Starting phenix.real_space_refine on Mon Aug 25 05:24:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqw_23490/08_2025/7lqw_23490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqw_23490/08_2025/7lqw_23490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqw_23490/08_2025/7lqw_23490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqw_23490/08_2025/7lqw_23490.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqw_23490/08_2025/7lqw_23490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqw_23490/08_2025/7lqw_23490.cif" } resolution = 4.47 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= 0.001 sd= 0.031 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 106 5.16 5 C 16021 2.51 5 N 4267 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25332 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 611 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 295 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 5, 'PHE:plan': 4, 'TYR:plan': 6, 'TRP:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 197 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 535 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 7, 'ARG:plan': 6, 'ASP:plan': 2, 'TRP:plan': 2, 'TYR:plan': 5, 'HIS:plan': 1, 'PHE:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 178 Chain: "B" Number of atoms: 8111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8111 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain breaks: 7 Chain: "C" Number of atoms: 7611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1066, 7605 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1011} Chain breaks: 6 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 998 Unresolved non-hydrogen dihedrals: 657 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 19, 'ARG:plan': 9, 'TYR:plan': 12, 'PHE:plan': 20, 'TRP:plan': 4, 'HIS:plan': 5, 'ASP:plan': 8, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 447 Conformer: "B" Number of residues, atoms: 1066, 7605 Classifications: {'peptide': 1066} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1011} Chain breaks: 6 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 998 Unresolved non-hydrogen dihedrals: 657 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 19, 'ARG:plan': 9, 'TYR:plan': 12, 'PHE:plan': 20, 'TRP:plan': 4, 'HIS:plan': 5, 'ASP:plan': 8, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 447 bond proxies already assigned to first conformer: 7733 Chain: "A" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8100 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.84, per 1000 atoms: 0.31 Number of scatterers: 25332 At special positions: 0 Unit cell: (136.482, 163.99, 199.962, 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 106 16.00 O 4938 8.00 N 4267 7.00 C 16021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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 Links applied NAG-ASN " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6308 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 53 sheets defined 22.0% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.874A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.166A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.929A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.675A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.579A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.702A pdb=" N GLN B 628 " --> pdb=" O HIS B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.838A pdb=" N ARG B 634 " --> pdb=" O THR B 630 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.791A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 4.043A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 3.620A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.778A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.915A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.764A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.137A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.090A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.630A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.839A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 981' Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.858A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 removed outlier: 4.144A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.876A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 619 through 624 removed outlier: 4.401A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.789A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.143A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.755A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 removed outlier: 3.981A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 4.025A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 857 removed outlier: 3.588A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 857 " --> pdb=" O LYS C 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 853 through 857' Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.579A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 904 removed outlier: 3.526A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 910 removed outlier: 3.831A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.193A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.730A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.596A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.210A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.539A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.672A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.028A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.996A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.545A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.687A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.701A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.581A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.630A pdb=" N PHE A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.116A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.586A pdb=" N ASN A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.502A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.626A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 removed outlier: 3.644A pdb=" N GLU A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 989 through 1032 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.679A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.918A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.918A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.529A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.686A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.912A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.544A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 316 removed outlier: 3.972A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 324 through 328 removed outlier: 7.033A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.808A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.173A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 654 through 655 removed outlier: 4.154A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AB8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.608A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.608A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC2, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.659A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.982A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.558A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 191 through 194 Processing sheet with id=AC6, first strand: chain 'C' and resid 101 through 105 removed outlier: 4.538A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.214A pdb=" N THR C 114 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE C 133 " --> pdb=" O THR C 114 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC9, first strand: chain 'C' and resid 276 through 279 removed outlier: 4.234A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.966A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.665A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.029A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'C' and resid 565 through 566 removed outlier: 7.028A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.647A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 666 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.401A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.055A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 722 removed outlier: 3.809A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.535A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.558A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.546A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.623A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.762A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.633A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.631A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.683A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.826A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.837A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.128A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.859A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A1070 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 727 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AF7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'A' and resid 1094 through 1097 767 hydrogen bonds defined for protein. 2066 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: 6.18 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8321 1.34 - 1.46: 6065 1.46 - 1.58: 11317 1.58 - 1.70: 0 1.70 - 1.82: 130 Bond restraints: 25833 Sorted by residual: bond pdb=" N PRO H 102 " pdb=" CD PRO H 102 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" CA ASP A 294 " pdb=" CB ASP A 294 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.58e-02 4.01e+03 3.40e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 ... (remaining 25828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 19.22: 35217 19.22 - 38.45: 0 38.45 - 57.67: 0 57.67 - 76.89: 0 76.89 - 96.12: 1 Bond angle restraints: 35218 Sorted by residual: angle pdb=" C ASP H 101 " pdb=" N PRO H 102 " pdb=" CD PRO H 102 " ideal model delta sigma weight residual 125.00 28.88 96.12 4.10e+00 5.95e-02 5.50e+02 angle pdb=" CA PRO H 102 " pdb=" N PRO H 102 " pdb=" CD PRO H 102 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.21e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.71 109.10 4.61 9.50e-01 1.11e+00 2.35e+01 angle pdb=" CA ASP A 294 " pdb=" CB ASP A 294 " pdb=" CG ASP A 294 " ideal model delta sigma weight residual 112.60 117.11 -4.51 1.00e+00 1.00e+00 2.03e+01 angle pdb=" CA LEU B1141 " pdb=" CB LEU B1141 " pdb=" CG LEU B1141 " ideal model delta sigma weight residual 116.30 129.06 -12.76 3.50e+00 8.16e-02 1.33e+01 ... (remaining 35213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14337 17.96 - 35.93: 1082 35.93 - 53.89: 234 53.89 - 71.86: 45 71.86 - 89.82: 23 Dihedral angle restraints: 15721 sinusoidal: 5940 harmonic: 9781 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -3.80 -82.20 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -12.36 -73.64 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta harmonic sigma weight residual -180.00 -142.86 -37.14 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 15718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3918 0.098 - 0.196: 224 0.196 - 0.294: 8 0.294 - 0.393: 1 0.393 - 0.491: 1 Chirality restraints: 4152 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA ASP A 294 " pdb=" N ASP A 294 " pdb=" C ASP A 294 " pdb=" CB ASP A 294 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4149 not shown) Planarity restraints: 4595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 101 " -0.151 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO H 102 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 102 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO H 102 " 0.106 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B 987 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO B 384 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.035 5.00e-02 4.00e+02 ... (remaining 4592 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.71: 1 1.71 - 2.51: 117 2.51 - 3.30: 27049 3.30 - 4.10: 56735 4.10 - 4.90: 99816 Warning: very small nonbonded interaction distances. Nonbonded interactions: 183718 Sorted by model distance: nonbonded pdb=" O ASP H 101 " pdb=" CD PRO H 102 " model vdw 0.911 2.752 nonbonded pdb=" O ASP H 101 " pdb=" CG PRO H 102 " model vdw 1.941 3.440 nonbonded pdb=" CA ASP H 101 " pdb=" CD PRO H 102 " model vdw 2.121 3.096 nonbonded pdb=" C ASP H 101 " pdb=" CG PRO H 102 " model vdw 2.197 2.936 nonbonded pdb=" OH TYR B 369 " pdb=" OG1 THR A 415 " model vdw 2.202 3.040 ... (remaining 183713 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 30 and (name N or name CA or name C or name O or name CB \ )) or (resid 33 through 34 and (name N or name CA or name C or name O or name CB \ )) or (resid 39 and (name N or name CA or name C or name O or name CB )) or (re \ sid 50 and (name N or name CA or name C or name O or name CB )) or (resid 55 and \ (name N or name CA or name C or name O or name CB )) or (resid 63 and (name N o \ r name CA or name C or name O or name CB )) or (resid 80 through 88 and (name N \ or name CA or name C or name O or name CB )) or resid 89 or (resid 90 through 10 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 103 or (resi \ d 104 through 106 and (name N or name CA or name C or name O or name CB )) or re \ sid 107 or (resid 108 through 141 and (name N or name CA or name C or name O or \ name CB )) or resid 142 or (resid 143 through 198 and (name N or name CA or name \ C or name O or name CB )) or resid 199 or (resid 200 through 218 and (name N or \ name CA or name C or name O or name CB )) or resid 219 or (resid 220 through 23 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 232 or (resi \ d 233 through 250 and (name N or name CA or name C or name O or name CB )) or (r \ esid 264 through 267 and (name N or name CA or name C or name O or name CB )) or \ resid 268 or (resid 269 through 270 and (name N or name CA or name C or name O \ or name CB )) or resid 271 through 492 or resid 494 through 828 or resid 851 thr \ ough 1308)) selection = (chain 'B' and ((resid 30 and (name N or name CA or name C or name O or name CB \ )) or (resid 33 through 34 and (name N or name CA or name C or name O or name CB \ )) or (resid 39 and (name N or name CA or name C or name O or name CB )) or (re \ sid 50 and (name N or name CA or name C or name O or name CB )) or (resid 55 and \ (name N or name CA or name C or name O or name CB )) or (resid 63 and (name N o \ r name CA or name C or name O or name CB )) or (resid 80 through 88 and (name N \ or name CA or name C or name O or name CB )) or resid 89 or (resid 90 through 10 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 103 or (resi \ d 104 through 106 and (name N or name CA or name C or name O or name CB )) or re \ sid 107 or (resid 108 through 141 and (name N or name CA or name C or name O or \ name CB )) or resid 142 or (resid 143 through 172 and (name N or name CA or name \ C or name O or name CB )) or (resid 186 through 198 and (name N or name CA or n \ ame C or name O or name CB )) or resid 199 or (resid 200 through 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 or (resid 220 through \ 231 and (name N or name CA or name C or name O or name CB )) or resid 232 or (r \ esid 233 through 267 and (name N or name CA or name C or name O or name CB )) or \ resid 268 or (resid 269 through 270 and (name N or name CA or name C or name O \ or name CB )) or resid 271 through 492 or resid 494 through 622 or resid 633 thr \ ough 828 or resid 851 through 1308)) selection = (chain 'C' and (resid 17 or resid 20 through 21 or resid 26 or resid 60 or resid \ 65 or resid 73 or resid 80 through 143 or resid 159 through 172 or resid 186 th \ rough 250 or resid 264 through 444 or resid 447 through 492 or resid 494 through \ 622 or resid 633 through 828 or resid 851 through 1308)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 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: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.510 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 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 : 0.003 0.048 25885 Z= 0.143 Angle : 0.794 96.117 35336 Z= 0.345 Chirality : 0.046 0.491 4152 Planarity : 0.005 0.111 4581 Dihedral : 13.526 89.820 9299 Min Nonbonded Distance : 0.911 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.65 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3316 helix: -0.64 (0.20), residues: 616 sheet: 0.54 (0.21), residues: 639 loop : -1.42 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A1014 TYR 0.020 0.001 TYR C 707 PHE 0.030 0.001 PHE A 43 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00287 (25833) covalent geometry : angle 0.78609 (35218) SS BOND : bond 0.00242 ( 38) SS BOND : angle 1.11143 ( 76) hydrogen bonds : bond 0.30608 ( 756) hydrogen bonds : angle 9.56447 ( 2066) link_NAG-ASN : bond 0.00580 ( 14) link_NAG-ASN : angle 3.22582 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.991 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: C 1050 MET cc_start: 0.5922 (ppp) cc_final: 0.5570 (ppp) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.1871 time to fit residues: 45.0389 Evaluate side-chains 69 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 239 GLN B 317 ASN B 370 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 519 HIS B 784 GLN B 954 GLN B1023 ASN B1101 HIS C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 644 GLN A 955 ASN A1011 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.039460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.030745 restraints weight = 392252.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.031740 restraints weight = 192699.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.032378 restraints weight = 118927.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.032829 restraints weight = 84956.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.033097 restraints weight = 66598.293| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 25885 Z= 0.302 Angle : 0.777 16.894 35336 Z= 0.402 Chirality : 0.047 0.463 4152 Planarity : 0.006 0.174 4581 Dihedral : 6.103 58.754 4114 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 0.12 % Allowed : 5.46 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.14), residues: 3316 helix: 0.09 (0.20), residues: 644 sheet: 0.13 (0.21), residues: 645 loop : -1.26 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 995 TYR 0.022 0.002 TYR A 741 PHE 0.042 0.002 PHE B1062 TRP 0.013 0.002 TRP A 353 HIS 0.008 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00582 (25833) covalent geometry : angle 0.76480 (35218) SS BOND : bond 0.00563 ( 38) SS BOND : angle 1.71803 ( 76) hydrogen bonds : bond 0.05438 ( 756) hydrogen bonds : angle 6.58588 ( 2066) link_NAG-ASN : bond 0.00711 ( 14) link_NAG-ASN : angle 3.39593 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.9833 (mmp) cc_final: 0.9455 (mmm) REVERT: C 340 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9129 (pm20) REVERT: C 532 ASN cc_start: 0.9389 (t0) cc_final: 0.9186 (t0) REVERT: C 740 MET cc_start: 0.9474 (ttm) cc_final: 0.9073 (ttm) REVERT: C 902 MET cc_start: 0.9652 (mmp) cc_final: 0.9238 (mmm) REVERT: C 1029 MET cc_start: 0.9844 (mmp) cc_final: 0.9466 (mmm) REVERT: C 1050 MET cc_start: 0.9162 (ppp) cc_final: 0.8873 (ppp) REVERT: A 269 TYR cc_start: 0.9200 (m-10) cc_final: 0.8958 (m-10) REVERT: A 740 MET cc_start: 0.9444 (ppp) cc_final: 0.9242 (ppp) REVERT: A 833 PHE cc_start: 0.7676 (t80) cc_final: 0.7375 (t80) REVERT: A 869 MET cc_start: 0.9519 (mtm) cc_final: 0.9150 (mtm) REVERT: A 1029 MET cc_start: 0.9812 (tpt) cc_final: 0.9465 (tpp) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1590 time to fit residues: 17.9654 Evaluate side-chains 47 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 111 optimal weight: 0.9990 chunk 286 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 142 optimal weight: 40.0000 chunk 200 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 370 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 448 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 644 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.039647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.030738 restraints weight = 458190.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.031811 restraints weight = 209491.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.032485 restraints weight = 124336.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032991 restraints weight = 86644.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.033278 restraints weight = 66195.210| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 25885 Z= 0.162 Angle : 0.581 11.360 35336 Z= 0.298 Chirality : 0.045 0.429 4152 Planarity : 0.004 0.141 4581 Dihedral : 5.554 59.135 4114 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.15), residues: 3316 helix: 0.64 (0.21), residues: 642 sheet: 0.15 (0.22), residues: 617 loop : -1.22 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 328 TYR 0.016 0.001 TYR B 917 PHE 0.026 0.001 PHE B 562 TRP 0.011 0.001 TRP C 633 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00319 (25833) covalent geometry : angle 0.56791 (35218) SS BOND : bond 0.00446 ( 38) SS BOND : angle 1.48346 ( 76) hydrogen bonds : bond 0.04310 ( 756) hydrogen bonds : angle 5.82669 ( 2066) link_NAG-ASN : bond 0.00525 ( 14) link_NAG-ASN : angle 3.05595 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.9379 (m-40) cc_final: 0.9145 (p0) REVERT: B 773 GLU cc_start: 0.9624 (mt-10) cc_final: 0.9287 (tp30) REVERT: B 856 ASN cc_start: 0.9416 (t0) cc_final: 0.8889 (p0) REVERT: B 858 LEU cc_start: 0.9612 (mt) cc_final: 0.9121 (mt) REVERT: B 902 MET cc_start: 0.9811 (mmp) cc_final: 0.9492 (mmm) REVERT: B 906 PHE cc_start: 0.9746 (m-80) cc_final: 0.9339 (m-80) REVERT: C 340 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9191 (pt0) REVERT: C 532 ASN cc_start: 0.9422 (t0) cc_final: 0.9209 (t0) REVERT: C 731 MET cc_start: 0.9015 (ppp) cc_final: 0.8787 (ppp) REVERT: C 740 MET cc_start: 0.9301 (ttm) cc_final: 0.8913 (ttm) REVERT: C 902 MET cc_start: 0.9679 (mmp) cc_final: 0.9178 (mmm) REVERT: C 1029 MET cc_start: 0.9875 (mmp) cc_final: 0.9351 (mmm) REVERT: A 365 TYR cc_start: 0.9698 (m-10) cc_final: 0.9379 (m-10) REVERT: A 739 THR cc_start: 0.9166 (m) cc_final: 0.8963 (p) REVERT: A 740 MET cc_start: 0.9379 (ppp) cc_final: 0.9020 (ppp) REVERT: A 869 MET cc_start: 0.9519 (mtm) cc_final: 0.9156 (mtm) REVERT: A 902 MET cc_start: 0.9587 (mmp) cc_final: 0.9313 (mmp) REVERT: A 1029 MET cc_start: 0.9830 (tpt) cc_final: 0.9571 (tpp) REVERT: A 1050 MET cc_start: 0.9591 (pmm) cc_final: 0.9266 (pmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1579 time to fit residues: 17.9788 Evaluate side-chains 51 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 297 optimal weight: 0.8980 chunk 156 optimal weight: 20.0000 chunk 210 optimal weight: 0.9980 chunk 17 optimal weight: 40.0000 chunk 301 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 ASN B 388 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 519 HIS A 762 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.037480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028826 restraints weight = 448903.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.029834 restraints weight = 209625.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.030467 restraints weight = 125525.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.030931 restraints weight = 88268.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.031199 restraints weight = 68167.260| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 25885 Z= 0.199 Angle : 0.628 13.190 35336 Z= 0.322 Chirality : 0.045 0.400 4152 Planarity : 0.005 0.130 4581 Dihedral : 5.393 58.749 4114 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 0.12 % Allowed : 3.42 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.15), residues: 3316 helix: 0.65 (0.21), residues: 646 sheet: 0.08 (0.21), residues: 672 loop : -1.25 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 509 TYR 0.015 0.002 TYR A 396 PHE 0.017 0.002 PHE B1062 TRP 0.010 0.002 TRP A 353 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00396 (25833) covalent geometry : angle 0.61490 (35218) SS BOND : bond 0.00788 ( 38) SS BOND : angle 1.62769 ( 76) hydrogen bonds : bond 0.04010 ( 756) hydrogen bonds : angle 5.73698 ( 2066) link_NAG-ASN : bond 0.00565 ( 14) link_NAG-ASN : angle 3.13398 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9052 (m-30) cc_final: 0.8540 (t70) REVERT: B 731 MET cc_start: 0.9334 (ppp) cc_final: 0.9094 (ppp) REVERT: B 773 GLU cc_start: 0.9587 (mt-10) cc_final: 0.9205 (tp30) REVERT: B 856 ASN cc_start: 0.9392 (t0) cc_final: 0.8648 (t0) REVERT: B 902 MET cc_start: 0.9818 (mmp) cc_final: 0.9451 (mmm) REVERT: B 906 PHE cc_start: 0.9803 (m-80) cc_final: 0.9387 (m-80) REVERT: B 1029 MET cc_start: 0.9695 (mmp) cc_final: 0.9445 (mmm) REVERT: C 340 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9264 (pm20) REVERT: C 731 MET cc_start: 0.9058 (ppp) cc_final: 0.8802 (ppp) REVERT: C 740 MET cc_start: 0.9397 (ttm) cc_final: 0.8968 (ttm) REVERT: C 902 MET cc_start: 0.9636 (mmp) cc_final: 0.9164 (mmm) REVERT: C 1029 MET cc_start: 0.9879 (mmp) cc_final: 0.9354 (mmm) REVERT: C 1050 MET cc_start: 0.9062 (ppp) cc_final: 0.8742 (ppp) REVERT: A 365 TYR cc_start: 0.9718 (m-10) cc_final: 0.9380 (m-10) REVERT: A 740 MET cc_start: 0.9438 (ppp) cc_final: 0.9204 (ppp) REVERT: A 869 MET cc_start: 0.9509 (mtm) cc_final: 0.9130 (mtm) REVERT: A 902 MET cc_start: 0.9612 (mmp) cc_final: 0.9372 (mmp) REVERT: A 1029 MET cc_start: 0.9800 (tpt) cc_final: 0.9537 (tpp) REVERT: A 1050 MET cc_start: 0.9625 (pmm) cc_final: 0.9329 (pmm) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1665 time to fit residues: 15.9924 Evaluate side-chains 47 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 13 optimal weight: 50.0000 chunk 57 optimal weight: 0.0030 chunk 191 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 9 optimal weight: 50.0000 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.036701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.028410 restraints weight = 381103.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.029310 restraints weight = 188961.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029903 restraints weight = 117143.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.030302 restraints weight = 83536.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.030592 restraints weight = 65745.677| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 25885 Z= 0.192 Angle : 0.604 12.913 35336 Z= 0.310 Chirality : 0.045 0.397 4152 Planarity : 0.004 0.124 4581 Dihedral : 5.379 59.499 4114 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 0.08 % Allowed : 2.16 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3316 helix: 0.65 (0.21), residues: 660 sheet: -0.26 (0.21), residues: 663 loop : -1.25 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 403 TYR 0.015 0.001 TYR B 789 PHE 0.015 0.002 PHE A 201 TRP 0.010 0.001 TRP B 633 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00380 (25833) covalent geometry : angle 0.58829 (35218) SS BOND : bond 0.00395 ( 38) SS BOND : angle 1.51339 ( 76) hydrogen bonds : bond 0.03758 ( 756) hydrogen bonds : angle 5.63875 ( 2066) link_NAG-ASN : bond 0.00646 ( 14) link_NAG-ASN : angle 3.60384 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9064 (m-30) cc_final: 0.8588 (t70) REVERT: B 731 MET cc_start: 0.9378 (ppp) cc_final: 0.8806 (ppp) REVERT: B 856 ASN cc_start: 0.9377 (t0) cc_final: 0.8570 (t0) REVERT: B 902 MET cc_start: 0.9827 (mmp) cc_final: 0.9457 (mmm) REVERT: B 906 PHE cc_start: 0.9838 (m-80) cc_final: 0.9408 (m-80) REVERT: B 1029 MET cc_start: 0.9731 (mmp) cc_final: 0.9451 (mmm) REVERT: C 731 MET cc_start: 0.9081 (ppp) cc_final: 0.8809 (ppp) REVERT: C 740 MET cc_start: 0.9355 (ttm) cc_final: 0.8900 (ttm) REVERT: C 902 MET cc_start: 0.9641 (mmp) cc_final: 0.9202 (mmm) REVERT: C 1029 MET cc_start: 0.9880 (mmp) cc_final: 0.9377 (mmm) REVERT: A 365 TYR cc_start: 0.9713 (m-10) cc_final: 0.9385 (m-10) REVERT: A 740 MET cc_start: 0.9443 (ppp) cc_final: 0.9240 (ppp) REVERT: A 869 MET cc_start: 0.9512 (mtm) cc_final: 0.9121 (mtm) REVERT: A 900 MET cc_start: 0.9701 (mmp) cc_final: 0.9478 (mmm) REVERT: A 902 MET cc_start: 0.9564 (mmp) cc_final: 0.9320 (mmp) REVERT: A 1050 MET cc_start: 0.9715 (pmm) cc_final: 0.9458 (pmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1576 time to fit residues: 14.6751 Evaluate side-chains 43 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 119 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 9.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 343 ASN B 370 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 779 GLN C 784 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 544 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 655 HIS A 690 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.031391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.023745 restraints weight = 463422.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.024542 restraints weight = 232389.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.025075 restraints weight = 145371.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.025357 restraints weight = 104626.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.025616 restraints weight = 85493.588| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 25885 Z= 0.500 Angle : 1.066 22.155 35336 Z= 0.560 Chirality : 0.053 0.424 4152 Planarity : 0.008 0.122 4581 Dihedral : 7.149 59.745 4114 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 35.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.98 % Favored : 89.95 % Rotamer: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % 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: -2.44 (0.13), residues: 3316 helix: -1.41 (0.17), residues: 668 sheet: -1.03 (0.20), residues: 637 loop : -1.96 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 454 TYR 0.037 0.004 TYR B 756 PHE 0.042 0.004 PHE B 464 TRP 0.023 0.004 TRP B 633 HIS 0.013 0.004 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00954 (25833) covalent geometry : angle 1.04838 (35218) SS BOND : bond 0.01194 ( 38) SS BOND : angle 2.93508 ( 76) hydrogen bonds : bond 0.06012 ( 756) hydrogen bonds : angle 7.63179 ( 2066) link_NAG-ASN : bond 0.01030 ( 14) link_NAG-ASN : angle 4.28950 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 314 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8953 (pp30) REVERT: B 731 MET cc_start: 0.9259 (ppp) cc_final: 0.8950 (ppp) REVERT: B 902 MET cc_start: 0.9844 (mmp) cc_final: 0.9505 (mmm) REVERT: B 906 PHE cc_start: 0.9899 (m-80) cc_final: 0.9514 (m-10) REVERT: B 1029 MET cc_start: 0.9808 (mmp) cc_final: 0.9496 (mmm) REVERT: C 340 GLU cc_start: 0.9756 (mm-30) cc_final: 0.9539 (pm20) REVERT: C 740 MET cc_start: 0.9473 (ttm) cc_final: 0.8968 (ttm) REVERT: C 902 MET cc_start: 0.9523 (mmp) cc_final: 0.9150 (mmm) REVERT: C 1029 MET cc_start: 0.9907 (mmp) cc_final: 0.9449 (mmm) REVERT: A 365 TYR cc_start: 0.9744 (m-10) cc_final: 0.9379 (m-10) REVERT: A 773 GLU cc_start: 0.9648 (tt0) cc_final: 0.9140 (tp30) REVERT: A 869 MET cc_start: 0.9589 (mtm) cc_final: 0.9299 (mtm) REVERT: A 1050 MET cc_start: 0.9733 (pmm) cc_final: 0.9375 (pmm) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.1591 time to fit residues: 13.9377 Evaluate side-chains 39 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 83 optimal weight: 4.9990 chunk 330 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 307 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 306 optimal weight: 8.9990 chunk 160 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 280 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 519 HIS ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.027956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.019247 restraints weight = 529844.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.020007 restraints weight = 302673.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.020552 restraints weight = 206403.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.020959 restraints weight = 156714.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.021248 restraints weight = 127458.539| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25885 Z= 0.184 Angle : 0.649 12.468 35336 Z= 0.336 Chirality : 0.046 0.413 4152 Planarity : 0.005 0.118 4581 Dihedral : 6.173 59.317 4114 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 0.12 % Allowed : 1.22 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.14), residues: 3316 helix: -0.16 (0.20), residues: 678 sheet: -0.89 (0.21), residues: 621 loop : -1.66 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 454 TYR 0.017 0.002 TYR A 873 PHE 0.032 0.002 PHE C 429 TRP 0.015 0.002 TRP C 886 HIS 0.004 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00373 (25833) covalent geometry : angle 0.63248 (35218) SS BOND : bond 0.00475 ( 38) SS BOND : angle 1.86001 ( 76) hydrogen bonds : bond 0.03920 ( 756) hydrogen bonds : angle 6.41202 ( 2066) link_NAG-ASN : bond 0.00515 ( 14) link_NAG-ASN : angle 3.56238 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9222 (m-30) cc_final: 0.8809 (t70) REVERT: B 697 MET cc_start: 0.9434 (ppp) cc_final: 0.9225 (ppp) REVERT: B 731 MET cc_start: 0.9336 (ppp) cc_final: 0.8931 (ppp) REVERT: B 902 MET cc_start: 0.9853 (mmp) cc_final: 0.9469 (mmm) REVERT: B 906 PHE cc_start: 0.9861 (m-80) cc_final: 0.9399 (m-80) REVERT: B 1029 MET cc_start: 0.9790 (mmp) cc_final: 0.9396 (mmm) REVERT: C 731 MET cc_start: 0.9128 (ppp) cc_final: 0.8892 (ppp) REVERT: C 740 MET cc_start: 0.9403 (ttm) cc_final: 0.8890 (ttm) REVERT: C 902 MET cc_start: 0.9532 (mmp) cc_final: 0.9187 (mmm) REVERT: C 1029 MET cc_start: 0.9841 (mmp) cc_final: 0.9272 (mmm) REVERT: A 365 TYR cc_start: 0.9771 (m-10) cc_final: 0.9423 (m-10) REVERT: A 773 GLU cc_start: 0.9673 (tt0) cc_final: 0.9176 (tp30) REVERT: A 869 MET cc_start: 0.9599 (mtm) cc_final: 0.9292 (mtm) REVERT: A 902 MET cc_start: 0.9647 (mmp) cc_final: 0.9367 (mmp) REVERT: A 1029 MET cc_start: 0.9827 (tpt) cc_final: 0.9622 (tpp) outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.1608 time to fit residues: 14.3306 Evaluate side-chains 40 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 240 optimal weight: 2.9990 chunk 139 optimal weight: 40.0000 chunk 228 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 325 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 312 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.034157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.026371 restraints weight = 417940.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.027257 restraints weight = 199621.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.027832 restraints weight = 121258.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.028165 restraints weight = 85472.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028482 restraints weight = 67658.600| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25885 Z= 0.167 Angle : 0.611 12.271 35336 Z= 0.314 Chirality : 0.045 0.394 4152 Planarity : 0.005 0.114 4581 Dihedral : 5.785 59.157 4114 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 0.08 % Allowed : 0.71 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3316 helix: 0.30 (0.20), residues: 677 sheet: -0.83 (0.20), residues: 627 loop : -1.57 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 454 TYR 0.014 0.002 TYR C 365 PHE 0.016 0.002 PHE B 220 TRP 0.010 0.001 TRP C 633 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00340 (25833) covalent geometry : angle 0.59515 (35218) SS BOND : bond 0.00623 ( 38) SS BOND : angle 1.82834 ( 76) hydrogen bonds : bond 0.03632 ( 756) hydrogen bonds : angle 6.00121 ( 2066) link_NAG-ASN : bond 0.00540 ( 14) link_NAG-ASN : angle 3.39657 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9231 (m-30) cc_final: 0.8841 (t70) REVERT: B 697 MET cc_start: 0.9423 (ppp) cc_final: 0.9205 (ppp) REVERT: B 731 MET cc_start: 0.9329 (ppp) cc_final: 0.8952 (ppp) REVERT: B 902 MET cc_start: 0.9846 (mmp) cc_final: 0.9474 (mmm) REVERT: B 906 PHE cc_start: 0.9869 (m-80) cc_final: 0.9403 (m-10) REVERT: B 1029 MET cc_start: 0.9771 (mmp) cc_final: 0.9401 (mmm) REVERT: C 731 MET cc_start: 0.9044 (ppp) cc_final: 0.8830 (ppp) REVERT: C 740 MET cc_start: 0.9341 (ttm) cc_final: 0.8812 (ttm) REVERT: C 902 MET cc_start: 0.9588 (mmp) cc_final: 0.9226 (mmm) REVERT: C 1029 MET cc_start: 0.9827 (mmp) cc_final: 0.9255 (mmm) REVERT: A 365 TYR cc_start: 0.9752 (m-10) cc_final: 0.9384 (m-10) REVERT: A 773 GLU cc_start: 0.9634 (tt0) cc_final: 0.9141 (tp30) REVERT: A 869 MET cc_start: 0.9571 (mtm) cc_final: 0.9250 (mtm) REVERT: A 902 MET cc_start: 0.9696 (mmp) cc_final: 0.9452 (mmp) REVERT: A 1010 GLN cc_start: 0.9703 (tp-100) cc_final: 0.9398 (tp-100) REVERT: A 1029 MET cc_start: 0.9829 (tpt) cc_final: 0.9606 (tpp) REVERT: A 1050 MET cc_start: 0.9593 (pmm) cc_final: 0.9369 (pmm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1578 time to fit residues: 12.5960 Evaluate side-chains 41 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 44 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 140 optimal weight: 40.0000 chunk 176 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.027593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.019395 restraints weight = 413246.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.020053 restraints weight = 257337.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.020524 restraints weight = 183812.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.020853 restraints weight = 143547.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.021133 restraints weight = 119678.963| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2500 r_free = 0.2500 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25885 Z= 0.208 Angle : 0.652 12.584 35336 Z= 0.337 Chirality : 0.045 0.385 4152 Planarity : 0.005 0.111 4581 Dihedral : 5.858 59.377 4114 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 0.08 % Allowed : 0.79 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.14), residues: 3316 helix: 0.23 (0.20), residues: 686 sheet: -0.82 (0.21), residues: 628 loop : -1.60 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 454 TYR 0.018 0.002 TYR B 756 PHE 0.018 0.002 PHE A 133 TRP 0.011 0.002 TRP C1102 HIS 0.006 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00410 (25833) covalent geometry : angle 0.63592 (35218) SS BOND : bond 0.00424 ( 38) SS BOND : angle 1.90891 ( 76) hydrogen bonds : bond 0.03779 ( 756) hydrogen bonds : angle 6.05499 ( 2066) link_NAG-ASN : bond 0.00595 ( 14) link_NAG-ASN : angle 3.49150 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9323 (m-30) cc_final: 0.8885 (t70) REVERT: B 697 MET cc_start: 0.9504 (ppp) cc_final: 0.9270 (ppp) REVERT: B 731 MET cc_start: 0.9298 (ppp) cc_final: 0.8966 (ppp) REVERT: B 902 MET cc_start: 0.9860 (mmp) cc_final: 0.9492 (mmm) REVERT: B 906 PHE cc_start: 0.9869 (m-80) cc_final: 0.9429 (m-10) REVERT: B 1029 MET cc_start: 0.9795 (mmp) cc_final: 0.9439 (mmm) REVERT: C 740 MET cc_start: 0.9340 (ttm) cc_final: 0.8853 (ttm) REVERT: C 902 MET cc_start: 0.9541 (mmp) cc_final: 0.9191 (mmm) REVERT: C 1029 MET cc_start: 0.9835 (mmp) cc_final: 0.9277 (mmm) REVERT: A 365 TYR cc_start: 0.9796 (m-10) cc_final: 0.9430 (m-10) REVERT: A 773 GLU cc_start: 0.9699 (tt0) cc_final: 0.9189 (tp30) REVERT: A 869 MET cc_start: 0.9593 (mtm) cc_final: 0.9237 (mtm) REVERT: A 902 MET cc_start: 0.9657 (mmp) cc_final: 0.9390 (mmp) REVERT: A 1010 GLN cc_start: 0.9691 (tp-100) cc_final: 0.9410 (tp-100) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1617 time to fit residues: 12.9428 Evaluate side-chains 41 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 278 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 chunk 138 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 30.0000 chunk 321 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 176 optimal weight: 0.0050 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 450 ASN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.034338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.026646 restraints weight = 386786.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.027517 restraints weight = 188782.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.028059 restraints weight = 115207.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.028442 restraints weight = 81434.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.028689 restraints weight = 63905.035| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 25885 Z= 0.136 Angle : 0.586 12.272 35336 Z= 0.299 Chirality : 0.045 0.384 4152 Planarity : 0.004 0.108 4581 Dihedral : 5.594 59.423 4114 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 0.12 % Allowed : 0.20 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.14), residues: 3316 helix: 0.54 (0.20), residues: 683 sheet: -0.70 (0.21), residues: 606 loop : -1.51 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 454 TYR 0.012 0.001 TYR B 917 PHE 0.015 0.001 PHE B 220 TRP 0.009 0.001 TRP C 633 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00287 (25833) covalent geometry : angle 0.57051 (35218) SS BOND : bond 0.00359 ( 38) SS BOND : angle 1.66292 ( 76) hydrogen bonds : bond 0.03374 ( 756) hydrogen bonds : angle 5.75203 ( 2066) link_NAG-ASN : bond 0.00542 ( 14) link_NAG-ASN : angle 3.32017 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6632 Ramachandran restraints generated. 3316 Oldfield, 0 Emsley, 3316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9204 (m-30) cc_final: 0.8773 (t70) REVERT: B 409 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8067 (mm110) REVERT: B 731 MET cc_start: 0.9305 (ppp) cc_final: 0.8944 (ppp) REVERT: B 902 MET cc_start: 0.9845 (mmp) cc_final: 0.9446 (mmm) REVERT: B 906 PHE cc_start: 0.9860 (m-80) cc_final: 0.9417 (m-80) REVERT: B 1029 MET cc_start: 0.9785 (mmp) cc_final: 0.9416 (mmm) REVERT: C 740 MET cc_start: 0.9287 (ttm) cc_final: 0.8773 (ttm) REVERT: C 902 MET cc_start: 0.9606 (mmp) cc_final: 0.9243 (mmm) REVERT: C 1029 MET cc_start: 0.9801 (mmp) cc_final: 0.9234 (mmm) REVERT: A 365 TYR cc_start: 0.9726 (m-10) cc_final: 0.9348 (m-10) REVERT: A 773 GLU cc_start: 0.9671 (tt0) cc_final: 0.9127 (tp30) REVERT: A 869 MET cc_start: 0.9592 (mtm) cc_final: 0.9279 (mtm) REVERT: A 902 MET cc_start: 0.9701 (mmp) cc_final: 0.9419 (mmp) REVERT: A 1010 GLN cc_start: 0.9675 (tp-100) cc_final: 0.9416 (tp-100) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1600 time to fit residues: 13.1235 Evaluate side-chains 41 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 243 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 chunk 294 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.027189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.019320 restraints weight = 393373.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.019932 restraints weight = 248677.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.020381 restraints weight = 179839.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.020716 restraints weight = 141344.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.020949 restraints weight = 117667.223| |-----------------------------------------------------------------------------| r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.7660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25885 Z= 0.257 Angle : 0.704 13.051 35336 Z= 0.366 Chirality : 0.046 0.387 4152 Planarity : 0.005 0.107 4581 Dihedral : 6.007 57.899 4114 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.36 % Favored : 91.58 % Rotamer: Outliers : 0.08 % Allowed : 0.35 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.14), residues: 3316 helix: 0.02 (0.19), residues: 704 sheet: -0.79 (0.21), residues: 599 loop : -1.67 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 454 TYR 0.025 0.002 TYR B 756 PHE 0.019 0.002 PHE A1103 TRP 0.010 0.002 TRP C1102 HIS 0.006 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00497 (25833) covalent geometry : angle 0.68698 (35218) SS BOND : bond 0.00493 ( 38) SS BOND : angle 2.09457 ( 76) hydrogen bonds : bond 0.04014 ( 756) hydrogen bonds : angle 6.24014 ( 2066) link_NAG-ASN : bond 0.00611 ( 14) link_NAG-ASN : angle 3.62730 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.34 seconds wall clock time: 73 minutes 39.34 seconds (4419.34 seconds total)