Starting phenix.real_space_refine on Tue Aug 26 00:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y13_38824/08_2025/8y13_38824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y13_38824/08_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_38824/08_2025/8y13_38824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y13_38824/08_2025/8y13_38824.map" model { file = "/net/cci-nas-00/data/ceres_data/8y13_38824/08_2025/8y13_38824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y13_38824/08_2025/8y13_38824.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.18, per 1000 atoms: 0.23 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.29 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: 6.80 Time building geometry restraints manager: 3.37 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: 7.490 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.300 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.850 ------------------------------------------------------------------------------- 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 : 7.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.66 (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 ARG 0.017 0.001 ARG D 587 TYR 0.033 0.004 TYR B 197 PHE 0.040 0.004 PHE D 722 TRP 0.032 0.004 TRP D 601 HIS 0.011 0.003 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00807 (32464) covalent geometry : angle 1.13236 (43735) hydrogen bonds : bond 0.14751 ( 1697) hydrogen bonds : angle 9.53277 ( 4971) *********************** 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 : 1.227 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: 0.4434 (p) REVERT: A 56 TYR cc_start: 0.2317 (t80) cc_final: -0.0585 (t80) REVERT: A 100 PHE cc_start: 0.4615 (t80) cc_final: 0.4329 (t80) REVERT: A 231 TRP cc_start: 0.1097 (t60) cc_final: 0.0849 (t-100) REVERT: A 557 LYS cc_start: 0.2927 (ttmt) cc_final: 0.2286 (mmtp) REVERT: A 704 MET cc_start: 0.0847 (mmt) cc_final: 0.0529 (mmt) REVERT: A 775 ILE cc_start: 0.5465 (mt) cc_final: 0.5213 (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: -0.4244 (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: -0.1697 (mtt) REVERT: B 667 LEU cc_start: 0.8570 (mp) cc_final: 0.8341 (mp) REVERT: B 742 PHE cc_start: 0.8058 (m-80) cc_final: 0.7165 (m-80) REVERT: B 771 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7854 (mp) REVERT: B 781 LEU cc_start: 0.8365 (mm) cc_final: 0.8136 (mm) 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: 0.2556 (pt) REVERT: C 585 LEU cc_start: 0.4040 (OUTLIER) cc_final: 0.3774 (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: 0.6605 (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: -0.2335 (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: 0.2171 time to fit residues: 186.6480 Evaluate side-chains 315 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 310 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 771 ILE 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 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 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 125 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 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 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.161726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.142119 restraints weight = 125241.942| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 3.81 r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32464 Z= 0.166 Angle : 0.677 14.687 43735 Z= 0.362 Chirality : 0.045 0.295 4649 Planarity : 0.005 0.065 5576 Dihedral : 6.057 48.417 4194 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.58 % Favored : 94.34 % Rotamer: Outliers : 1.89 % Allowed : 9.35 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.12), residues: 3764 helix: -1.10 (0.09), residues: 2480 sheet: -4.08 (0.36), residues: 108 loop : -2.77 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 802 TYR 0.027 0.002 TYR C 755 PHE 0.026 0.002 PHE B 45 TRP 0.023 0.002 TRP C 448 HIS 0.023 0.002 HIS D 852 Details of bonding type rmsd covalent geometry : bond 0.00366 (32464) covalent geometry : angle 0.67674 (43735) hydrogen bonds : bond 0.04321 ( 1697) hydrogen bonds : angle 5.80977 ( 4971) *********************** 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 406 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 340 time to evaluate : 1.145 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: A 35 GLU cc_start: 0.6291 (tp30) cc_final: 0.5690 (tt0) REVERT: A 85 LEU cc_start: 0.6624 (tp) cc_final: 0.6386 (pp) REVERT: A 139 ASP cc_start: 0.1865 (OUTLIER) cc_final: 0.0404 (m-30) REVERT: A 231 TRP cc_start: 0.1741 (t60) cc_final: 0.0749 (m-10) REVERT: A 307 GLU cc_start: 0.5409 (tp30) cc_final: 0.5002 (pt0) REVERT: A 473 LEU cc_start: 0.5096 (mp) cc_final: 0.4438 (mt) REVERT: A 531 MET cc_start: -0.2684 (mmt) cc_final: -0.3264 (mmm) REVERT: A 694 GLU cc_start: 0.2144 (tp30) cc_final: 0.1560 (tp30) REVERT: A 825 LEU cc_start: 0.4545 (pp) cc_final: 0.4024 (tt) REVERT: A 936 MET cc_start: -0.3382 (mpp) cc_final: -0.5047 (ttm) REVERT: B 804 TYR cc_start: 0.7230 (m-80) cc_final: 0.6795 (m-80) REVERT: B 842 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7594 (tt) REVERT: B 844 LEU cc_start: 0.8574 (mm) cc_final: 0.8296 (tp) REVERT: B 930 MET cc_start: 0.1021 (tpt) cc_final: 0.0676 (mtt) REVERT: B 936 MET cc_start: 0.3076 (OUTLIER) cc_final: 0.2474 (ptm) REVERT: C 607 GLU cc_start: 0.5446 (tt0) cc_final: 0.5136 (mt-10) REVERT: C 612 ILE cc_start: 0.5696 (mm) cc_final: 0.5269 (mm) REVERT: C 658 HIS cc_start: 0.4356 (m-70) cc_final: 0.2897 (m-70) REVERT: C 711 GLN cc_start: 0.7350 (mt0) cc_final: 0.6766 (tm-30) REVERT: C 742 PHE cc_start: 0.4132 (OUTLIER) cc_final: 0.3197 (m-80) REVERT: C 774 ILE cc_start: 0.8523 (mm) cc_final: 0.8164 (tp) REVERT: C 913 MET cc_start: -0.1979 (tpt) cc_final: -0.2932 (mtt) REVERT: C 976 MET cc_start: 0.2805 (mpt) cc_final: 0.2344 (mpt) REVERT: C 1001 MET cc_start: 0.4636 (ttm) cc_final: 0.4392 (ttp) REVERT: D 60 TRP cc_start: 0.5690 (t60) cc_final: 0.5423 (t60) REVERT: D 105 LYS cc_start: 0.7073 (tppt) cc_final: 0.6508 (tppt) REVERT: D 755 TYR cc_start: 0.8394 (t80) cc_final: 0.8188 (t80) REVERT: D 781 LEU cc_start: 0.8446 (mm) cc_final: 0.7969 (tt) REVERT: D 870 ARG cc_start: 0.5535 (tpm170) cc_final: 0.5140 (tpt170) REVERT: D 913 MET cc_start: -0.3304 (tpt) cc_final: -0.3515 (ptt) outliers start: 66 outliers final: 23 residues processed: 392 average time/residue: 0.2070 time to fit residues: 128.4062 Evaluate side-chains 269 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 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 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 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 261 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 358 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 136 ASN A 343 ASN A 614 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS A 979 HIS B 93 ASN B 349 HIS B 475 GLN B 563 ASN B 666 ASN ** B 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 810 HIS B 852 HIS B 881 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 591 ASN C 614 ASN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN C 789 GLN C 852 HIS D 136 ASN D 182 ASN D 211 HIS D 765 ASN ** D 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.147712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.126939 restraints weight = 118363.745| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.65 r_work: 0.4103 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 32464 Z= 0.319 Angle : 0.851 10.233 43735 Z= 0.450 Chirality : 0.051 0.287 4649 Planarity : 0.006 0.062 5576 Dihedral : 6.362 45.401 4188 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.75 % Favored : 93.15 % Rotamer: Outliers : 2.89 % Allowed : 11.18 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.12), residues: 3764 helix: -0.77 (0.10), residues: 2464 sheet: -4.08 (0.42), residues: 100 loop : -2.74 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 447 TYR 0.031 0.003 TYR A 313 PHE 0.033 0.003 PHE B 559 TRP 0.035 0.004 TRP A 757 HIS 0.011 0.002 HIS D 978 Details of bonding type rmsd covalent geometry : bond 0.00738 (32464) covalent geometry : angle 0.85148 (43735) hydrogen bonds : bond 0.05328 ( 1697) hydrogen bonds : angle 5.92616 ( 4971) *********************** 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 420 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 319 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.2692 (OUTLIER) cc_final: -0.1468 (mp0) REVERT: A 158 VAL cc_start: -0.0136 (OUTLIER) cc_final: -0.1116 (p) REVERT: A 189 ASP cc_start: 0.2614 (OUTLIER) cc_final: -0.0234 (t0) REVERT: A 197 TYR cc_start: 0.2425 (m-10) cc_final: 0.1524 (m-80) REVERT: A 200 ILE cc_start: 0.1771 (tt) cc_final: 0.0315 (tt) REVERT: A 204 MET cc_start: 0.2869 (mtp) cc_final: 0.1702 (ttt) REVERT: A 261 TYR cc_start: 0.1943 (OUTLIER) cc_final: -0.0340 (m-80) REVERT: A 263 ASN cc_start: 0.5244 (m-40) cc_final: 0.5019 (p0) REVERT: A 566 ARG cc_start: 0.1282 (ttt90) cc_final: 0.0568 (mtp180) REVERT: A 578 MET cc_start: 0.2948 (ttt) cc_final: 0.0912 (mtt) REVERT: A 611 TYR cc_start: 0.1370 (t80) cc_final: 0.0649 (m-10) REVERT: A 614 ASN cc_start: 0.1399 (m110) cc_final: 0.0661 (t0) REVERT: A 647 MET cc_start: -0.0613 (ttm) cc_final: -0.1000 (ttp) REVERT: A 694 GLU cc_start: 0.2306 (tp30) cc_final: 0.1739 (tp30) REVERT: A 825 LEU cc_start: 0.5521 (pp) cc_final: 0.5169 (tt) REVERT: A 839 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5796 (t80) REVERT: A 936 MET cc_start: -0.2306 (mpp) cc_final: -0.3452 (ttm) REVERT: B 124 MET cc_start: 0.8575 (mmm) cc_final: 0.8313 (mmm) REVERT: B 339 HIS cc_start: 0.7208 (t70) cc_final: 0.6907 (t70) REVERT: B 525 ASP cc_start: 0.8329 (t0) cc_final: 0.8019 (t0) REVERT: B 625 TYR cc_start: 0.6035 (t80) cc_final: 0.5834 (t80) REVERT: B 747 ARG cc_start: 0.7794 (ptt180) cc_final: 0.7527 (ptt90) REVERT: B 842 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 930 MET cc_start: 0.1396 (tpt) cc_final: 0.0576 (mtt) REVERT: B 936 MET cc_start: 0.2620 (ptp) cc_final: 0.2366 (ptm) REVERT: C 119 ASP cc_start: 0.6696 (m-30) cc_final: 0.5683 (t70) REVERT: C 222 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: C 421 MET cc_start: 0.8454 (mtp) cc_final: 0.8249 (mtp) REVERT: C 482 TYR cc_start: 0.8468 (t80) cc_final: 0.7880 (t80) REVERT: C 578 MET cc_start: 0.2583 (tmm) cc_final: 0.2362 (ttp) REVERT: C 655 ILE cc_start: 0.7272 (mt) cc_final: 0.7050 (mt) REVERT: C 658 HIS cc_start: 0.7635 (m-70) cc_final: 0.6971 (m-70) REVERT: C 711 GLN cc_start: 0.8062 (mt0) cc_final: 0.7802 (mm-40) REVERT: C 913 MET cc_start: -0.1053 (tpt) cc_final: -0.2571 (mtt) REVERT: C 936 MET cc_start: -0.4766 (mtm) cc_final: -0.5099 (mtm) REVERT: C 976 MET cc_start: 0.1936 (mpt) cc_final: 0.1727 (mpt) REVERT: D 9 LYS cc_start: 0.8136 (tmtm) cc_final: 0.7822 (ttpp) REVERT: D 98 MET cc_start: 0.3875 (pmm) cc_final: 0.2934 (pmm) REVERT: D 357 MET cc_start: 0.7461 (mmm) cc_final: 0.7023 (mmm) REVERT: D 578 MET cc_start: 0.4201 (ppp) cc_final: 0.3592 (ppp) REVERT: D 755 TYR cc_start: 0.8346 (t80) cc_final: 0.8070 (t80) REVERT: D 913 MET cc_start: -0.1471 (tpt) cc_final: -0.3287 (mmp) outliers start: 101 outliers final: 40 residues processed: 402 average time/residue: 0.2100 time to fit residues: 134.9546 Evaluate side-chains 309 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 139 ASP 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 741 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 1004 PHE 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 283 LEU 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 695 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 980 VAL 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 585 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 606 HIS 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 838 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 113 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 326 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 202 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 371 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 241 HIS A 382 ASN A 614 ASN A 698 GLN A 834 GLN B 93 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 339 HIS ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 ASN D 789 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.149424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.127819 restraints weight = 118659.946| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.72 r_work: 0.4225 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32464 Z= 0.148 Angle : 0.614 9.701 43735 Z= 0.325 Chirality : 0.043 0.213 4649 Planarity : 0.004 0.067 5576 Dihedral : 5.508 52.071 4188 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 2.29 % Allowed : 13.24 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.13), residues: 3764 helix: -0.08 (0.10), residues: 2476 sheet: -3.92 (0.36), residues: 120 loop : -2.61 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 10 TYR 0.026 0.002 TYR A 755 PHE 0.039 0.002 PHE B 559 TRP 0.021 0.002 TRP B 143 HIS 0.009 0.001 HIS C 978 Details of bonding type rmsd covalent geometry : bond 0.00329 (32464) covalent geometry : angle 0.61354 (43735) hydrogen bonds : bond 0.03935 ( 1697) hydrogen bonds : angle 5.13114 ( 4971) *********************** 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 358 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 278 time to evaluate : 1.385 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 56 TYR cc_start: 0.5003 (t80) cc_final: 0.2997 (t80) REVERT: A 139 ASP cc_start: 0.1600 (OUTLIER) cc_final: 0.0358 (m-30) REVERT: A 158 VAL cc_start: -0.1182 (OUTLIER) cc_final: -0.1433 (t) REVERT: A 186 LYS cc_start: 0.2021 (OUTLIER) cc_final: -0.0549 (ptmt) REVERT: A 189 ASP cc_start: 0.2623 (OUTLIER) cc_final: 0.0030 (t0) REVERT: A 197 TYR cc_start: 0.1703 (m-10) cc_final: 0.0261 (m-80) REVERT: A 204 MET cc_start: 0.2666 (mtp) cc_final: 0.1639 (ttt) REVERT: A 290 MET cc_start: 0.2543 (mtt) cc_final: 0.2027 (mtm) REVERT: A 492 PHE cc_start: 0.5934 (t80) cc_final: 0.5678 (t80) REVERT: A 519 MET cc_start: 0.0015 (mmp) cc_final: -0.0731 (mmp) REVERT: A 566 ARG cc_start: 0.1517 (ttt90) cc_final: 0.0682 (ptp-170) REVERT: A 578 MET cc_start: 0.1904 (ttt) cc_final: -0.0491 (mtt) REVERT: A 611 TYR cc_start: 0.1290 (t80) cc_final: 0.0823 (m-10) REVERT: A 825 LEU cc_start: 0.4897 (pp) cc_final: 0.4471 (tt) REVERT: A 834 GLN cc_start: 0.2867 (OUTLIER) cc_final: 0.2596 (mm110) REVERT: A 866 MET cc_start: 0.2610 (OUTLIER) cc_final: 0.2321 (mpp) REVERT: A 936 MET cc_start: -0.3658 (mpp) cc_final: -0.4588 (ttm) REVERT: A 1001 MET cc_start: 0.4787 (ptm) cc_final: 0.3797 (mtt) REVERT: B 98 MET cc_start: 0.8040 (mmm) cc_final: 0.7798 (mmt) REVERT: B 339 HIS cc_start: 0.7233 (t70) cc_final: 0.6954 (t70) REVERT: B 525 ASP cc_start: 0.8375 (t0) cc_final: 0.8005 (t0) REVERT: B 722 PHE cc_start: 0.8893 (t80) cc_final: 0.8676 (t80) REVERT: B 747 ARG cc_start: 0.7950 (ptt180) cc_final: 0.7578 (ptt90) REVERT: B 804 TYR cc_start: 0.7415 (m-80) cc_final: 0.7214 (m-80) REVERT: B 842 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7872 (mp) REVERT: B 930 MET cc_start: 0.1858 (tpt) cc_final: 0.1105 (mtt) REVERT: B 936 MET cc_start: 0.3253 (OUTLIER) cc_final: 0.2816 (ptm) REVERT: C 119 ASP cc_start: 0.6673 (m-30) cc_final: 0.5794 (t70) REVERT: C 222 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6679 (m-30) REVERT: C 482 TYR cc_start: 0.8286 (t80) cc_final: 0.7480 (t80) REVERT: C 578 MET cc_start: 0.2748 (tmm) cc_final: 0.2083 (mtp) REVERT: C 589 TYR cc_start: 0.5744 (m-10) cc_final: 0.5499 (m-10) REVERT: C 612 ILE cc_start: 0.7265 (mm) cc_final: 0.6959 (mm) REVERT: C 704 MET cc_start: 0.6596 (mmm) cc_final: 0.6338 (mmm) REVERT: C 913 MET cc_start: -0.1919 (tpt) cc_final: -0.3359 (mtt) REVERT: C 976 MET cc_start: 0.2208 (mpt) cc_final: 0.1820 (mpt) REVERT: C 1004 PHE cc_start: 0.3335 (OUTLIER) cc_final: 0.2182 (m-10) REVERT: D 60 TRP cc_start: 0.5642 (t60) cc_final: 0.5238 (t60) REVERT: D 84 TYR cc_start: 0.6144 (m-80) cc_final: 0.5862 (m-10) REVERT: D 98 MET cc_start: 0.3826 (pmm) cc_final: 0.3093 (pmm) REVERT: D 222 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6769 (t0) REVERT: D 564 LYS cc_start: 0.5666 (mptt) cc_final: 0.5216 (mtpt) REVERT: D 913 MET cc_start: -0.2706 (tpt) cc_final: -0.3948 (mmp) outliers start: 80 outliers final: 40 residues processed: 344 average time/residue: 0.2082 time to fit residues: 116.7323 Evaluate side-chains 294 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 TYR 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 186 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 834 GLN 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 199 LEU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 666 ASN 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 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 283 LEU 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 792 SER Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 204 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 487 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 826 CYS 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 285 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 77 optimal weight: 0.3980 chunk 315 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 366 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- 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 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN D 789 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.147391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.128305 restraints weight = 117463.109| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 3.06 r_work: 0.4188 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.7498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32464 Z= 0.142 Angle : 0.604 12.240 43735 Z= 0.315 Chirality : 0.042 0.245 4649 Planarity : 0.004 0.069 5576 Dihedral : 5.264 52.848 4186 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.77 % Favored : 94.21 % Rotamer: Outliers : 2.46 % Allowed : 13.41 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 3764 helix: 0.28 (0.10), residues: 2474 sheet: -3.66 (0.40), residues: 106 loop : -2.47 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 267 TYR 0.027 0.002 TYR C 479 PHE 0.037 0.002 PHE B 559 TRP 0.026 0.002 TRP C 60 HIS 0.008 0.001 HIS C 978 Details of bonding type rmsd covalent geometry : bond 0.00317 (32464) covalent geometry : angle 0.60359 (43735) hydrogen bonds : bond 0.03724 ( 1697) hydrogen bonds : angle 4.91836 ( 4971) *********************** 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 361 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 1.211 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: A 56 TYR cc_start: 0.4757 (t80) cc_final: 0.4507 (t80) REVERT: A 119 ASP cc_start: 0.3292 (t0) cc_final: 0.3082 (t0) REVERT: A 139 ASP cc_start: 0.1827 (OUTLIER) cc_final: 0.0443 (m-30) REVERT: A 158 VAL cc_start: -0.0571 (OUTLIER) cc_final: -0.0909 (t) REVERT: A 186 LYS cc_start: 0.2156 (OUTLIER) cc_final: 0.0526 (ptmt) REVERT: A 189 ASP cc_start: 0.2591 (OUTLIER) cc_final: 0.0088 (m-30) REVERT: A 190 TYR cc_start: 0.4880 (m-80) cc_final: 0.4249 (m-10) REVERT: A 261 TYR cc_start: 0.1596 (OUTLIER) cc_final: -0.0953 (m-80) REVERT: A 519 MET cc_start: 0.0456 (mmp) cc_final: 0.0051 (mmm) REVERT: A 578 MET cc_start: 0.2875 (ttt) cc_final: 0.0565 (mtt) REVERT: A 611 TYR cc_start: 0.1626 (t80) cc_final: 0.0950 (m-10) REVERT: A 825 LEU cc_start: 0.4531 (pp) cc_final: 0.4288 (tt) REVERT: A 936 MET cc_start: -0.3102 (mpp) cc_final: -0.4339 (ttm) REVERT: A 967 LEU cc_start: 0.4008 (mp) cc_final: 0.3775 (mp) REVERT: A 1001 MET cc_start: 0.5128 (ptm) cc_final: 0.4374 (mtt) REVERT: B 525 ASP cc_start: 0.8056 (t0) cc_final: 0.7821 (t0) REVERT: B 722 PHE cc_start: 0.8694 (t80) cc_final: 0.8464 (t80) REVERT: B 772 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8117 (tp) REVERT: B 842 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7791 (mp) REVERT: B 930 MET cc_start: 0.2016 (tpt) cc_final: 0.1129 (mtt) REVERT: B 936 MET cc_start: 0.3112 (OUTLIER) cc_final: 0.2742 (ptm) REVERT: C 101 ASP cc_start: 0.4392 (m-30) cc_final: 0.4107 (p0) REVERT: C 119 ASP cc_start: 0.6957 (m-30) cc_final: 0.5997 (t70) REVERT: C 482 TYR cc_start: 0.8142 (t80) cc_final: 0.7501 (t80) REVERT: C 578 MET cc_start: 0.2448 (tmm) cc_final: 0.1883 (mtp) REVERT: C 837 PHE cc_start: 0.5090 (t80) cc_final: 0.4770 (t80) REVERT: C 913 MET cc_start: -0.1479 (tpt) cc_final: -0.2958 (mtt) REVERT: C 976 MET cc_start: 0.2457 (mpt) cc_final: 0.2193 (mpt) REVERT: C 1004 PHE cc_start: 0.3841 (OUTLIER) cc_final: 0.2701 (m-10) REVERT: D 61 ARG cc_start: 0.6039 (mmm160) cc_final: 0.5671 (mtm180) REVERT: D 84 TYR cc_start: 0.6534 (m-80) cc_final: 0.6144 (m-10) REVERT: D 98 MET cc_start: 0.3911 (pmm) cc_final: 0.3288 (pmm) REVERT: D 222 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7000 (t0) REVERT: D 357 MET cc_start: 0.7402 (mmm) cc_final: 0.7091 (mmm) REVERT: D 578 MET cc_start: 0.4731 (ppp) cc_final: 0.4171 (ppp) REVERT: D 582 ILE cc_start: 0.7383 (mm) cc_final: 0.7148 (mt) REVERT: D 691 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7330 (tt) REVERT: D 694 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: D 772 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7808 (tp) REVERT: D 913 MET cc_start: -0.2257 (tpt) cc_final: -0.3395 (pmm) REVERT: D 936 MET cc_start: 0.2393 (mmp) cc_final: 0.1339 (mmm) outliers start: 86 outliers final: 41 residues processed: 342 average time/residue: 0.2179 time to fit residues: 120.3626 Evaluate side-chains 296 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR 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 186 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 666 ASN 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 772 ILE 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 134 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 694 GLU Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 838 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 230 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 349 optimal weight: 7.9990 chunk 332 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 334 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 93 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 241 HIS A 483 GLN A 606 HIS A 614 ASN A 765 ASN ** A 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 ASN D 810 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.144781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.122603 restraints weight = 114757.250| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.29 r_work: 0.4072 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.8351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32464 Z= 0.173 Angle : 0.637 10.442 43735 Z= 0.334 Chirality : 0.044 0.228 4649 Planarity : 0.004 0.081 5576 Dihedral : 5.314 52.895 4186 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 2.57 % Allowed : 14.30 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.13), residues: 3764 helix: 0.32 (0.10), residues: 2450 sheet: -3.67 (0.41), residues: 104 loop : -2.36 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 587 TYR 0.033 0.002 TYR A1003 PHE 0.026 0.002 PHE B 559 TRP 0.028 0.002 TRP C 143 HIS 0.011 0.001 HIS D 810 Details of bonding type rmsd covalent geometry : bond 0.00395 (32464) covalent geometry : angle 0.63668 (43735) hydrogen bonds : bond 0.03950 ( 1697) hydrogen bonds : angle 4.94888 ( 4971) *********************** 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 359 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 269 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1458 (p0) cc_final: -0.1971 (p0) REVERT: A 139 ASP cc_start: 0.1721 (OUTLIER) cc_final: 0.0178 (m-30) REVERT: A 155 GLU cc_start: 0.0893 (OUTLIER) cc_final: -0.2935 (pt0) REVERT: A 158 VAL cc_start: -0.0067 (OUTLIER) cc_final: -0.0383 (t) REVERT: A 186 LYS cc_start: 0.3093 (OUTLIER) cc_final: 0.0479 (ptmt) REVERT: A 189 ASP cc_start: 0.3400 (OUTLIER) cc_final: -0.0277 (t0) REVERT: A 190 TYR cc_start: 0.5299 (m-80) cc_final: 0.4702 (m-10) REVERT: A 245 PHE cc_start: 0.6076 (t80) cc_final: 0.5528 (t80) REVERT: A 261 TYR cc_start: 0.1796 (OUTLIER) cc_final: -0.1254 (m-80) REVERT: A 306 ASP cc_start: 0.6799 (m-30) cc_final: 0.6286 (m-30) REVERT: A 455 TYR cc_start: 0.1023 (m-80) cc_final: 0.0799 (m-10) REVERT: A 578 MET cc_start: 0.3114 (ttt) cc_final: 0.0742 (mtt) REVERT: A 601 TRP cc_start: 0.3263 (t-100) cc_final: 0.2437 (t-100) REVERT: A 611 TYR cc_start: 0.1839 (t80) cc_final: 0.1206 (m-10) REVERT: A 839 PHE cc_start: 0.6288 (m-10) cc_final: 0.5953 (t80) REVERT: A 866 MET cc_start: 0.2880 (OUTLIER) cc_final: 0.2138 (mpp) REVERT: A 870 ARG cc_start: 0.6978 (tpm170) cc_final: 0.6055 (ptp-170) REVERT: A 936 MET cc_start: -0.2496 (mpp) cc_final: -0.3927 (ttm) REVERT: A 1001 MET cc_start: 0.5262 (ptm) cc_final: 0.4497 (mtt) REVERT: B 525 ASP cc_start: 0.8139 (t0) cc_final: 0.7838 (t0) REVERT: B 531 MET cc_start: 0.8684 (mmt) cc_final: 0.8376 (mmt) REVERT: B 722 PHE cc_start: 0.8820 (t80) cc_final: 0.8591 (t80) REVERT: B 772 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8143 (tp) REVERT: B 804 TYR cc_start: 0.7379 (m-80) cc_final: 0.6571 (m-80) REVERT: B 842 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 930 MET cc_start: 0.2114 (tpt) cc_final: 0.1144 (mtt) REVERT: B 936 MET cc_start: 0.3093 (OUTLIER) cc_final: 0.2198 (ptm) REVERT: C 71 TYR cc_start: 0.3170 (m-10) cc_final: 0.2003 (m-80) REVERT: C 222 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: C 309 ILE cc_start: 0.6770 (mm) cc_final: 0.6453 (mt) REVERT: C 479 TYR cc_start: 0.8214 (t80) cc_final: 0.7963 (t80) REVERT: C 482 TYR cc_start: 0.8329 (t80) cc_final: 0.7661 (t80) REVERT: C 606 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8021 (m-70) REVERT: C 913 MET cc_start: -0.1202 (tpt) cc_final: -0.2724 (mtt) REVERT: D 9 LYS cc_start: 0.6560 (mptt) cc_final: 0.6188 (ttpp) REVERT: D 61 ARG cc_start: 0.6267 (mmm160) cc_final: 0.6045 (mmm160) REVERT: D 229 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8769 (mt) REVERT: D 357 MET cc_start: 0.7376 (mmm) cc_final: 0.6777 (mmm) REVERT: D 362 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8119 (mt-10) REVERT: D 396 MET cc_start: 0.7859 (tpt) cc_final: 0.7598 (mmt) REVERT: D 522 PHE cc_start: 0.4201 (OUTLIER) cc_final: 0.3496 (t80) REVERT: D 564 LYS cc_start: 0.5669 (mptt) cc_final: 0.5266 (mtpt) REVERT: D 578 MET cc_start: 0.4517 (ppp) cc_final: 0.3812 (ppp) REVERT: D 582 ILE cc_start: 0.7473 (mm) cc_final: 0.7196 (tp) REVERT: D 691 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7446 (tt) REVERT: D 694 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: D 772 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (tp) REVERT: D 781 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8247 (tt) REVERT: D 837 PHE cc_start: 0.7642 (t80) cc_final: 0.7274 (t80) REVERT: D 936 MET cc_start: 0.3411 (mmp) cc_final: 0.2774 (mmm) outliers start: 90 outliers final: 50 residues processed: 340 average time/residue: 0.2181 time to fit residues: 119.0915 Evaluate side-chains 314 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 246 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR 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 186 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 750 ASP 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 117 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 606 HIS Chi-restraints excluded: chain B residue 666 ASN 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 772 ILE 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 844 LEU Chi-restraints excluded: chain B residue 936 MET 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 170 VAL 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 606 HIS Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 694 GLU Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 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 810 HIS Chi-restraints excluded: chain D residue 838 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 79 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 273 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 339 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 313 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 598 ASN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN B 666 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 391 ASN ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 GLN C 765 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.143269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.122112 restraints weight = 117969.782| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.34 r_work: 0.4050 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.9056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32464 Z= 0.192 Angle : 0.645 10.403 43735 Z= 0.339 Chirality : 0.044 0.242 4649 Planarity : 0.004 0.069 5576 Dihedral : 5.291 49.433 4186 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.70 % Rotamer: Outliers : 2.83 % Allowed : 14.53 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.13), residues: 3764 helix: 0.27 (0.10), residues: 2497 sheet: -3.37 (0.46), residues: 92 loop : -2.42 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 754 TYR 0.026 0.002 TYR A 755 PHE 0.030 0.002 PHE A 511 TRP 0.028 0.002 TRP A 448 HIS 0.033 0.001 HIS D 810 Details of bonding type rmsd covalent geometry : bond 0.00442 (32464) covalent geometry : angle 0.64513 (43735) hydrogen bonds : bond 0.04007 ( 1697) hydrogen bonds : angle 4.96211 ( 4971) *********************** 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 375 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 276 time to evaluate : 1.410 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: A 31 LYS cc_start: 0.6796 (mmtm) cc_final: 0.6496 (ttpp) REVERT: A 35 GLU cc_start: 0.6001 (tp30) cc_final: 0.5799 (tp30) REVERT: A 119 ASP cc_start: 0.3397 (t0) cc_final: 0.3118 (t0) REVERT: A 139 ASP cc_start: 0.1748 (OUTLIER) cc_final: 0.0318 (m-30) REVERT: A 155 GLU cc_start: 0.1031 (OUTLIER) cc_final: -0.2909 (pt0) REVERT: A 186 LYS cc_start: 0.3564 (OUTLIER) cc_final: 0.3308 (mmtm) REVERT: A 189 ASP cc_start: 0.2758 (OUTLIER) cc_final: 0.0778 (m-30) REVERT: A 261 TYR cc_start: 0.1996 (OUTLIER) cc_final: -0.0402 (m-80) REVERT: A 306 ASP cc_start: 0.6442 (m-30) cc_final: 0.5847 (m-30) REVERT: A 310 ASP cc_start: 0.5640 (m-30) cc_final: 0.5365 (m-30) REVERT: A 578 MET cc_start: 0.2693 (ttt) cc_final: 0.0705 (mtt) REVERT: A 601 TRP cc_start: 0.3588 (t-100) cc_final: 0.2394 (t-100) REVERT: A 611 TYR cc_start: 0.1975 (t80) cc_final: 0.1313 (m-10) REVERT: A 721 TYR cc_start: 0.2154 (OUTLIER) cc_final: 0.1371 (m-80) REVERT: A 756 VAL cc_start: 0.0863 (t) cc_final: 0.0582 (p) REVERT: A 865 LEU cc_start: 0.4508 (tt) cc_final: 0.4304 (tt) REVERT: A 866 MET cc_start: 0.2665 (OUTLIER) cc_final: 0.0805 (mpp) REVERT: A 870 ARG cc_start: 0.6805 (tpm170) cc_final: 0.6019 (mtt180) REVERT: A 936 MET cc_start: -0.2411 (mpp) cc_final: -0.3672 (ttm) REVERT: A 967 LEU cc_start: 0.4491 (mp) cc_final: 0.4074 (tp) REVERT: A 1001 MET cc_start: 0.5505 (ptm) cc_final: 0.4630 (mtt) REVERT: B 98 MET cc_start: 0.8171 (mmm) cc_final: 0.7782 (mmt) REVERT: B 525 ASP cc_start: 0.8041 (t0) cc_final: 0.7770 (t0) REVERT: B 578 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5312 (ttt) REVERT: B 772 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8321 (tp) REVERT: B 930 MET cc_start: 0.1501 (tpt) cc_final: 0.0478 (mtt) REVERT: B 936 MET cc_start: 0.3066 (OUTLIER) cc_final: 0.2694 (ptm) REVERT: C 109 GLN cc_start: 0.6504 (OUTLIER) cc_final: 0.6148 (tp40) REVERT: C 222 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: C 309 ILE cc_start: 0.6989 (mm) cc_final: 0.6613 (mt) REVERT: C 479 TYR cc_start: 0.8220 (t80) cc_final: 0.7952 (t80) REVERT: C 482 TYR cc_start: 0.8216 (t80) cc_final: 0.7691 (t80) REVERT: C 525 ASP cc_start: 0.6384 (t0) cc_final: 0.6168 (t70) REVERT: C 578 MET cc_start: 0.2508 (tpt) cc_final: 0.1655 (mtt) REVERT: C 913 MET cc_start: -0.1777 (tpt) cc_final: -0.3154 (mtt) REVERT: D 357 MET cc_start: 0.7549 (mmm) cc_final: 0.6910 (mmm) REVERT: D 362 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7900 (mm-30) REVERT: D 522 PHE cc_start: 0.4514 (OUTLIER) cc_final: 0.3848 (t80) REVERT: D 564 LYS cc_start: 0.5969 (mptt) cc_final: 0.5546 (mtpt) REVERT: D 578 MET cc_start: 0.4981 (ppp) cc_final: 0.4581 (ppp) REVERT: D 582 ILE cc_start: 0.7431 (mm) cc_final: 0.7178 (tp) REVERT: D 691 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7598 (tt) REVERT: D 694 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: D 772 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7876 (tp) REVERT: D 781 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8268 (tt) REVERT: D 837 PHE cc_start: 0.7408 (t80) cc_final: 0.7175 (t80) REVERT: D 913 MET cc_start: -0.0398 (tpp) cc_final: -0.3214 (mmp) REVERT: D 936 MET cc_start: 0.2492 (mmp) cc_final: 0.1611 (mmm) outliers start: 99 outliers final: 56 residues processed: 354 average time/residue: 0.2176 time to fit residues: 124.0584 Evaluate side-chains 312 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 134 TYR 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 186 LYS Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 757 TRP 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 117 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 MET 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 772 ILE Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 678 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 367 CYS Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 694 GLU Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 838 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 72 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 264 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 199 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 ASN D 67 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.144019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.124420 restraints weight = 119150.252| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 3.11 r_work: 0.4111 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.9263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32464 Z= 0.132 Angle : 0.595 10.972 43735 Z= 0.312 Chirality : 0.042 0.204 4649 Planarity : 0.004 0.069 5576 Dihedral : 5.009 46.876 4186 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.17 % Allowed : 15.33 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 3764 helix: 0.52 (0.10), residues: 2502 sheet: -3.12 (0.48), residues: 87 loop : -2.34 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 61 TYR 0.032 0.001 TYR A 452 PHE 0.051 0.002 PHE A 441 TRP 0.033 0.002 TRP C 143 HIS 0.006 0.001 HIS D 978 Details of bonding type rmsd covalent geometry : bond 0.00291 (32464) covalent geometry : angle 0.59467 (43735) hydrogen bonds : bond 0.03609 ( 1697) hydrogen bonds : angle 4.75333 ( 4971) *********************** 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: 76 poor density : 262 time to evaluate : 1.236 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 31 LYS cc_start: 0.6823 (mmtm) cc_final: 0.6539 (ttpp) REVERT: A 61 ARG cc_start: 0.6028 (ttp80) cc_final: 0.5476 (ptt90) REVERT: A 197 TYR cc_start: 0.1299 (m-80) cc_final: -0.0445 (m-80) REVERT: A 261 TYR cc_start: 0.1535 (OUTLIER) cc_final: -0.1492 (m-80) REVERT: A 306 ASP cc_start: 0.6336 (m-30) cc_final: 0.5857 (m-30) REVERT: A 310 ASP cc_start: 0.5857 (m-30) cc_final: 0.5612 (m-30) REVERT: A 578 MET cc_start: 0.2479 (ttt) cc_final: 0.1009 (tpt) REVERT: A 601 TRP cc_start: 0.3072 (t-100) cc_final: 0.1942 (t-100) REVERT: A 611 TYR cc_start: 0.1875 (t80) cc_final: 0.1025 (m-10) REVERT: A 614 ASN cc_start: 0.1712 (m110) cc_final: 0.1339 (t0) REVERT: A 666 ASN cc_start: 0.2989 (m-40) cc_final: 0.1527 (p0) REVERT: A 757 TRP cc_start: -0.0424 (OUTLIER) cc_final: -0.0749 (m-90) REVERT: A 819 ARG cc_start: 0.6864 (mtm-85) cc_final: 0.5735 (tpp80) REVERT: A 865 LEU cc_start: 0.4625 (tt) cc_final: 0.4379 (tt) REVERT: A 866 MET cc_start: 0.2681 (OUTLIER) cc_final: 0.2474 (mpp) REVERT: A 889 LEU cc_start: -0.2716 (OUTLIER) cc_final: -0.2949 (tt) REVERT: A 936 MET cc_start: -0.2837 (mpp) cc_final: -0.4230 (ttm) REVERT: A 967 LEU cc_start: 0.4700 (mp) cc_final: 0.4294 (tp) REVERT: A 1001 MET cc_start: 0.5307 (ptm) cc_final: 0.4598 (mtt) REVERT: B 525 ASP cc_start: 0.7892 (t0) cc_final: 0.7643 (t0) REVERT: B 772 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 784 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 804 TYR cc_start: 0.7359 (m-80) cc_final: 0.6371 (m-80) REVERT: B 842 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7651 (mp) REVERT: B 930 MET cc_start: 0.1861 (tpt) cc_final: 0.0858 (mtt) REVERT: B 936 MET cc_start: 0.3160 (OUTLIER) cc_final: 0.2157 (ptm) REVERT: C 109 GLN cc_start: 0.6126 (tp-100) cc_final: 0.5872 (tp40) REVERT: C 222 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: C 309 ILE cc_start: 0.7042 (mm) cc_final: 0.6659 (mt) REVERT: C 479 TYR cc_start: 0.8177 (t80) cc_final: 0.7974 (t80) REVERT: C 482 TYR cc_start: 0.8135 (t80) cc_final: 0.7782 (t80) REVERT: C 525 ASP cc_start: 0.6277 (t0) cc_final: 0.5958 (t70) REVERT: C 578 MET cc_start: 0.2626 (tpt) cc_final: 0.1714 (mtt) REVERT: C 647 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.5215 (mmm) REVERT: C 913 MET cc_start: -0.1412 (tpt) cc_final: -0.2905 (mtt) REVERT: D 229 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8731 (mt) REVERT: D 357 MET cc_start: 0.7435 (mmm) cc_final: 0.6898 (mmm) REVERT: D 362 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7960 (mm-30) REVERT: D 522 PHE cc_start: 0.4295 (OUTLIER) cc_final: 0.3558 (t80) REVERT: D 578 MET cc_start: 0.4833 (ppp) cc_final: 0.4411 (ppp) REVERT: D 582 ILE cc_start: 0.7381 (mm) cc_final: 0.7120 (tp) REVERT: D 691 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7397 (tt) REVERT: D 704 MET cc_start: 0.7281 (mmm) cc_final: 0.6957 (mmm) REVERT: D 772 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7960 (tp) REVERT: D 781 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8287 (tt) REVERT: D 837 PHE cc_start: 0.7529 (t80) cc_final: 0.7286 (t80) REVERT: D 913 MET cc_start: -0.0069 (tpp) cc_final: -0.2983 (mmp) REVERT: D 936 MET cc_start: 0.2424 (mmp) cc_final: 0.1986 (mmm) outliers start: 76 outliers final: 49 residues processed: 320 average time/residue: 0.2080 time to fit residues: 108.5642 Evaluate side-chains 304 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 241 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 110 VAL 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 158 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 757 TRP Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 552 TYR 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 772 ILE Chi-restraints excluded: chain B residue 779 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 134 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 678 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 691 ILE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 761 LEU Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 838 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 369 optimal weight: 20.0000 chunk 367 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 292 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 765 ASN D 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.142039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.119202 restraints weight = 110234.547| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.18 r_work: 0.4028 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.9756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32464 Z= 0.176 Angle : 0.646 11.821 43735 Z= 0.338 Chirality : 0.044 0.219 4649 Planarity : 0.004 0.070 5576 Dihedral : 5.174 49.853 4186 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.46 % Favored : 93.52 % Rotamer: Outliers : 2.14 % Allowed : 15.78 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.13), residues: 3764 helix: 0.44 (0.10), residues: 2494 sheet: -3.29 (0.47), residues: 87 loop : -2.43 (0.16), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 747 TYR 0.027 0.002 TYR D 625 PHE 0.055 0.002 PHE A 441 TRP 0.031 0.002 TRP A 448 HIS 0.010 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00403 (32464) covalent geometry : angle 0.64582 (43735) hydrogen bonds : bond 0.03872 ( 1697) hydrogen bonds : angle 4.88171 ( 4971) *********************** 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 340 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 265 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.6826 (mmtm) cc_final: 0.6485 (ttpp) REVERT: A 119 ASP cc_start: 0.3367 (t0) cc_final: 0.3157 (t0) REVERT: A 186 LYS cc_start: 0.3629 (OUTLIER) cc_final: 0.2384 (mtmm) REVERT: A 197 TYR cc_start: 0.1895 (m-80) cc_final: 0.1656 (m-80) REVERT: A 261 TYR cc_start: 0.1743 (OUTLIER) cc_final: -0.1648 (m-80) REVERT: A 310 ASP cc_start: 0.5961 (m-30) cc_final: 0.5736 (m-30) REVERT: A 578 MET cc_start: 0.2511 (ttt) cc_final: 0.1077 (tpt) REVERT: A 601 TRP cc_start: 0.3409 (t-100) cc_final: 0.2170 (t-100) REVERT: A 611 TYR cc_start: 0.1963 (t80) cc_final: 0.1029 (m-80) REVERT: A 614 ASN cc_start: 0.1919 (m110) cc_final: 0.1212 (t0) REVERT: A 666 ASN cc_start: 0.3110 (m-40) cc_final: 0.1528 (p0) REVERT: A 721 TYR cc_start: 0.2215 (OUTLIER) cc_final: 0.1814 (m-80) REVERT: A 819 ARG cc_start: 0.6278 (mtm-85) cc_final: 0.5456 (tpp80) REVERT: A 866 MET cc_start: 0.2399 (OUTLIER) cc_final: 0.0528 (mpp) REVERT: A 870 ARG cc_start: 0.7155 (tpm170) cc_final: 0.6115 (ptp-170) REVERT: A 893 LYS cc_start: 0.3838 (tttt) cc_final: 0.3580 (ttpp) REVERT: A 936 MET cc_start: -0.2857 (mpp) cc_final: -0.3720 (ttm) REVERT: A 967 LEU cc_start: 0.4837 (mp) cc_final: 0.4419 (tp) REVERT: A 1001 MET cc_start: 0.5136 (ptm) cc_final: 0.4172 (mtt) REVERT: B 98 MET cc_start: 0.8178 (mmm) cc_final: 0.7798 (mmt) REVERT: B 525 ASP cc_start: 0.8036 (t0) cc_final: 0.7778 (t0) REVERT: B 578 MET cc_start: 0.5257 (tpp) cc_final: 0.4813 (tpt) REVERT: B 772 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 784 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 842 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7737 (mp) REVERT: B 925 ILE cc_start: 0.4293 (OUTLIER) cc_final: 0.3402 (tt) REVERT: B 936 MET cc_start: 0.2966 (OUTLIER) cc_final: 0.1901 (ptm) REVERT: C 109 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6218 (tp40) REVERT: C 222 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: C 309 ILE cc_start: 0.7281 (mm) cc_final: 0.6879 (mt) REVERT: C 482 TYR cc_start: 0.8169 (t80) cc_final: 0.7747 (t80) REVERT: C 578 MET cc_start: 0.2531 (tpt) cc_final: 0.1780 (mtt) REVERT: C 725 TYR cc_start: 0.5148 (m-80) cc_final: 0.4629 (m-80) REVERT: C 782 GLN cc_start: 0.6213 (mt0) cc_final: 0.5898 (mt0) REVERT: C 792 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.7962 (m) REVERT: C 913 MET cc_start: -0.1935 (tpt) cc_final: -0.3262 (mtt) REVERT: D 305 ASP cc_start: 0.8170 (p0) cc_final: 0.7802 (p0) REVERT: D 357 MET cc_start: 0.7415 (mmm) cc_final: 0.6996 (mmp) REVERT: D 362 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7884 (mm-30) REVERT: D 396 MET cc_start: 0.7635 (mmt) cc_final: 0.7216 (mmt) REVERT: D 522 PHE cc_start: 0.4268 (OUTLIER) cc_final: 0.3520 (t80) REVERT: D 578 MET cc_start: 0.5125 (ppp) cc_final: 0.4642 (ppp) REVERT: D 582 ILE cc_start: 0.7429 (mm) cc_final: 0.7178 (tp) REVERT: D 704 MET cc_start: 0.7271 (mmm) cc_final: 0.6978 (mmm) REVERT: D 772 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7958 (tp) REVERT: D 781 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8242 (tt) REVERT: D 839 PHE cc_start: 0.7655 (m-80) cc_final: 0.7386 (m-80) REVERT: D 913 MET cc_start: -0.0663 (tpp) cc_final: -0.3506 (mmp) REVERT: D 936 MET cc_start: 0.2278 (mmp) cc_final: 0.1863 (mmm) outliers start: 75 outliers final: 52 residues processed: 323 average time/residue: 0.2136 time to fit residues: 110.9960 Evaluate side-chains 313 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 110 VAL 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 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 441 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 757 TRP 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 117 ILE Chi-restraints excluded: chain B residue 162 THR 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 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 772 ILE Chi-restraints excluded: chain B residue 779 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 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 678 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 60 TRP Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 619 LEU 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 737 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 838 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 301 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 89 optimal weight: 8.9990 chunk 299 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 563 ASN A 863 ASN B 666 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.146099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.122747 restraints weight = 100703.819| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 3.57 r_work: 0.4080 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.9894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32464 Z= 0.138 Angle : 0.612 11.755 43735 Z= 0.320 Chirality : 0.042 0.204 4649 Planarity : 0.004 0.069 5576 Dihedral : 5.005 49.120 4186 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.94 % Allowed : 16.36 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.14), residues: 3764 helix: 0.63 (0.10), residues: 2484 sheet: -3.19 (0.47), residues: 87 loop : -2.35 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 10 TYR 0.028 0.001 TYR D 625 PHE 0.052 0.002 PHE A 441 TRP 0.024 0.002 TRP A 448 HIS 0.006 0.001 HIS D 978 Details of bonding type rmsd covalent geometry : bond 0.00308 (32464) covalent geometry : angle 0.61157 (43735) hydrogen bonds : bond 0.03590 ( 1697) hydrogen bonds : angle 4.74424 ( 4971) ********************** 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: 68 poor density : 259 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.6883 (mmtm) cc_final: 0.6542 (ttpp) REVERT: A 44 PHE cc_start: 0.7264 (m-80) cc_final: 0.6774 (m-80) REVERT: A 155 GLU cc_start: 0.0835 (OUTLIER) cc_final: -0.2267 (pt0) REVERT: A 186 LYS cc_start: 0.3293 (OUTLIER) cc_final: 0.0796 (ptmt) REVERT: A 190 TYR cc_start: 0.5560 (m-80) cc_final: 0.4868 (m-10) REVERT: A 261 TYR cc_start: 0.1501 (OUTLIER) cc_final: -0.1648 (m-80) REVERT: A 310 ASP cc_start: 0.6056 (m-30) cc_final: 0.5833 (m-30) REVERT: A 578 MET cc_start: 0.3050 (ttt) cc_final: 0.1245 (mtt) REVERT: A 601 TRP cc_start: 0.3019 (t-100) cc_final: 0.1639 (t-100) REVERT: A 611 TYR cc_start: 0.1986 (t80) cc_final: 0.0943 (m-80) REVERT: A 614 ASN cc_start: 0.2012 (m110) cc_final: 0.1251 (t0) REVERT: A 721 TYR cc_start: 0.2033 (OUTLIER) cc_final: 0.1769 (m-80) REVERT: A 819 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6133 (tpp80) REVERT: A 866 MET cc_start: 0.2521 (OUTLIER) cc_final: 0.1011 (mpp) REVERT: A 870 ARG cc_start: 0.6904 (tpm170) cc_final: 0.6015 (ptp-170) REVERT: A 936 MET cc_start: -0.2523 (mpp) cc_final: -0.3158 (mmm) REVERT: A 967 LEU cc_start: 0.5222 (mp) cc_final: 0.4846 (tp) REVERT: A 1001 MET cc_start: 0.5157 (ptm) cc_final: 0.4420 (mtt) REVERT: B 98 MET cc_start: 0.8068 (mmm) cc_final: 0.7739 (mmt) REVERT: B 525 ASP cc_start: 0.8009 (t0) cc_final: 0.7750 (t0) REVERT: B 578 MET cc_start: 0.5155 (tpp) cc_final: 0.4728 (tpt) REVERT: B 772 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8347 (tp) REVERT: B 784 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 842 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7572 (mp) REVERT: B 925 ILE cc_start: 0.4221 (OUTLIER) cc_final: 0.3457 (tt) REVERT: B 936 MET cc_start: 0.3134 (OUTLIER) cc_final: 0.2123 (ptm) REVERT: C 222 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6921 (m-30) REVERT: C 309 ILE cc_start: 0.7511 (mm) cc_final: 0.7094 (mt) REVERT: C 482 TYR cc_start: 0.8225 (t80) cc_final: 0.7794 (t80) REVERT: C 578 MET cc_start: 0.2372 (tpt) cc_final: 0.1455 (mtt) REVERT: C 725 TYR cc_start: 0.5297 (m-80) cc_final: 0.4501 (m-80) REVERT: C 757 TRP cc_start: 0.7112 (m-10) cc_final: 0.6713 (m-10) REVERT: C 782 GLN cc_start: 0.6213 (mt0) cc_final: 0.5906 (mt0) REVERT: C 792 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7782 (m) REVERT: C 913 MET cc_start: -0.1346 (tpt) cc_final: -0.2872 (mtt) REVERT: D 357 MET cc_start: 0.7252 (mmm) cc_final: 0.6904 (mmp) REVERT: D 362 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7984 (mm-30) REVERT: D 396 MET cc_start: 0.7777 (mmt) cc_final: 0.7379 (mmt) REVERT: D 522 PHE cc_start: 0.3964 (OUTLIER) cc_final: 0.3298 (t80) REVERT: D 578 MET cc_start: 0.5101 (ppp) cc_final: 0.4636 (ppp) REVERT: D 582 ILE cc_start: 0.7371 (mm) cc_final: 0.7128 (tp) REVERT: D 704 MET cc_start: 0.7253 (mmm) cc_final: 0.6976 (mmm) REVERT: D 781 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8282 (tt) REVERT: D 839 PHE cc_start: 0.7639 (m-80) cc_final: 0.7400 (m-80) REVERT: D 913 MET cc_start: 0.0140 (tpp) cc_final: -0.2739 (mmp) REVERT: D 936 MET cc_start: 0.2894 (mmp) cc_final: 0.2497 (mmm) REVERT: D 976 MET cc_start: 0.6293 (ttt) cc_final: 0.5513 (tpp) outliers start: 68 outliers final: 47 residues processed: 312 average time/residue: 0.1966 time to fit residues: 99.4954 Evaluate side-chains 304 residues out of total 3500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 110 VAL 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 441 PHE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 721 TYR Chi-restraints excluded: chain A residue 757 TRP 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 117 ILE Chi-restraints excluded: chain B residue 162 THR 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 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 772 ILE Chi-restraints excluded: chain B residue 779 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 925 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 647 MET Chi-restraints excluded: chain C residue 678 PHE Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1004 PHE Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 552 TYR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 737 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 838 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 258 optimal weight: 0.7980 chunk 302 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 237 optimal weight: 0.0870 chunk 288 optimal weight: 0.6980 chunk 370 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- 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 563 ASN A 786 HIS ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 789 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.143639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.124086 restraints weight = 118376.054| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 3.16 r_work: 0.4119 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 1.0039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32464 Z= 0.123 Angle : 0.603 12.498 43735 Z= 0.315 Chirality : 0.042 0.192 4649 Planarity : 0.004 0.071 5576 Dihedral : 4.884 52.045 4186 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.63 % Allowed : 16.79 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3764 helix: 0.75 (0.11), residues: 2490 sheet: -3.05 (0.44), residues: 100 loop : -2.28 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 61 TYR 0.037 0.001 TYR C 66 PHE 0.051 0.002 PHE A 441 TRP 0.031 0.002 TRP A 231 HIS 0.006 0.001 HIS D 978 Details of bonding type rmsd covalent geometry : bond 0.00271 (32464) covalent geometry : angle 0.60278 (43735) hydrogen bonds : bond 0.03444 ( 1697) hydrogen bonds : angle 4.63982 ( 4971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10211.60 seconds wall clock time: 175 minutes 39.11 seconds (10539.11 seconds total)