Starting phenix.real_space_refine on Sun Jul 5 04:25:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_23490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_23490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_23490.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_23490.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_23490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_23490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqw_23490/07_2026/7lqw_23490.map" } 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-dev-6108/lib/python3.11/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 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 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 chiralities: 9 Time building chain proxies: 6.17, per 1000 atoms: 0.24 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.91 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: 5.18 Time building geometry restraints manager: 2.89 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: 13857 17.96 - 35.93: 1048 35.93 - 53.89: 208 53.89 - 71.86: 39 71.86 - 89.82: 23 Dihedral angle restraints: 15175 sinusoidal: 5394 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 15172 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: 6.590 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.270 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 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 : 13.506 89.820 8753 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 are 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/Z covalent geometry : bond 0.00287 / 0.14 (25833) covalent geometry : angle 0.78609 / 0.34 (35218) SS BOND : bond 0.00242 / 0.18 ( 38) SS BOND : angle 1.11143 / 0.77 ( 76) hydrogen bonds : bond 0.30608 / 23.01 ( 756) hydrogen bonds : angle 9.56447 / 6.86 ( 2066) link_NAG-ASN : bond 0.00580 / 0.50 ( 14) link_NAG-ASN : angle 3.22582 / 2.24 ( 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 : 0.973 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: 0.1537 time to fit residues: 37.5065 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 : 0.937 ------------------------------------------------------------------------------- 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... 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 954 GLN B1023 ASN B1101 HIS C 779 GLN C 872 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 ASN ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.039735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.030934 restraints weight = 391453.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.031950 restraints weight = 192053.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.032590 restraints weight = 117901.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.033038 restraints weight = 83509.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.033310 restraints weight = 65623.330| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 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 = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 25885 Z= 0.304 Angle : 0.768 16.622 35336 Z= 0.398 Chirality : 0.047 0.453 4152 Planarity : 0.006 0.179 4581 Dihedral : 4.415 33.810 3568 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 0.16 % Allowed : 5.22 % Favored : 94.62 % 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 are not related in a simple way. whole: -1.00 (0.14), residues: 3316 helix: 0.16 (0.20), residues: 649 sheet: 0.17 (0.22), residues: 628 loop : -1.25 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 995 TYR 0.021 0.002 TYR B 313 PHE 0.037 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/Z covalent geometry : bond 0.00586 / 0.30 (25833) covalent geometry : angle 0.75703 / 0.39 (35218) SS BOND : bond 0.00558 / 0.42 ( 38) SS BOND : angle 1.67693 / 1.23 ( 76) hydrogen bonds : bond 0.05442 / 4.13 ( 756) hydrogen bonds : angle 6.55364 / 4.70 ( 2066) link_NAG-ASN : bond 0.00672 / 0.49 ( 14) link_NAG-ASN : angle 3.26413 / 2.26 ( 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: 2 poor density : 62 time to evaluate : 0.863 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: 0.9836 (mmp) cc_final: 0.9454 (mmm) REVERT: C 340 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9119 (pm20) REVERT: C 532 ASN cc_start: 0.9375 (t0) cc_final: 0.9169 (t0) REVERT: C 740 MET cc_start: 0.9480 (ttm) cc_final: 0.9079 (ttm) REVERT: C 902 MET cc_start: 0.9655 (mmp) cc_final: 0.9164 (mmm) REVERT: C 1029 MET cc_start: 0.9840 (mmp) cc_final: 0.9420 (mmm) REVERT: C 1050 MET cc_start: 0.9170 (ppp) cc_final: 0.8850 (ppp) REVERT: A 269 TYR cc_start: 0.9177 (m-10) cc_final: 0.8932 (m-10) REVERT: A 740 MET cc_start: 0.9440 (ppp) cc_final: 0.9234 (ppp) REVERT: A 833 PHE cc_start: 0.7676 (t80) cc_final: 0.7389 (t80) REVERT: A 869 MET cc_start: 0.9532 (mtm) cc_final: 0.9164 (mtm) REVERT: A 902 MET cc_start: 0.9637 (mmp) cc_final: 0.9432 (mmm) REVERT: A 1029 MET cc_start: 0.9811 (tpt) cc_final: 0.9467 (tpp) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1484 time to fit residues: 16.4759 Evaluate side-chains 46 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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: 0.8980 chunk 286 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 chunk 200 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 258 optimal weight: 0.0070 chunk 249 optimal weight: 20.0000 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 B 784 GLN B 856 ASN C 448 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 955 ASN A1036 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.041391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.032275 restraints weight = 448677.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.033400 restraints weight = 202880.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.034129 restraints weight = 119832.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.034609 restraints weight = 82509.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.034906 restraints weight = 63127.061| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 25885 Z= 0.114 Angle : 0.551 10.857 35336 Z= 0.278 Chirality : 0.045 0.418 4152 Planarity : 0.004 0.143 4581 Dihedral : 4.003 33.885 3568 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.72 % 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 are not related in a simple way. whole: -0.81 (0.14), residues: 3316 helix: 0.55 (0.21), residues: 644 sheet: 0.28 (0.22), residues: 598 loop : -1.19 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 328 TYR 0.014 0.001 TYR A 873 PHE 0.022 0.001 PHE B 562 TRP 0.009 0.001 TRP C 633 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (25833) covalent geometry : angle 0.53948 / 0.28 (35218) SS BOND : bond 0.00298 / 0.23 ( 38) SS BOND : angle 1.21901 / 0.86 ( 76) hydrogen bonds : bond 0.04186 / 3.17 ( 756) hydrogen bonds : angle 5.78210 / 4.15 ( 2066) link_NAG-ASN : bond 0.00532 / 0.46 ( 14) link_NAG-ASN : angle 2.90571 / 2.01 ( 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 68 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.980 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: B 370 ASN cc_start: 0.9315 (m-40) cc_final: 0.9070 (p0) REVERT: B 731 MET cc_start: 0.9418 (ptm) cc_final: 0.8656 (ppp) REVERT: B 856 ASN cc_start: 0.9401 (t0) cc_final: 0.8914 (p0) REVERT: B 858 LEU cc_start: 0.9689 (mt) cc_final: 0.9277 (mt) REVERT: B 902 MET cc_start: 0.9776 (mmp) cc_final: 0.9460 (mmm) REVERT: B 906 PHE cc_start: 0.9652 (m-80) cc_final: 0.9205 (m-80) REVERT: C 340 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9133 (pt0) REVERT: C 532 ASN cc_start: 0.9373 (t0) cc_final: 0.9152 (t0) REVERT: C 731 MET cc_start: 0.9009 (ppp) cc_final: 0.8791 (ppp) REVERT: C 740 MET cc_start: 0.9337 (ttm) cc_final: 0.8947 (ttm) REVERT: C 902 MET cc_start: 0.9680 (mmp) cc_final: 0.9267 (mmm) REVERT: C 1029 MET cc_start: 0.9859 (mmp) cc_final: 0.9330 (mmm) REVERT: A 269 TYR cc_start: 0.9203 (m-10) cc_final: 0.8958 (m-10) REVERT: A 740 MET cc_start: 0.9345 (ppp) cc_final: 0.8974 (ppp) REVERT: A 869 MET cc_start: 0.9498 (mtm) cc_final: 0.9173 (mtm) REVERT: A 902 MET cc_start: 0.9569 (mmp) cc_final: 0.9351 (mmm) REVERT: A 1029 MET cc_start: 0.9806 (tpt) cc_final: 0.9508 (tpp) REVERT: A 1050 MET cc_start: 0.9481 (pmm) cc_final: 0.9216 (pmm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1262 time to fit residues: 15.5743 Evaluate side-chains 56 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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: 8.9990 chunk 101 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 17 optimal weight: 40.0000 chunk 301 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 282 ASN B 388 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 779 GLN ** 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** A 87 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 544 ASN A 675 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.035926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.027456 restraints weight = 458907.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.028426 restraints weight = 216926.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.029050 restraints weight = 131141.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.029488 restraints weight = 92224.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.029743 restraints weight = 71741.369| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 25885 Z= 0.307 Angle : 0.787 17.345 35336 Z= 0.406 Chirality : 0.047 0.406 4152 Planarity : 0.006 0.130 4581 Dihedral : 4.920 29.806 3568 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % 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 are not related in a simple way. whole: -1.23 (0.14), residues: 3316 helix: 0.12 (0.20), residues: 646 sheet: -0.18 (0.21), residues: 651 loop : -1.39 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 273 TYR 0.023 0.003 TYR A 741 PHE 0.028 0.003 PHE B1062 TRP 0.017 0.002 TRP A 353 HIS 0.009 0.002 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.31 (25833) covalent geometry : angle 0.77448 / 0.40 (35218) SS BOND : bond 0.01379 / 1.00 ( 38) SS BOND : angle 1.99000 / 1.40 ( 76) hydrogen bonds : bond 0.04737 / 3.56 ( 756) hydrogen bonds : angle 6.29383 / 4.52 ( 2066) link_NAG-ASN : bond 0.00712 / 0.52 ( 14) link_NAG-ASN : angle 3.37911 / 2.36 ( 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 57 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 731 MET cc_start: 0.9407 (ptm) cc_final: 0.8998 (ptm) REVERT: B 773 GLU cc_start: 0.9614 (mt-10) cc_final: 0.9303 (tp30) REVERT: B 856 ASN cc_start: 0.9307 (t0) cc_final: 0.8571 (t0) REVERT: B 902 MET cc_start: 0.9838 (mmp) cc_final: 0.9544 (mmm) REVERT: B 906 PHE cc_start: 0.9837 (m-80) cc_final: 0.9566 (m-10) REVERT: B 1029 MET cc_start: 0.9705 (mmp) cc_final: 0.9427 (mmm) REVERT: C 340 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9357 (pm20) REVERT: C 740 MET cc_start: 0.9393 (ttm) cc_final: 0.8978 (ttm) REVERT: C 902 MET cc_start: 0.9629 (mmp) cc_final: 0.9185 (mmm) REVERT: C 1029 MET cc_start: 0.9898 (mmp) cc_final: 0.9377 (mmm) REVERT: A 365 TYR cc_start: 0.9726 (m-10) cc_final: 0.9407 (m-10) REVERT: A 740 MET cc_start: 0.9451 (ppp) cc_final: 0.9216 (ppp) REVERT: A 869 MET cc_start: 0.9533 (mtm) cc_final: 0.9293 (mtm) REVERT: A 1029 MET cc_start: 0.9819 (tpt) cc_final: 0.9586 (tpp) REVERT: A 1050 MET cc_start: 0.9616 (pmm) cc_final: 0.9343 (pmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1601 time to fit residues: 16.3273 Evaluate side-chains 44 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 0.0980 chunk 191 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 9 optimal weight: 50.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** 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** ** 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** A1071 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.027742 restraints weight = 386446.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.028636 restraints weight = 190893.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.029218 restraints weight = 117900.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.029628 restraints weight = 84539.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.029868 restraints weight = 66471.550| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 25885 Z= 0.226 Angle : 0.646 14.787 35336 Z= 0.333 Chirality : 0.045 0.401 4152 Planarity : 0.005 0.124 4581 Dihedral : 4.743 28.457 3568 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % 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 are not related in a simple way. whole: -1.23 (0.14), residues: 3316 helix: 0.34 (0.20), residues: 661 sheet: -0.45 (0.21), residues: 646 loop : -1.39 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 983 TYR 0.017 0.002 TYR B 789 PHE 0.016 0.002 PHE A1103 TRP 0.012 0.002 TRP A 353 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.23 (25833) covalent geometry : angle 0.63054 / 0.33 (35218) SS BOND : bond 0.00647 / 0.53 ( 38) SS BOND : angle 1.70390 / 1.21 ( 76) hydrogen bonds : bond 0.04082 / 3.06 ( 756) hydrogen bonds : angle 5.99250 / 4.30 ( 2066) link_NAG-ASN : bond 0.00482 / 0.39 ( 14) link_NAG-ASN : angle 3.60440 / 2.32 ( 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 : 1.132 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: 0.9076 (m-30) cc_final: 0.8603 (t70) REVERT: B 773 GLU cc_start: 0.9588 (mt-10) cc_final: 0.9294 (tp30) REVERT: B 776 LYS cc_start: 0.9789 (mtmt) cc_final: 0.9575 (ptmm) REVERT: B 856 ASN cc_start: 0.9314 (t0) cc_final: 0.8554 (t0) REVERT: B 902 MET cc_start: 0.9839 (mmp) cc_final: 0.9478 (mmm) REVERT: B 906 PHE cc_start: 0.9843 (m-80) cc_final: 0.9442 (m-80) REVERT: B 1029 MET cc_start: 0.9743 (mmp) cc_final: 0.9461 (mmm) REVERT: C 731 MET cc_start: 0.9049 (ppp) cc_final: 0.8774 (ppp) REVERT: C 740 MET cc_start: 0.9378 (ttm) cc_final: 0.8932 (ttm) REVERT: C 902 MET cc_start: 0.9629 (mmp) cc_final: 0.9204 (mmm) REVERT: C 1029 MET cc_start: 0.9889 (mmp) cc_final: 0.9374 (mmm) REVERT: A 365 TYR cc_start: 0.9728 (m-10) cc_final: 0.9408 (m-10) REVERT: A 740 MET cc_start: 0.9367 (ppp) cc_final: 0.9149 (ppp) REVERT: A 869 MET cc_start: 0.9520 (mtm) cc_final: 0.9141 (mtm) REVERT: A 900 MET cc_start: 0.9769 (mmm) cc_final: 0.9534 (mmm) REVERT: A 902 MET cc_start: 0.9591 (mmp) cc_final: 0.9320 (mmp) REVERT: A 1050 MET cc_start: 0.9717 (pmm) cc_final: 0.9481 (pmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1635 time to fit residues: 14.7452 Evaluate side-chains 42 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A1010 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.024490 restraints weight = 486023.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.025361 restraints weight = 232805.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025915 restraints weight = 141638.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.026287 restraints weight = 99896.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.026560 restraints weight = 78558.996| |-----------------------------------------------------------------------------| r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 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 = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 25885 Z= 0.383 Angle : 0.907 18.865 35336 Z= 0.473 Chirality : 0.049 0.414 4152 Planarity : 0.006 0.121 4581 Dihedral : 5.920 26.849 3568 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 29.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.87 % Favored : 91.07 % Rotamer: Outliers : 0.12 % Allowed : 2.59 % Favored : 97.29 % 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 are not related in a simple way. whole: -2.06 (0.14), residues: 3316 helix: -0.71 (0.18), residues: 663 sheet: -0.90 (0.21), residues: 631 loop : -1.81 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 466 TYR 0.029 0.003 TYR A 313 PHE 0.032 0.003 PHE B 464 TRP 0.019 0.003 TRP B 353 HIS 0.012 0.003 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.38 (25833) covalent geometry : angle 0.89151 / 0.47 (35218) SS BOND : bond 0.01124 / 0.92 ( 38) SS BOND : angle 2.45787 / 1.73 ( 76) hydrogen bonds : bond 0.05173 / 3.87 ( 756) hydrogen bonds : angle 7.04393 / 5.06 ( 2066) link_NAG-ASN : bond 0.00793 / 0.53 ( 14) link_NAG-ASN : angle 3.86210 / 2.67 ( 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 47 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8849 (tm-30) REVERT: B 731 MET cc_start: 0.9308 (ppp) cc_final: 0.9046 (ppp) REVERT: B 902 MET cc_start: 0.9853 (mmp) cc_final: 0.9465 (mmm) REVERT: B 906 PHE cc_start: 0.9900 (m-80) cc_final: 0.9493 (m-10) REVERT: B 1029 MET cc_start: 0.9815 (mmp) cc_final: 0.9505 (mmm) REVERT: C 740 MET cc_start: 0.9375 (ttm) cc_final: 0.8853 (ttm) REVERT: C 902 MET cc_start: 0.9569 (mmp) cc_final: 0.9189 (mmm) REVERT: C 1029 MET cc_start: 0.9905 (mmp) cc_final: 0.9439 (mmm) REVERT: A 365 TYR cc_start: 0.9779 (m-10) cc_final: 0.9450 (m-10) REVERT: A 773 GLU cc_start: 0.9645 (tt0) cc_final: 0.9084 (tp30) REVERT: A 869 MET cc_start: 0.9575 (mtm) cc_final: 0.9295 (mtm) REVERT: A 1029 MET cc_start: 0.9843 (tpt) cc_final: 0.9642 (tpp) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.1618 time to fit residues: 13.8521 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 : 0.997 ------------------------------------------------------------------------------- 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: 3.9990 chunk 330 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 306 optimal weight: 0.0570 chunk 160 optimal weight: 40.0000 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN B 280 ASN B 409 GLN B 519 HIS ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** 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 ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.027079 restraints weight = 528608.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028119 restraints weight = 227956.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.028787 restraints weight = 130480.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.029210 restraints weight = 88308.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.029511 restraints weight = 67496.581| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6238 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= 0.131 Angle : 0.606 11.491 35336 Z= 0.310 Chirality : 0.046 0.397 4152 Planarity : 0.004 0.117 4581 Dihedral : 4.967 27.326 3568 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 0.12 % Allowed : 0.82 % Favored : 99.06 % 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 are not related in a simple way. whole: -1.36 (0.14), residues: 3316 helix: 0.54 (0.20), residues: 666 sheet: -0.67 (0.21), residues: 626 loop : -1.53 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 454 TYR 0.018 0.001 TYR A 873 PHE 0.029 0.002 PHE C 429 TRP 0.015 0.001 TRP C 886 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (25833) covalent geometry : angle 0.59145 / 0.31 (35218) SS BOND : bond 0.00381 / 0.29 ( 38) SS BOND : angle 1.59622 / 1.12 ( 76) hydrogen bonds : bond 0.03542 / 2.66 ( 756) hydrogen bonds : angle 5.94288 / 4.28 ( 2066) link_NAG-ASN : bond 0.00506 / 0.44 ( 14) link_NAG-ASN : angle 3.28750 / 2.24 ( 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 53 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9086 (m-30) cc_final: 0.8689 (t70) REVERT: B 731 MET cc_start: 0.9290 (ppp) cc_final: 0.9072 (ppp) REVERT: B 902 MET cc_start: 0.9850 (mmp) cc_final: 0.9554 (mmm) REVERT: B 906 PHE cc_start: 0.9855 (m-80) cc_final: 0.9483 (m-10) REVERT: B 1029 MET cc_start: 0.9778 (mmp) cc_final: 0.9381 (mmm) REVERT: C 731 MET cc_start: 0.9061 (ppp) cc_final: 0.8799 (ppp) REVERT: C 740 MET cc_start: 0.9337 (ttm) cc_final: 0.8838 (ttm) REVERT: C 902 MET cc_start: 0.9574 (mmp) cc_final: 0.9188 (mmm) REVERT: C 1029 MET cc_start: 0.9827 (mmp) cc_final: 0.9251 (mmm) REVERT: A 365 TYR cc_start: 0.9752 (m-10) cc_final: 0.9392 (m-10) REVERT: A 773 GLU cc_start: 0.9641 (tt0) cc_final: 0.9115 (tp30) REVERT: A 869 MET cc_start: 0.9568 (mtm) cc_final: 0.9251 (mtm) REVERT: A 902 MET cc_start: 0.9633 (mmp) cc_final: 0.9379 (mmp) REVERT: A 1010 GLN cc_start: 0.9587 (tp40) cc_final: 0.9367 (tp-100) REVERT: A 1029 MET cc_start: 0.9820 (tpt) cc_final: 0.9600 (tpp) REVERT: A 1050 MET cc_start: 0.9634 (pmm) cc_final: 0.9309 (pmm) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.1832 time to fit residues: 16.6210 Evaluate side-chains 43 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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: 9.9990 chunk 139 optimal weight: 50.0000 chunk 228 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 325 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 312 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 370 ASN B 409 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** ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** 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** ** C1011 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 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.032729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.025083 restraints weight = 431190.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025925 restraints weight = 209302.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.026462 restraints weight = 128630.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.026776 restraints weight = 91736.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.027068 restraints weight = 73572.060| |-----------------------------------------------------------------------------| r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 25885 Z= 0.297 Angle : 0.746 14.760 35336 Z= 0.387 Chirality : 0.046 0.392 4152 Planarity : 0.005 0.114 4581 Dihedral : 5.355 26.812 3568 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.08 % Favored : 91.86 % Rotamer: Outliers : 0.08 % Allowed : 1.26 % 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 are not related in a simple way. whole: -1.71 (0.14), residues: 3316 helix: -0.07 (0.19), residues: 673 sheet: -0.89 (0.20), residues: 655 loop : -1.65 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 454 TYR 0.024 0.003 TYR B 756 PHE 0.021 0.002 PHE B 220 TRP 0.011 0.002 TRP C 633 HIS 0.008 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.30 (25833) covalent geometry : angle 0.73111 / 0.38 (35218) SS BOND : bond 0.00540 / 0.42 ( 38) SS BOND : angle 2.06980 / 1.48 ( 76) hydrogen bonds : bond 0.04358 / 3.27 ( 756) hydrogen bonds : angle 6.42619 / 4.62 ( 2066) link_NAG-ASN : bond 0.00679 / 0.48 ( 14) link_NAG-ASN : angle 3.55890 / 2.47 ( 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 44 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9279 (m-30) cc_final: 0.8879 (t70) REVERT: B 697 MET cc_start: 0.9427 (ppp) cc_final: 0.9187 (ppp) REVERT: B 902 MET cc_start: 0.9858 (mmp) cc_final: 0.9460 (mmm) REVERT: B 906 PHE cc_start: 0.9884 (m-80) cc_final: 0.9463 (m-10) REVERT: B 1029 MET cc_start: 0.9798 (mmp) cc_final: 0.9447 (mmm) REVERT: C 740 MET cc_start: 0.9350 (ttm) cc_final: 0.8842 (ttm) REVERT: C 902 MET cc_start: 0.9583 (mmp) cc_final: 0.9239 (mmm) REVERT: C 1029 MET cc_start: 0.9889 (mmp) cc_final: 0.9335 (mmm) REVERT: A 365 TYR cc_start: 0.9779 (m-10) cc_final: 0.9440 (m-10) REVERT: A 773 GLU cc_start: 0.9633 (tt0) cc_final: 0.9077 (tp30) REVERT: A 869 MET cc_start: 0.9565 (mtm) cc_final: 0.9232 (mtm) REVERT: A 902 MET cc_start: 0.9601 (mmp) cc_final: 0.9334 (mmp) REVERT: A 1010 GLN cc_start: 0.9542 (tp40) cc_final: 0.9226 (tp-100) REVERT: A 1050 MET cc_start: 0.9645 (pmm) cc_final: 0.9409 (pmm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1548 time to fit residues: 12.3795 Evaluate side-chains 40 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 9.9990 chunk 327 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 140 optimal weight: 40.0000 chunk 176 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 199 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.026482 restraints weight = 419635.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.027377 restraints weight = 198473.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.027932 restraints weight = 119614.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.028317 restraints weight = 84132.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.028604 restraints weight = 65537.446| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.6837 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= 0.150 Angle : 0.606 11.879 35336 Z= 0.310 Chirality : 0.045 0.387 4152 Planarity : 0.004 0.111 4581 Dihedral : 4.980 27.590 3568 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.08 % Allowed : 0.63 % Favored : 99.29 % 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 are not related in a simple way. whole: -1.44 (0.14), residues: 3316 helix: 0.46 (0.20), residues: 675 sheet: -0.72 (0.21), residues: 616 loop : -1.59 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 454 TYR 0.014 0.001 TYR B 917 PHE 0.017 0.001 PHE C 429 TRP 0.010 0.001 TRP C 633 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (25833) covalent geometry : angle 0.59094 / 0.31 (35218) SS BOND : bond 0.00432 / 0.34 ( 38) SS BOND : angle 1.70418 / 1.21 ( 76) hydrogen bonds : bond 0.03530 / 2.66 ( 756) hydrogen bonds : angle 5.94869 / 4.28 ( 2066) link_NAG-ASN : bond 0.00501 / 0.43 ( 14) link_NAG-ASN : angle 3.32750 / 2.29 ( 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 : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9226 (m-30) cc_final: 0.8832 (t70) REVERT: B 731 MET cc_start: 0.9342 (ppp) cc_final: 0.9100 (ppp) REVERT: B 902 MET cc_start: 0.9848 (mmp) cc_final: 0.9452 (mmm) REVERT: B 906 PHE cc_start: 0.9862 (m-80) cc_final: 0.9366 (m-10) REVERT: B 1029 MET cc_start: 0.9786 (mmp) cc_final: 0.9408 (mmm) REVERT: C 731 MET cc_start: 0.9017 (ppp) cc_final: 0.8815 (ppp) REVERT: C 740 MET cc_start: 0.9301 (ttm) cc_final: 0.8792 (ttm) REVERT: C 902 MET cc_start: 0.9600 (mmp) cc_final: 0.9245 (mmm) REVERT: C 1029 MET cc_start: 0.9835 (mmp) cc_final: 0.9257 (mmm) REVERT: A 365 TYR cc_start: 0.9759 (m-10) cc_final: 0.9392 (m-10) REVERT: A 773 GLU cc_start: 0.9658 (tt0) cc_final: 0.9127 (tp30) REVERT: A 869 MET cc_start: 0.9571 (mtm) cc_final: 0.9248 (mtm) REVERT: A 902 MET cc_start: 0.9603 (mmp) cc_final: 0.9333 (mmp) REVERT: A 1010 GLN cc_start: 0.9562 (tp40) cc_final: 0.9360 (tp-100) REVERT: A 1050 MET cc_start: 0.9657 (pmm) cc_final: 0.9334 (pmm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1515 time to fit residues: 12.1518 Evaluate side-chains 40 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 20.0000 chunk 277 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 321 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 325 optimal weight: 9.9990 chunk 236 optimal weight: 0.0030 chunk 176 optimal weight: 0.7980 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** 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 A 460 ASN A 498 GLN A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.027289 restraints weight = 382574.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.028161 restraints weight = 184954.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.028749 restraints weight = 112587.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029062 restraints weight = 78448.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.029376 restraints weight = 62809.253| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.6741 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= 0.118 Angle : 0.571 11.695 35336 Z= 0.289 Chirality : 0.045 0.371 4152 Planarity : 0.004 0.108 4581 Dihedral : 4.562 28.272 3568 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 0.08 % Allowed : 0.27 % Favored : 99.65 % 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 are not related in a simple way. whole: -1.18 (0.15), residues: 3316 helix: 0.85 (0.21), residues: 670 sheet: -0.53 (0.21), residues: 603 loop : -1.48 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 454 TYR 0.013 0.001 TYR B 917 PHE 0.014 0.001 PHE C 429 TRP 0.008 0.001 TRP C 633 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (25833) covalent geometry : angle 0.55802 / 0.29 (35218) SS BOND : bond 0.00291 / 0.22 ( 38) SS BOND : angle 1.44639 / 1.02 ( 76) hydrogen bonds : bond 0.03284 / 2.48 ( 756) hydrogen bonds : angle 5.47870 / 3.94 ( 2066) link_NAG-ASN : bond 0.00522 / 0.45 ( 14) link_NAG-ASN : angle 3.13662 / 2.16 ( 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 46 residues out of total 2933 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 198 ASP cc_start: 0.9128 (m-30) cc_final: 0.8733 (t70) REVERT: B 731 MET cc_start: 0.9327 (ppp) cc_final: 0.9124 (ppp) REVERT: B 902 MET cc_start: 0.9843 (mmp) cc_final: 0.9456 (mmm) REVERT: B 906 PHE cc_start: 0.9856 (m-80) cc_final: 0.9381 (m-80) REVERT: B 1029 MET cc_start: 0.9765 (mmp) cc_final: 0.9398 (mmm) REVERT: C 697 MET cc_start: 0.8707 (mmp) cc_final: 0.8432 (mmm) REVERT: C 740 MET cc_start: 0.9269 (ttm) cc_final: 0.8758 (ttm) REVERT: C 902 MET cc_start: 0.9608 (mmp) cc_final: 0.9237 (mmm) REVERT: C 1018 ILE cc_start: 0.9785 (mm) cc_final: 0.9401 (tp) REVERT: C 1029 MET cc_start: 0.9808 (mmp) cc_final: 0.9231 (mmm) REVERT: A 365 TYR cc_start: 0.9735 (m-10) cc_final: 0.9370 (m-10) REVERT: A 773 GLU cc_start: 0.9679 (tt0) cc_final: 0.9115 (tp30) REVERT: A 902 MET cc_start: 0.9638 (mmp) cc_final: 0.9334 (mmp) REVERT: A 1010 GLN cc_start: 0.9544 (tp40) cc_final: 0.9309 (tp-100) REVERT: A 1050 MET cc_start: 0.9680 (pmm) cc_final: 0.9337 (pmm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1474 time to fit residues: 12.5173 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 : 1.024 ------------------------------------------------------------------------------- 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: 2.9990 chunk 81 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 294 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.026645 restraints weight = 384798.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.027501 restraints weight = 187615.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.028037 restraints weight = 114942.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.028416 restraints weight = 81496.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.028672 restraints weight = 64338.186| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.6951 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= 0.151 Angle : 0.582 11.910 35336 Z= 0.296 Chirality : 0.045 0.371 4152 Planarity : 0.004 0.105 4581 Dihedral : 4.567 28.067 3568 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % 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 are not related in a simple way. whole: -1.18 (0.15), residues: 3316 helix: 0.82 (0.20), residues: 675 sheet: -0.52 (0.22), residues: 598 loop : -1.49 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 454 TYR 0.013 0.001 TYR B 917 PHE 0.014 0.001 PHE C 429 TRP 0.008 0.001 TRP C1102 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (25833) covalent geometry : angle 0.56725 / 0.29 (35218) SS BOND : bond 0.00350 / 0.28 ( 38) SS BOND : angle 1.52624 / 1.08 ( 76) hydrogen bonds : bond 0.03355 / 2.53 ( 756) hydrogen bonds : angle 5.53452 / 3.98 ( 2066) link_NAG-ASN : bond 0.00515 / 0.44 ( 14) link_NAG-ASN : angle 3.24527 / 2.24 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3960.86 seconds wall clock time: 70 minutes 6.42 seconds (4206.42 seconds total)