 878 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 92 optimal weight: 4.9990 chunk 331 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 311 optimal weight: 0.6980 chunk 193 optimal weight: 0.0670 chunk 284 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 ASN D 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.148399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.126510 restraints weight = 111966.763| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 3.61 r_work: 0.4063 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.9575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32464 Z= 0.176 Angle : 0.655 11.538 43735 Z= 0.345 Chirality : 0.044 0.307 4649 Planarity : 0.004 0.069 5576 Dihedral : 5.175 49.688 4186 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.66 % Allowed : 15.41 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3764 helix: 0.46 (0.10), residues: 2489 sheet: -3.42 (0.46), residues: 81 loop : -2.33 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 601 HIS 0.010 0.001 HIS A 609 PHE 0.035 0.002 PHE C 778 TYR 0.047 0.002 TYR A1003 ARG 0.007 0.001 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 1697) hydrogen bonds : angle 4.76509 ( 4971) covalent geometry : bond 0.00406 (32464) covalent geometry : angle 0.65486 (43735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TRP cc_start: 0.5789 (p90) cc_final: 0.5563 (p-90) REVERT: A 68 GLU cc_start: 0.5282 (pt0) cc_final: 0.4945 (pt0) REVERT: A 155 GLU cc_start: 0.0391 (OUTLIER) cc_final: -0.1688 (mp0) REVERT: A 186 LYS cc_start: 0.4068 (OUTLIER) cc_final: 0.2171 (tttt) REVERT: A 189 ASP cc_start: 0.2276 (OUTLIER) cc_final: 0.0192 (m-30) REVERT: A 190 TYR cc_start: 0.5766 (m-80) cc_final: 0.5240 (m-10) REVERT: A 197 TYR cc_start: 0.1355 (m-10) cc_final: 0.0819 (m-80) REVERT: A 261 TYR cc_start: 0.1769 (OUTLIER) cc_final: -0.1604 (m-80) REVERT: A 519 MET cc_start: 0.0687 (mmp) cc_final: 0.0254 (mpp) REVERT: A 531 MET cc_start: -0.1951 (mtt) cc_final: -0.3357 (ttt) REVERT: A 578 MET cc_start: 0.2913 (ttt) cc_final: 0.1055 (mtt) REVERT: A 611 TYR cc_start: 0.2114 (t80) cc_final: 0.1485 (m-80) REVERT: A 694 GLU cc_start: 0.2909 (tp30) cc_final: 0.2185 (tp30) REVERT: A 866 MET cc_start: 0.2763 (mmm) cc_final: 0.1815 (mmm) REVERT: A 870 ARG cc_start: 0.6274 (tpm170) cc_final: 0.5742 (ptp-170) REVERT: A 889 LEU cc_start: -0.2440 (OUTLIER) cc_final: -0.2684 (tt) REVERT: A 936 MET cc_start: -0.3505 (mpp) cc_final: -0.4826 (ttm) REVERT: A 1001 MET cc_start: 0.5277 (ptm) cc_final: 0.4517 (mtt) REVERT: B 525 ASP cc_start: 0.8279 (t0) cc_final: 0.8008 (t0) REVERT: B 559 PHE cc_start: 0.5180 (t80) cc_final: 0.4578 (t80) REVERT: B 578 MET cc_start: 0.5313 (tpp) cc_final: 0.4701 (tpt) REVERT: B 722 PHE cc_start: 0.8803 (t80) cc_final: 0.8590 (t80) REVERT: B 842 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 866 MET cc_start: 0.3229 (mmt) cc_final: 0.2784 (ttm) REVERT: B 913 MET cc_start: 0.1836 (tpt) cc_final: 0.0762 (mmm) REVERT: B 930 MET cc_start: 0.1251 (tpt) cc_final: 0.0361 (mtt) REVERT: B 936 MET cc_start: 0.2630 (ptp) cc_final: 0.2202 (ptp) REVERT: C 309 ILE cc_start: 0.7377 (mm) cc_final: 0.6989 (mt) REVERT: C 482 TYR cc_start: 0.8228 (t80) cc_final: 0.7938 (t80) REVERT: C 523 ASN cc_start: 0.6452 (t0) cc_final: 0.6243 (t0) REVERT: C 535 PHE cc_start: 0.7601 (t80) cc_final: 0.7342 (t80) REVERT: C 647 MET cc_start: 0.6011 (tpp) cc_final: 0.5540 (mmp) REVERT: C 725 TYR cc_start: 0.5011 (m-80) cc_final: 0.4722 (m-80) REVERT: C 792 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7861 (m) REVERT: C 913 MET cc_start: -0.0961 (tpt) cc_final: -0.1997 (mtt) REVERT: D 305 ASP cc_start: 0.8146 (p0) cc_final: 0.7742 (p0) REVERT: D 362 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8036 (mm-30) REVERT: D 396 MET cc_start: 0.7972 (tpt) cc_final: 0.7693 (mmt) REVERT: D 519 MET cc_start: 0.6811 (ppp) cc_final: 0.6035 (ptm) REVERT: D 578 MET cc_start: 0.5194 (ppp) cc_final: 0.4732 (ppp) REVERT: D 704 MET cc_start: 0.7222 (mmm) cc_final: 0.6992 (mmm) REVERT: D 870 ARG cc_start: 0.6901 (tpm170) cc_final: 0.6028 (ttt90) REVERT: D 913 MET cc_start: 0.0541 (tpp) cc_final: -0.1956 (mmp) REVERT: D 936 MET cc_start: 0.3115 (mmp) cc_final: 0.2539 (mmm) REVERT: D 976 MET cc_start: 0.6462 (ttt) cc_final: 0.5501 (tpp) outliers start: 58 outliers final: 44 residues processed: 310 average time/residue: 0.4771 time to fit residues: 237.2954 Evaluate side-chains 292 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 4.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 601 TRP Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 878 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 115 optimal weight: 0.0770 chunk 233 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 160 optimal weight: 0.0030 chunk 75 optimal weight: 0.9990 chunk 368 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.0020 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 563 ASN B 782 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.145010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.124711 restraints weight = 117203.664| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 3.30 r_work: 0.4131 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.9704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32464 Z= 0.119 Angle : 0.608 12.397 43735 Z= 0.317 Chirality : 0.042 0.186 4649 Planarity : 0.004 0.073 5576 Dihedral : 4.821 53.281 4186 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.23 % Allowed : 16.19 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3764 helix: 0.74 (0.11), residues: 2481 sheet: -3.20 (0.43), residues: 105 loop : -2.21 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 757 HIS 0.014 0.001 HIS A 609 PHE 0.047 0.002 PHE A 441 TYR 0.043 0.001 TYR A1003 ARG 0.016 0.000 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 1697) hydrogen bonds : angle 4.51645 ( 4971) covalent geometry : bond 0.00261 (32464) covalent geometry : angle 0.60801 (43735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21656.76 seconds wall clock time: 382 minutes 25.86 seconds (22945.86 seconds total)