Starting phenix.real_space_refine on Thu Mar 5 17:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8u_22731/03_2026/7k8u_22731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8u_22731/03_2026/7k8u_22731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k8u_22731/03_2026/7k8u_22731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8u_22731/03_2026/7k8u_22731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k8u_22731/03_2026/7k8u_22731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8u_22731/03_2026/7k8u_22731.map" } resolution = 3.8 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= 0.014 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 102 5.16 5 C 15257 2.51 5 N 4016 2.21 5 O 4540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23915 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7619 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 48, 'TRANS': 942} Chain breaks: 9 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7586 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7612 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 9, 'GLN:plan1': 2, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 519 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 7, 'TRP:plan': 5, 'GLU:plan': 3, 'TYR:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 171 Chain: "L" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 7, 'ARG:plan': 6, 'TRP:plan': 2, 'TYR:plan': 6, 'ASP:plan': 3, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 171 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.10, per 1000 atoms: 0.26 Number of scatterers: 23915 At special positions: 0 Unit cell: (131.252, 133.76, 203.148, 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 102 16.00 O 4540 8.00 N 4016 7.00 C 15257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.06 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG C1301 " - " ASN C 331 " " NAG D 1 " - " ASN B 331 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 50 sheets defined 25.2% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.675A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.685A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.568A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 4.624A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.063A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.179A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.080A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.051A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.904A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.566A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.057A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.642A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.533A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.677A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.864A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.649A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.978A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.518A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.702A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.512A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1034 removed outlier: 3.666A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.533A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.881A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.668A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.676A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.586A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.683A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.504A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.513A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.521A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.822A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.129A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.388A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.718A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C1018 " --> pdb=" O ARG C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 4.029A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1125 through 1129' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.201A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.212A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.509A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 319 removed outlier: 5.442A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.752A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.599A pdb=" N PHE A 392 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.619A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.032A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.767A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.589A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.589A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.872A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 30 removed outlier: 4.603A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.528A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.511A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.378A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.590A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.593A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.709A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.195A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.195A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.652A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.739A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.519A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.909A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.025A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.162A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.510A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.765A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.780A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.780A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.142A pdb=" N GLY H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.278A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.533A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.615A pdb=" N VAL L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.615A pdb=" N VAL L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) 985 hydrogen bonds defined for protein. 2682 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: 5.91 Time building geometry restraints manager: 2.85 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: 7784 1.34 - 1.47: 6282 1.47 - 1.60: 10233 1.60 - 1.72: 0 1.72 - 1.85: 126 Bond restraints: 24425 Sorted by residual: bond pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" CA ASN B1098 " pdb=" C ASN B1098 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.80e-02 3.09e+03 1.47e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.19e-02 7.06e+03 9.26e+00 bond pdb=" N THR B 333 " pdb=" CA THR B 333 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.98e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 ... (remaining 24420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 32000 1.95 - 3.89: 1105 3.89 - 5.84: 135 5.84 - 7.79: 47 7.79 - 9.73: 11 Bond angle restraints: 33298 Sorted by residual: angle pdb=" C THR B 333 " pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 122.59 114.29 8.30 1.57e+00 4.06e-01 2.80e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.17 106.67 6.50 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 114.75 108.56 6.19 1.26e+00 6.30e-01 2.41e+01 angle pdb=" C ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta sigma weight residual 110.42 120.15 -9.73 1.99e+00 2.53e-01 2.39e+01 angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" C PRO A 337 " ideal model delta sigma weight residual 112.47 122.19 -9.72 2.06e+00 2.36e-01 2.22e+01 ... (remaining 33293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13429 17.92 - 35.84: 899 35.84 - 53.76: 146 53.76 - 71.68: 28 71.68 - 89.61: 26 Dihedral angle restraints: 14528 sinusoidal: 5310 harmonic: 9218 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -171.60 85.60 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.97 83.03 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 173.28 -80.28 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 14525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3801 0.120 - 0.240: 74 0.240 - 0.360: 4 0.360 - 0.480: 0 0.480 - 0.599: 2 Chirality restraints: 3881 Sorted by residual: chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 7.87e+00 chirality pdb=" CA ASN C 331 " pdb=" N ASN C 331 " pdb=" C ASN C 331 " pdb=" CB ASN C 331 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 3878 not shown) Planarity restraints: 4324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.320 2.00e-02 2.50e+03 2.71e-01 9.18e+02 pdb=" C7 NAG D 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.471 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.283 2.00e-02 2.50e+03 2.38e-01 7.09e+02 pdb=" C7 NAG A1301 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.085 2.00e-02 2.50e+03 6.98e-02 6.09e+01 pdb=" C7 NAG D 2 " -0.023 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.064 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.111 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.015 2.00e-02 2.50e+03 ... (remaining 4321 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 12 2.14 - 2.83: 9037 2.83 - 3.52: 33843 3.52 - 4.21: 54927 4.21 - 4.90: 92641 Nonbonded interactions: 190460 Sorted by model distance: nonbonded pdb=" CG2 THR B 333 " pdb=" CG1 VAL B 362 " model vdw 1.449 3.880 nonbonded pdb=" O3 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.053 3.040 nonbonded pdb=" OH TYR B 369 " pdb=" O PRO B 384 " model vdw 2.079 3.040 nonbonded pdb=" O CYS B1032 " pdb=" OG SER B1051 " model vdw 2.092 3.040 nonbonded pdb=" O GLU B 309 " pdb=" OH TYR B 313 " model vdw 2.093 3.040 ... (remaining 190455 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 528 or (resid 529 and (name N or name CA or name C or name O or name CB )) \ or resid 530 through 553 or (resid 554 and (name N or name CA or name C or name \ O or name CB )) or resid 555 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 or (resid 796 and (name N or name C \ A or name C or name O or name CB )) or resid 797 through 810 or (resid 811 and ( \ name N or name CA or name C or name O or name CB )) or resid 813 through 827 or \ resid 856 through 866 or (resid 867 through 868 and (name N or name CA or name C \ or name O or name CB )) or resid 869 through 939 or (resid 940 and (name N or n \ ame CA or name C or name O or name CB )) or resid 941 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 98 \ 7 or (resid 988 through 989 and (name N or name CA or name C or name O or name C \ B )) or resid 990 through 1141 or (resid 1142 and (name N or name CA or name C o \ r name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 an \ d (name N or name CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 585 or (resid 586 and (name N or name CA or name C or name O or name CB ) \ ) or resid 587 through 613 or (resid 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 676 or resid 690 through \ 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) or re \ sid 746 through 810 or (resid 811 and (name N or name CA or name C or name O or \ name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 939 or (resid 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 527 or (resid 528 thro \ ugh 529 and (name N or name CA or name C or name O or name CB )) or resid 530 th \ rough 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) \ or resid 555 through 567 or (resid 568 and (name N or name CA or name C or name \ O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name CA o \ r name C or name O or name CB )) or resid 572 through 581 or (resid 582 through \ 583 and (name N or name CA or name C or name O or name CB )) or resid 584 throug \ h 585 or (resid 586 and (name N or name CA or name C or name O or name CB )) or \ resid 587 through 618 or (resid 619 and (name N or name CA or name C or name O o \ r name CB )) or resid 620 through 645 or (resid 646 through 647 and (name N or n \ ame CA or name C or name O or name CB )) or resid 648 through 793 or (resid 794 \ and (name N or name CA or name C or name O or name CB )) or resid 795 or (resid \ 796 and (name N or name CA or name C or name O or name CB )) or resid 797 throug \ h 811 or resid 813 through 920 or (resid 921 and (name N or name CA or name C or \ name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name N or na \ me CA or name C or name O or name CB )) or resid 1074 through 1117 or (resid 111 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 1119 through \ 1141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or \ resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.410 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.140 Find NCS groups from input model: 0.460 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: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 : 0.010 0.107 24468 Z= 0.453 Angle : 0.885 18.462 33388 Z= 0.479 Chirality : 0.052 0.599 3881 Planarity : 0.007 0.271 4321 Dihedral : 12.565 89.605 8471 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.25 % Favored : 91.69 % Rotamer: Outliers : 0.20 % Allowed : 0.60 % Favored : 99.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: -2.36 (0.14), residues: 3117 helix: -1.29 (0.19), residues: 635 sheet: -1.22 (0.19), residues: 726 loop : -1.84 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 357 TYR 0.028 0.003 TYR B 453 PHE 0.040 0.003 PHE A 906 TRP 0.044 0.002 TRP A 886 HIS 0.009 0.002 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00979 (24425) covalent geometry : angle 0.86564 (33298) SS BOND : bond 0.00944 ( 39) SS BOND : angle 2.55982 ( 78) hydrogen bonds : bond 0.28285 ( 955) hydrogen bonds : angle 10.84839 ( 2682) link_BETA1-4 : bond 0.00061 ( 1) link_BETA1-4 : angle 0.93606 ( 3) link_NAG-ASN : bond 0.04795 ( 3) link_NAG-ASN : angle 8.63423 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9437 (tp) cc_final: 0.9153 (tp) REVERT: C 697 MET cc_start: 0.8883 (ppp) cc_final: 0.8604 (ppp) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 0.1433 time to fit residues: 16.8929 Evaluate side-chains 47 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 50.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 540 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.071301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.045233 restraints weight = 122068.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.046614 restraints weight = 56988.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047470 restraints weight = 34628.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048071 restraints weight = 24999.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.048358 restraints weight = 20237.333| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 24468 Z= 0.185 Angle : 0.663 17.721 33388 Z= 0.344 Chirality : 0.046 0.291 3881 Planarity : 0.005 0.063 4321 Dihedral : 5.705 55.392 3459 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.44 % Allowed : 4.74 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3117 helix: 0.42 (0.20), residues: 642 sheet: -0.86 (0.19), residues: 714 loop : -1.47 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 408 TYR 0.022 0.002 TYR A 369 PHE 0.021 0.002 PHE A 906 TRP 0.017 0.001 TRP A 886 HIS 0.010 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00410 (24425) covalent geometry : angle 0.65304 (33298) SS BOND : bond 0.00531 ( 39) SS BOND : angle 1.68998 ( 78) hydrogen bonds : bond 0.05444 ( 955) hydrogen bonds : angle 6.85892 ( 2682) link_BETA1-4 : bond 0.00387 ( 1) link_BETA1-4 : angle 3.42349 ( 3) link_NAG-ASN : bond 0.00991 ( 3) link_NAG-ASN : angle 4.68115 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9429 (tp) cc_final: 0.9143 (tp) REVERT: A 740 MET cc_start: 0.8718 (tpp) cc_final: 0.8345 (tpp) REVERT: A 858 LEU cc_start: 0.9088 (pt) cc_final: 0.8808 (pt) REVERT: B 191 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8509 (pm20) REVERT: B 1005 GLN cc_start: 0.8776 (pm20) cc_final: 0.8545 (pm20) REVERT: C 298 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 596 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.8985 (p) REVERT: C 697 MET cc_start: 0.8902 (ppp) cc_final: 0.8396 (ppp) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 0.1418 time to fit residues: 19.6152 Evaluate side-chains 55 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 83 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 44 optimal weight: 0.0370 chunk 66 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 139 optimal weight: 30.0000 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.071638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045500 restraints weight = 120493.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046891 restraints weight = 56116.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047791 restraints weight = 34003.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.048345 restraints weight = 24422.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048744 restraints weight = 19734.364| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24468 Z= 0.154 Angle : 0.586 17.950 33388 Z= 0.300 Chirality : 0.044 0.212 3881 Planarity : 0.004 0.061 4321 Dihedral : 5.255 59.864 3459 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.00 % Allowed : 7.74 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3117 helix: 0.92 (0.21), residues: 651 sheet: -0.69 (0.19), residues: 730 loop : -1.30 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.019 0.001 TYR A 369 PHE 0.016 0.001 PHE B 392 TRP 0.011 0.001 TRP A 886 HIS 0.010 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00348 (24425) covalent geometry : angle 0.57995 (33298) SS BOND : bond 0.00444 ( 39) SS BOND : angle 1.34369 ( 78) hydrogen bonds : bond 0.04447 ( 955) hydrogen bonds : angle 6.03755 ( 2682) link_BETA1-4 : bond 0.00088 ( 1) link_BETA1-4 : angle 1.80769 ( 3) link_NAG-ASN : bond 0.00936 ( 3) link_NAG-ASN : angle 3.81489 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9462 (tp) cc_final: 0.9153 (tp) REVERT: A 756 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8507 (t80) REVERT: A 858 LEU cc_start: 0.9117 (pt) cc_final: 0.8817 (pt) REVERT: B 191 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8497 (pm20) REVERT: B 332 ILE cc_start: 0.4463 (OUTLIER) cc_final: 0.4151 (mm) REVERT: B 392 PHE cc_start: 0.7706 (m-80) cc_final: 0.7494 (m-80) REVERT: B 432 CYS cc_start: 0.4990 (OUTLIER) cc_final: 0.4578 (p) REVERT: B 981 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9188 (mm) REVERT: B 1005 GLN cc_start: 0.8844 (pm20) cc_final: 0.8609 (pp30) REVERT: C 200 TYR cc_start: 0.9153 (m-80) cc_final: 0.8946 (t80) REVERT: C 298 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7639 (mt-10) REVERT: C 596 SER cc_start: 0.9363 (m) cc_final: 0.8967 (p) REVERT: C 697 MET cc_start: 0.8914 (ppp) cc_final: 0.8345 (ppp) REVERT: C 1017 GLU cc_start: 0.8849 (tp30) cc_final: 0.8554 (tp30) outliers start: 25 outliers final: 12 residues processed: 78 average time/residue: 0.1306 time to fit residues: 18.7784 Evaluate side-chains 66 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 112 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 216 optimal weight: 0.1980 chunk 121 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.071009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.044387 restraints weight = 119868.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045762 restraints weight = 55219.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.046654 restraints weight = 33594.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.047198 restraints weight = 24207.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.047597 restraints weight = 19696.029| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24468 Z= 0.203 Angle : 0.596 15.785 33388 Z= 0.303 Chirality : 0.043 0.186 3881 Planarity : 0.004 0.060 4321 Dihedral : 5.113 55.007 3459 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.28 % Allowed : 9.75 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3117 helix: 1.11 (0.21), residues: 644 sheet: -0.67 (0.19), residues: 744 loop : -1.23 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.017 0.001 TYR A1067 PHE 0.014 0.001 PHE A 201 TRP 0.010 0.001 TRP A 886 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00455 (24425) covalent geometry : angle 0.58795 (33298) SS BOND : bond 0.00465 ( 39) SS BOND : angle 1.45811 ( 78) hydrogen bonds : bond 0.04176 ( 955) hydrogen bonds : angle 5.76836 ( 2682) link_BETA1-4 : bond 0.00166 ( 1) link_BETA1-4 : angle 3.36287 ( 3) link_NAG-ASN : bond 0.00611 ( 3) link_NAG-ASN : angle 4.22318 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9426 (tp) cc_final: 0.9123 (tp) REVERT: A 756 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8658 (t80) REVERT: A 869 MET cc_start: 0.9667 (ptt) cc_final: 0.9399 (ptt) REVERT: A 935 GLN cc_start: 0.9547 (OUTLIER) cc_final: 0.9342 (tt0) REVERT: B 191 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8635 (mp0) REVERT: B 332 ILE cc_start: 0.5212 (OUTLIER) cc_final: 0.4967 (mm) REVERT: B 432 CYS cc_start: 0.5043 (OUTLIER) cc_final: 0.4614 (p) REVERT: C 200 TYR cc_start: 0.9224 (m-80) cc_final: 0.8956 (t80) REVERT: C 298 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7609 (mt-10) REVERT: C 596 SER cc_start: 0.9434 (m) cc_final: 0.9029 (p) REVERT: C 697 MET cc_start: 0.8935 (ppp) cc_final: 0.8198 (ppp) REVERT: C 1017 GLU cc_start: 0.8998 (tp30) cc_final: 0.8686 (tp30) outliers start: 32 outliers final: 16 residues processed: 83 average time/residue: 0.1237 time to fit residues: 18.8192 Evaluate side-chains 68 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 202 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 284 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 241 optimal weight: 0.6980 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.070863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044867 restraints weight = 119739.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046189 restraints weight = 56031.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.047076 restraints weight = 34285.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.047653 restraints weight = 24819.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048037 restraints weight = 19952.351| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24468 Z= 0.172 Angle : 0.558 14.671 33388 Z= 0.285 Chirality : 0.043 0.201 3881 Planarity : 0.004 0.058 4321 Dihedral : 4.845 53.017 3459 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.16 % Allowed : 11.00 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: -0.73 (0.15), residues: 3117 helix: 1.30 (0.21), residues: 645 sheet: -0.57 (0.19), residues: 746 loop : -1.14 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.016 0.001 TYR A 369 PHE 0.012 0.001 PHE B1095 TRP 0.009 0.001 TRP A 64 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00384 (24425) covalent geometry : angle 0.55147 (33298) SS BOND : bond 0.00448 ( 39) SS BOND : angle 1.36710 ( 78) hydrogen bonds : bond 0.03931 ( 955) hydrogen bonds : angle 5.54061 ( 2682) link_BETA1-4 : bond 0.00078 ( 1) link_BETA1-4 : angle 2.21087 ( 3) link_NAG-ASN : bond 0.00872 ( 3) link_NAG-ASN : angle 3.19831 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8766 (m-80) cc_final: 0.8560 (m-10) REVERT: A 756 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8544 (t80) REVERT: A 858 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8742 (pt) REVERT: A 869 MET cc_start: 0.9592 (ptt) cc_final: 0.9340 (ptt) REVERT: A 935 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.9217 (tt0) REVERT: B 191 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8558 (mp0) REVERT: B 332 ILE cc_start: 0.4714 (OUTLIER) cc_final: 0.4441 (mm) REVERT: B 392 PHE cc_start: 0.7538 (m-80) cc_final: 0.7101 (t80) REVERT: B 432 CYS cc_start: 0.4948 (OUTLIER) cc_final: 0.4554 (p) REVERT: B 900 MET cc_start: 0.9128 (mmt) cc_final: 0.8817 (mmt) REVERT: C 697 MET cc_start: 0.8966 (ppp) cc_final: 0.8201 (ppp) REVERT: C 990 GLU cc_start: 0.9092 (pp20) cc_final: 0.8802 (pp20) REVERT: C 1017 GLU cc_start: 0.8834 (tp30) cc_final: 0.8575 (tp30) outliers start: 29 outliers final: 15 residues processed: 77 average time/residue: 0.1369 time to fit residues: 19.1091 Evaluate side-chains 67 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 189 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 235 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 282 optimal weight: 0.7980 chunk 233 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.072693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045615 restraints weight = 115729.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.047013 restraints weight = 53822.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047930 restraints weight = 33120.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048533 restraints weight = 24042.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.048860 restraints weight = 19496.161| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24468 Z= 0.124 Angle : 0.524 13.646 33388 Z= 0.266 Chirality : 0.042 0.203 3881 Planarity : 0.004 0.058 4321 Dihedral : 4.587 50.935 3459 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.28 % Allowed : 11.44 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: -0.51 (0.15), residues: 3117 helix: 1.57 (0.21), residues: 648 sheet: -0.47 (0.19), residues: 740 loop : -1.02 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.015 0.001 TYR A 369 PHE 0.016 0.001 PHE A 201 TRP 0.009 0.001 TRP A 64 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00278 (24425) covalent geometry : angle 0.51887 (33298) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.23100 ( 78) hydrogen bonds : bond 0.03681 ( 955) hydrogen bonds : angle 5.29868 ( 2682) link_BETA1-4 : bond 0.00096 ( 1) link_BETA1-4 : angle 1.95154 ( 3) link_NAG-ASN : bond 0.00536 ( 3) link_NAG-ASN : angle 2.92048 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8582 (t80) REVERT: A 858 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8837 (pt) REVERT: A 935 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.9131 (tt0) REVERT: B 191 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8577 (mp0) REVERT: B 332 ILE cc_start: 0.4882 (OUTLIER) cc_final: 0.4662 (mm) REVERT: B 432 CYS cc_start: 0.4917 (OUTLIER) cc_final: 0.4473 (p) REVERT: B 900 MET cc_start: 0.9162 (mmt) cc_final: 0.8781 (mmt) REVERT: B 902 MET cc_start: 0.9650 (tpp) cc_final: 0.9439 (tpp) REVERT: C 200 TYR cc_start: 0.9191 (m-80) cc_final: 0.8982 (t80) REVERT: C 697 MET cc_start: 0.8915 (ppp) cc_final: 0.8138 (ppp) REVERT: C 990 GLU cc_start: 0.9076 (pp20) cc_final: 0.8813 (pp20) REVERT: C 1017 GLU cc_start: 0.8983 (tp30) cc_final: 0.8665 (tp30) outliers start: 32 outliers final: 16 residues processed: 82 average time/residue: 0.1340 time to fit residues: 20.3309 Evaluate side-chains 69 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 923 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 314 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 309 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 227 optimal weight: 50.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** C 901 GLN ** 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 = 0.3570 r_free = 0.3570 target = 0.071828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.044808 restraints weight = 116475.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046168 restraints weight = 54396.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047064 restraints weight = 33521.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047647 restraints weight = 24342.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.047967 restraints weight = 19743.179| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24468 Z= 0.178 Angle : 0.548 12.351 33388 Z= 0.279 Chirality : 0.042 0.231 3881 Planarity : 0.004 0.057 4321 Dihedral : 4.607 50.446 3459 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.65 % Allowed : 11.68 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: -0.47 (0.15), residues: 3117 helix: 1.63 (0.21), residues: 646 sheet: -0.45 (0.19), residues: 739 loop : -1.01 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.015 0.001 TYR A1067 PHE 0.035 0.001 PHE A 392 TRP 0.009 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00396 (24425) covalent geometry : angle 0.54246 (33298) SS BOND : bond 0.00406 ( 39) SS BOND : angle 1.28354 ( 78) hydrogen bonds : bond 0.03739 ( 955) hydrogen bonds : angle 5.31330 ( 2682) link_BETA1-4 : bond 0.00448 ( 1) link_BETA1-4 : angle 2.61240 ( 3) link_NAG-ASN : bond 0.00307 ( 3) link_NAG-ASN : angle 3.04543 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 48 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8635 (t80) REVERT: A 858 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8859 (pt) REVERT: A 869 MET cc_start: 0.9512 (ptt) cc_final: 0.9211 (ptt) REVERT: A 935 GLN cc_start: 0.9483 (OUTLIER) cc_final: 0.9178 (tt0) REVERT: B 191 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8583 (mp0) REVERT: B 392 PHE cc_start: 0.7592 (m-80) cc_final: 0.7195 (t80) REVERT: B 432 CYS cc_start: 0.4964 (OUTLIER) cc_final: 0.4499 (p) REVERT: B 900 MET cc_start: 0.9182 (mmt) cc_final: 0.8812 (mmt) REVERT: C 200 TYR cc_start: 0.9223 (m-80) cc_final: 0.8979 (t80) REVERT: C 697 MET cc_start: 0.8885 (ppp) cc_final: 0.8001 (ppp) REVERT: C 1017 GLU cc_start: 0.9004 (tp30) cc_final: 0.8661 (tp30) outliers start: 41 outliers final: 24 residues processed: 86 average time/residue: 0.1336 time to fit residues: 21.3653 Evaluate side-chains 75 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 315 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 138 optimal weight: 40.0000 chunk 218 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** C 901 GLN ** 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 = 0.3617 r_free = 0.3617 target = 0.072347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.046273 restraints weight = 117611.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.047647 restraints weight = 54835.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048543 restraints weight = 33462.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.049084 restraints weight = 24067.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049496 restraints weight = 19581.438| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24468 Z= 0.119 Angle : 0.512 11.941 33388 Z= 0.260 Chirality : 0.042 0.151 3881 Planarity : 0.004 0.058 4321 Dihedral : 4.408 49.025 3457 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.40 % Allowed : 12.28 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: -0.32 (0.15), residues: 3117 helix: 1.78 (0.21), residues: 648 sheet: -0.38 (0.19), residues: 746 loop : -0.91 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.014 0.001 TYR A 369 PHE 0.029 0.001 PHE A 392 TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00266 (24425) covalent geometry : angle 0.50755 (33298) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.16949 ( 78) hydrogen bonds : bond 0.03539 ( 955) hydrogen bonds : angle 5.15058 ( 2682) link_BETA1-4 : bond 0.00170 ( 1) link_BETA1-4 : angle 1.96708 ( 3) link_NAG-ASN : bond 0.00416 ( 3) link_NAG-ASN : angle 2.76855 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8435 (t80) REVERT: A 858 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8565 (pt) REVERT: A 935 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: B 191 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8455 (mp0) REVERT: B 392 PHE cc_start: 0.7408 (m-80) cc_final: 0.6994 (t80) REVERT: B 432 CYS cc_start: 0.5088 (OUTLIER) cc_final: 0.4667 (p) REVERT: C 697 MET cc_start: 0.8790 (ppp) cc_final: 0.8121 (ppp) REVERT: C 1017 GLU cc_start: 0.8689 (tp30) cc_final: 0.8384 (tp30) outliers start: 35 outliers final: 24 residues processed: 83 average time/residue: 0.1362 time to fit residues: 20.6978 Evaluate side-chains 75 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 135 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 223 optimal weight: 0.3980 chunk 194 optimal weight: 0.0030 chunk 263 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 229 optimal weight: 40.0000 chunk 182 optimal weight: 0.9980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN C 87 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.073412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047532 restraints weight = 116853.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048882 restraints weight = 56265.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049780 restraints weight = 34860.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050324 restraints weight = 25186.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050699 restraints weight = 20473.201| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24468 Z= 0.090 Angle : 0.506 11.574 33388 Z= 0.256 Chirality : 0.042 0.150 3881 Planarity : 0.004 0.058 4321 Dihedral : 4.244 47.576 3457 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.16 % Allowed : 12.52 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: -0.20 (0.15), residues: 3117 helix: 1.90 (0.21), residues: 649 sheet: -0.30 (0.19), residues: 767 loop : -0.85 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.015 0.001 TYR C 200 PHE 0.027 0.001 PHE A 392 TRP 0.009 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00199 (24425) covalent geometry : angle 0.49975 (33298) SS BOND : bond 0.00330 ( 39) SS BOND : angle 1.50507 ( 78) hydrogen bonds : bond 0.03367 ( 955) hydrogen bonds : angle 4.97906 ( 2682) link_BETA1-4 : bond 0.00650 ( 1) link_BETA1-4 : angle 1.69622 ( 3) link_NAG-ASN : bond 0.00580 ( 3) link_NAG-ASN : angle 2.40960 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8440 (t80) REVERT: A 935 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: B 191 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8417 (mp0) REVERT: B 392 PHE cc_start: 0.7346 (m-80) cc_final: 0.6879 (t80) REVERT: B 432 CYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4829 (p) REVERT: C 1017 GLU cc_start: 0.8618 (tp30) cc_final: 0.8307 (tp30) outliers start: 29 outliers final: 24 residues processed: 86 average time/residue: 0.1351 time to fit residues: 21.3147 Evaluate side-chains 74 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 265 optimal weight: 7.9990 chunk 272 optimal weight: 0.0020 chunk 192 optimal weight: 0.0020 chunk 174 optimal weight: 0.0970 chunk 32 optimal weight: 20.0000 chunk 306 optimal weight: 0.0270 chunk 155 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 213 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 overall best weight: 0.0430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.073767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047810 restraints weight = 118204.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049254 restraints weight = 54804.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050189 restraints weight = 33073.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.050815 restraints weight = 23653.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051157 restraints weight = 18984.541| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 24468 Z= 0.095 Angle : 0.510 10.812 33388 Z= 0.257 Chirality : 0.042 0.188 3881 Planarity : 0.004 0.058 4321 Dihedral : 4.180 52.331 3457 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.28 % Allowed : 12.84 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: -0.06 (0.15), residues: 3117 helix: 1.99 (0.21), residues: 650 sheet: -0.20 (0.18), residues: 772 loop : -0.75 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.015 0.001 TYR A 380 PHE 0.029 0.001 PHE A 392 TRP 0.010 0.001 TRP B 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00207 (24425) covalent geometry : angle 0.50407 (33298) SS BOND : bond 0.00358 ( 39) SS BOND : angle 1.46094 ( 78) hydrogen bonds : bond 0.03256 ( 955) hydrogen bonds : angle 4.87233 ( 2682) link_BETA1-4 : bond 0.00239 ( 1) link_BETA1-4 : angle 1.37956 ( 3) link_NAG-ASN : bond 0.00461 ( 3) link_NAG-ASN : angle 2.35016 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 935 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: B 191 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8548 (mp0) REVERT: B 392 PHE cc_start: 0.7476 (m-80) cc_final: 0.7066 (t80) REVERT: B 432 CYS cc_start: 0.5245 (OUTLIER) cc_final: 0.4799 (p) REVERT: C 1017 GLU cc_start: 0.8600 (tp30) cc_final: 0.8305 (tp30) outliers start: 32 outliers final: 23 residues processed: 92 average time/residue: 0.1346 time to fit residues: 22.5352 Evaluate side-chains 76 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 98 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 204 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.073183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047924 restraints weight = 117831.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049888 restraints weight = 58575.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050146 restraints weight = 27135.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050283 restraints weight = 23023.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050394 restraints weight = 21932.421| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24468 Z= 0.102 Angle : 0.513 16.638 33388 Z= 0.256 Chirality : 0.042 0.145 3881 Planarity : 0.004 0.059 4321 Dihedral : 4.131 51.749 3457 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.28 % Allowed : 13.00 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.65 % Cis-general : 0.00 % 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: 0.01 (0.15), residues: 3117 helix: 2.05 (0.21), residues: 650 sheet: -0.14 (0.19), residues: 765 loop : -0.71 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 357 TYR 0.012 0.001 TYR C1067 PHE 0.030 0.001 PHE A 392 TRP 0.019 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00233 (24425) covalent geometry : angle 0.50749 (33298) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.40141 ( 78) hydrogen bonds : bond 0.03236 ( 955) hydrogen bonds : angle 4.84246 ( 2682) link_BETA1-4 : bond 0.00223 ( 1) link_BETA1-4 : angle 1.36528 ( 3) link_NAG-ASN : bond 0.00389 ( 3) link_NAG-ASN : angle 2.25384 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4392.39 seconds wall clock time: 76 minutes 35.71 seconds (4595.71 seconds total)