Starting phenix.real_space_refine on Fri Mar 6 10:41:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xdb_33142/03_2026/7xdb_33142_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdb_33142/03_2026/7xdb_33142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xdb_33142/03_2026/7xdb_33142_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdb_33142/03_2026/7xdb_33142_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xdb_33142/03_2026/7xdb_33142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdb_33142/03_2026/7xdb_33142.map" } resolution = 2.62 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= -0.000 sd= 0.077 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 132 5.16 5 C 19301 2.51 5 N 4957 2.21 5 O 5799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 30189 Number of models: 1 Model: "" Number of chains: 23 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8126 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 929 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 929 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8121 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 56, 'TRANS': 976} Chain breaks: 8 Chain: "B" Number of atoms: 8169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8169 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 57, 'TRANS': 982} Chain breaks: 7 Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 929 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "O" 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: "S" 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: "U" 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: "Z" 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: "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: "f" 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: "i" 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: "J" 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: "K" 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: "L" 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: "M" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.93, per 1000 atoms: 0.23 Number of scatterers: 30189 At special positions: 0 Unit cell: (138.672, 171.2, 192.6, 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 132 16.00 O 5799 8.00 N 4957 7.00 C 19301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG f 1 " - " NAG f 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A1201 " - " ASN A1134 " " NAG A1202 " - " ASN A 709 " " NAG A1203 " - " ASN A1074 " " NAG A1204 " - " ASN A 616 " " NAG B1201 " - " ASN B1134 " " NAG B1202 " - " ASN B 709 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 616 " " NAG B1205 " - " ASN B 234 " " NAG B1206 " - " ASN B 163 " " NAG B1207 " - " ASN B 64 " " NAG C1201 " - " ASN C1134 " " NAG C1202 " - " ASN C 709 " " NAG C1203 " - " ASN C1074 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 331 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 343 " " NAG O 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG Z 1 " - " ASN B1098 " " NAG d 1 " - " ASN B 717 " " NAG f 1 " - " ASN B 801 " " NAG i 1 " - " ASN B 343 " Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7054 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 69 sheets defined 21.8% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.590A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.100A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.386A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.936A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.728A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.517A 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 912 through 919 removed outlier: 3.987A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.805A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.617A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.684A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.902A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.085A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.558A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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 783 Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.589A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.948A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.694A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.683A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 958 " --> pdb=" O HIS C 954 " (cutoff:3.500A) 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 1032 removed outlier: 3.575A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.902A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.085A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.992A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.911A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.856A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.624A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.015A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.542A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.542A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 33 removed outlier: 4.186A pdb=" N ALA A 30 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN A 64 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A 269 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 264 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 199 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP A 228 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.007A pdb=" N PHE A 46 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 58 removed outlier: 3.936A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.245A pdb=" N LEU A 142 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.102A pdb=" N ALA A 243 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 102 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 166 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.890A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.383A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.451A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.385A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.490A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.584A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.484A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 61 removed outlier: 3.593A pdb=" N ILE D 51 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 35 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP D 34 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 58 through 61 removed outlier: 3.593A pdb=" N ILE D 51 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 35 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP D 34 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.813A pdb=" N THR G 118 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 35 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP G 58 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.813A pdb=" N THR G 118 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU G 110 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.651A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.493A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 30 through 33 removed outlier: 4.237A pdb=" N ALA C 30 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASN C 64 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR C 269 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 39 through 40 removed outlier: 7.069A pdb=" N VAL C 39 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 45 through 46 removed outlier: 5.463A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 58 removed outlier: 3.516A pdb=" N ASP C 56 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.067A pdb=" N ALA C 243 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE C 102 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.540A pdb=" N LEU C 142 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.128A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.681A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.424A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.918A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.513A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.442A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.626A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.521A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 31 through 33 removed outlier: 7.722A pdb=" N ASN B 64 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR B 269 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS B 205 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ALA B 222 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 39 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 50 through 58 removed outlier: 3.998A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AF7, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.614A pdb=" N GLY B 104 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 243 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 102 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 166 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 135 through 136 removed outlier: 6.951A pdb=" N GLN B 135 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.146A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.680A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.594A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AG4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.918A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.900A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.439A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.439A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.697A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.650A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AH3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.494A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AH5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.814A pdb=" N THR I 118 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE I 35 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE I 51 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP I 58 " --> pdb=" O TYR I 53 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.814A pdb=" N THR I 118 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU I 110 " --> pdb=" O ARG I 99 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3462 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: 7.72 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4972 1.32 - 1.45: 8857 1.45 - 1.58: 16924 1.58 - 1.70: 0 1.70 - 1.83: 168 Bond restraints: 30921 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" O PRO C 986 " ideal model delta sigma weight residual 1.240 1.195 0.045 1.12e-02 7.97e+03 1.61e+01 bond pdb=" N VAL C 534 " pdb=" CA VAL C 534 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.63e+00 bond pdb=" N VAL C 327 " pdb=" CA VAL C 327 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.20e-02 6.94e+03 9.30e+00 bond pdb=" N THR C 581 " pdb=" CA THR C 581 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.33e-02 5.65e+03 9.27e+00 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.97e+00 ... (remaining 30916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 40553 1.50 - 2.99: 1205 2.99 - 4.49: 253 4.49 - 5.98: 33 5.98 - 7.48: 12 Bond angle restraints: 42056 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.99 -7.29 1.22e+00 6.72e-01 3.57e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 111.21 116.67 -5.46 1.04e+00 9.25e-01 2.76e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 124.04 -6.11 1.20e+00 6.94e-01 2.59e+01 angle pdb=" C LYS C 528 " pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 122.95 115.93 7.02 1.44e+00 4.82e-01 2.38e+01 angle pdb=" CA LYS C 528 " pdb=" C LYS C 528 " pdb=" O LYS C 528 " ideal model delta sigma weight residual 121.94 116.37 5.57 1.15e+00 7.56e-01 2.34e+01 ... (remaining 42051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 17517 17.88 - 35.76: 1084 35.76 - 53.64: 188 53.64 - 71.52: 42 71.52 - 89.40: 24 Dihedral angle restraints: 18855 sinusoidal: 7871 harmonic: 10984 Sorted by residual: dihedral pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" N THR B 618 " pdb=" CA THR B 618 " ideal model delta harmonic sigma weight residual 180.00 146.61 33.39 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 47.06 45.94 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 49.18 43.82 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 18852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 4792 0.202 - 0.404: 13 0.404 - 0.606: 5 0.606 - 0.809: 0 0.809 - 1.011: 1 Chirality restraints: 4811 Sorted by residual: chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C1 NAG B1201 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1201 " pdb=" O5 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 4808 not shown) Planarity restraints: 5372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1204 " -0.318 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C7 NAG C1204 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C1204 " -0.192 2.00e-02 2.50e+03 pdb=" N2 NAG C1204 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG C1204 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1205 " -0.274 2.00e-02 2.50e+03 2.30e-01 6.62e+02 pdb=" C7 NAG C1205 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1205 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG C1205 " 0.390 2.00e-02 2.50e+03 pdb=" O7 NAG C1205 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " 0.052 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO A 230 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.043 5.00e-02 4.00e+02 ... (remaining 5369 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 391 2.67 - 3.23: 27920 3.23 - 3.78: 47794 3.78 - 4.34: 68833 4.34 - 4.90: 110813 Nonbonded interactions: 255751 Sorted by model distance: nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.111 3.120 nonbonded pdb=" OG SER E 63 " pdb=" OG1 THR E 74 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR B 110 " pdb=" OG1 THR B 115 " model vdw 2.150 3.040 nonbonded pdb=" O ASP B 81 " pdb=" OH TYR B 265 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR D 70 " pdb=" O GLN D 83 " model vdw 2.223 3.040 ... (remaining 255746 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 29 through 620 or resid 629 through 827 or resid 848 throu \ gh 1204)) selection = (chain 'B' and (resid 29 through 620 or resid 629 through 1204)) selection = (chain 'C' and (resid 29 through 827 or resid 848 through 1204)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'U' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.530 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.010 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.004 0.053 31004 Z= 0.188 Angle : 0.673 18.190 42260 Z= 0.362 Chirality : 0.052 1.011 4811 Planarity : 0.007 0.267 5345 Dihedral : 12.333 89.397 11666 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.54 (0.13), residues: 3715 helix: 1.28 (0.20), residues: 734 sheet: 0.81 (0.15), residues: 1061 loop : -0.21 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 765 TYR 0.043 0.002 TYR C 198 PHE 0.028 0.002 PHE C 906 TRP 0.031 0.002 TRP C 886 HIS 0.012 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00360 (30921) covalent geometry : angle 0.63794 (42056) SS BOND : bond 0.00538 ( 45) SS BOND : angle 1.37837 ( 90) hydrogen bonds : bond 0.12684 ( 1232) hydrogen bonds : angle 7.44090 ( 3462) link_BETA1-4 : bond 0.00625 ( 11) link_BETA1-4 : angle 1.69302 ( 33) link_NAG-ASN : bond 0.00674 ( 27) link_NAG-ASN : angle 4.69337 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7922 (ptmt) REVERT: A 118 LEU cc_start: 0.6706 (mp) cc_final: 0.6444 (mt) REVERT: A 130 LYS cc_start: 0.8017 (mppt) cc_final: 0.7741 (mptt) REVERT: A 309 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 955 ASN cc_start: 0.7243 (t0) cc_final: 0.6774 (m110) REVERT: G 3 GLN cc_start: 0.7975 (mt0) cc_final: 0.7533 (pm20) REVERT: C 280 ASN cc_start: 0.7452 (p0) cc_final: 0.7222 (p0) REVERT: C 811 LYS cc_start: 0.6916 (mtmm) cc_final: 0.6196 (tptp) REVERT: B 100 ASN cc_start: 0.7921 (m-40) cc_final: 0.7578 (t0) REVERT: B 239 GLN cc_start: 0.7746 (tt0) cc_final: 0.7440 (tt0) REVERT: B 360 ASN cc_start: 0.8156 (m-40) cc_final: 0.7942 (m-40) REVERT: B 428 ASP cc_start: 0.7350 (p0) cc_final: 0.7101 (p0) REVERT: H 4 MET cc_start: 0.0444 (mmt) cc_final: -0.0385 (ttp) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.5918 time to fit residues: 263.9507 Evaluate side-chains 268 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.0670 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 505 HIS A 677 GLN A 779 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN C 33 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN C 907 ASN C1010 GLN C1125 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1010 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN I 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.192017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123136 restraints weight = 37465.512| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.48 r_work: 0.3155 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31004 Z= 0.188 Angle : 0.626 16.775 42260 Z= 0.319 Chirality : 0.049 0.757 4811 Planarity : 0.005 0.054 5345 Dihedral : 6.268 59.372 4862 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.12 % Allowed : 6.97 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.49 (0.13), residues: 3715 helix: 1.52 (0.19), residues: 730 sheet: 0.77 (0.16), residues: 1008 loop : -0.33 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.032 0.002 TYR B 265 PHE 0.033 0.002 PHE C 906 TRP 0.023 0.002 TRP C 886 HIS 0.006 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00440 (30921) covalent geometry : angle 0.59598 (42056) SS BOND : bond 0.00358 ( 45) SS BOND : angle 1.56328 ( 90) hydrogen bonds : bond 0.04818 ( 1232) hydrogen bonds : angle 6.11979 ( 3462) link_BETA1-4 : bond 0.00453 ( 11) link_BETA1-4 : angle 1.19477 ( 33) link_NAG-ASN : bond 0.00512 ( 27) link_NAG-ASN : angle 4.05172 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8196 (ttpt) cc_final: 0.7897 (ptmt) REVERT: A 130 LYS cc_start: 0.7816 (mppt) cc_final: 0.7569 (mptt) REVERT: A 309 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 326 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 516 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 964 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8184 (tppt) REVERT: A 1038 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8182 (mmtm) REVERT: D 3 GLN cc_start: 0.7795 (pm20) cc_final: 0.7564 (pm20) REVERT: D 37 TRP cc_start: 0.7920 (m100) cc_final: 0.6709 (m100) REVERT: D 41 MET cc_start: 0.7781 (tpt) cc_final: 0.7534 (mmm) REVERT: D 60 ARG cc_start: 0.8372 (ttm170) cc_final: 0.8010 (ttm-80) REVERT: D 96 TYR cc_start: 0.8173 (m-80) cc_final: 0.7530 (m-10) REVERT: D 97 CYS cc_start: 0.8044 (t) cc_final: 0.7573 (t) REVERT: G 40 GLN cc_start: 0.7423 (tt0) cc_final: 0.7049 (tt0) REVERT: G 94 MET cc_start: 0.6612 (tmm) cc_final: 0.6334 (tpp) REVERT: C 239 GLN cc_start: 0.6417 (tt0) cc_final: 0.5855 (mp10) REVERT: C 675 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6936 (mp10) REVERT: C 811 LYS cc_start: 0.6479 (mtmm) cc_final: 0.5799 (tptp) REVERT: C 988 GLU cc_start: 0.7756 (mp0) cc_final: 0.6716 (tp30) REVERT: B 100 ASN cc_start: 0.8026 (m-40) cc_final: 0.7467 (t0) REVERT: B 360 ASN cc_start: 0.8387 (m-40) cc_final: 0.8091 (m-40) REVERT: B 428 ASP cc_start: 0.7698 (p0) cc_final: 0.7464 (p0) REVERT: B 957 GLN cc_start: 0.8509 (tt0) cc_final: 0.8286 (tt0) REVERT: H 4 MET cc_start: 0.1622 (mmt) cc_final: 0.0263 (ttp) outliers start: 37 outliers final: 16 residues processed: 307 average time/residue: 0.5717 time to fit residues: 210.8349 Evaluate side-chains 267 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 145 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 239 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 417 ASN A 779 GLN A 895 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1125 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.192668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123976 restraints weight = 37554.017| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.53 r_work: 0.3176 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31004 Z= 0.137 Angle : 0.560 16.516 42260 Z= 0.284 Chirality : 0.047 0.729 4811 Planarity : 0.004 0.047 5345 Dihedral : 5.790 59.309 4862 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.61 % Allowed : 8.40 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.46 (0.13), residues: 3715 helix: 1.65 (0.20), residues: 713 sheet: 0.70 (0.16), residues: 1003 loop : -0.37 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 403 TYR 0.027 0.001 TYR B 265 PHE 0.015 0.001 PHE C 906 TRP 0.015 0.001 TRP F 96 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00310 (30921) covalent geometry : angle 0.53180 (42056) SS BOND : bond 0.00298 ( 45) SS BOND : angle 1.20822 ( 90) hydrogen bonds : bond 0.04239 ( 1232) hydrogen bonds : angle 5.77797 ( 3462) link_BETA1-4 : bond 0.00379 ( 11) link_BETA1-4 : angle 1.26550 ( 33) link_NAG-ASN : bond 0.00512 ( 27) link_NAG-ASN : angle 3.77137 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7885 (ptmt) REVERT: A 130 LYS cc_start: 0.7773 (mppt) cc_final: 0.7467 (mptt) REVERT: A 233 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6825 (tp) REVERT: A 309 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 326 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8033 (mp) REVERT: A 357 ARG cc_start: 0.8442 (ttt-90) cc_final: 0.8151 (ttt-90) REVERT: A 580 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.6555 (mp10) REVERT: A 964 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8218 (tppt) REVERT: A 1038 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8172 (mmtt) REVERT: D 3 GLN cc_start: 0.7894 (pm20) cc_final: 0.7535 (pm20) REVERT: D 37 TRP cc_start: 0.8027 (m100) cc_final: 0.7207 (m100) REVERT: D 49 MET cc_start: 0.8545 (mtp) cc_final: 0.8033 (mtm) REVERT: D 60 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8145 (ttm-80) REVERT: D 96 TYR cc_start: 0.8185 (m-80) cc_final: 0.7943 (m-80) REVERT: D 97 CYS cc_start: 0.7865 (t) cc_final: 0.7103 (t) REVERT: G 40 GLN cc_start: 0.7355 (tt0) cc_final: 0.7127 (tt0) REVERT: G 49 MET cc_start: 0.8222 (mtm) cc_final: 0.7937 (mtp) REVERT: G 94 MET cc_start: 0.6621 (tmm) cc_final: 0.6182 (tpp) REVERT: F 88 CYS cc_start: 0.6285 (p) cc_final: 0.6041 (p) REVERT: F 89 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: C 239 GLN cc_start: 0.6338 (tt0) cc_final: 0.5810 (mm-40) REVERT: C 281 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: C 309 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8248 (mm-30) REVERT: C 675 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: C 811 LYS cc_start: 0.6552 (mtmm) cc_final: 0.5828 (tptp) REVERT: C 988 GLU cc_start: 0.7706 (mp0) cc_final: 0.6578 (tp30) REVERT: B 100 ASN cc_start: 0.7956 (m-40) cc_final: 0.7355 (t0) REVERT: B 360 ASN cc_start: 0.8386 (m-40) cc_final: 0.8106 (m-40) REVERT: B 428 ASP cc_start: 0.7723 (p0) cc_final: 0.7475 (p0) REVERT: B 430 THR cc_start: 0.7980 (m) cc_final: 0.7701 (t) REVERT: B 465 GLU cc_start: 0.7356 (tp30) cc_final: 0.6897 (pt0) REVERT: B 556 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7695 (p0) REVERT: B 957 GLN cc_start: 0.8504 (tt0) cc_final: 0.8248 (tt0) REVERT: H 4 MET cc_start: 0.1452 (mmt) cc_final: 0.0048 (ptp) outliers start: 53 outliers final: 22 residues processed: 303 average time/residue: 0.5432 time to fit residues: 198.9774 Evaluate side-chains 278 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 156 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 505 HIS B 762 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118336 restraints weight = 37200.659| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.70 r_work: 0.3071 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 31004 Z= 0.280 Angle : 0.659 17.753 42260 Z= 0.334 Chirality : 0.051 0.850 4811 Planarity : 0.005 0.057 5345 Dihedral : 6.035 59.764 4862 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.21 % Allowed : 9.43 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.11 (0.13), residues: 3715 helix: 1.16 (0.19), residues: 712 sheet: 0.47 (0.16), residues: 1027 loop : -0.50 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 403 TYR 0.031 0.002 TYR B 265 PHE 0.021 0.002 PHE C 898 TRP 0.015 0.002 TRP A 886 HIS 0.007 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00670 (30921) covalent geometry : angle 0.62919 (42056) SS BOND : bond 0.00363 ( 45) SS BOND : angle 1.61303 ( 90) hydrogen bonds : bond 0.05181 ( 1232) hydrogen bonds : angle 6.02228 ( 3462) link_BETA1-4 : bond 0.00303 ( 11) link_BETA1-4 : angle 1.39287 ( 33) link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 4.12540 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7857 (ptmt) REVERT: A 103 ARG cc_start: 0.6940 (mtt180) cc_final: 0.6275 (mmt90) REVERT: A 130 LYS cc_start: 0.7789 (mppt) cc_final: 0.7472 (mptt) REVERT: A 233 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7017 (tp) REVERT: A 309 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8320 (mm-30) REVERT: A 516 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 580 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.6500 (mp10) REVERT: A 1038 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8247 (mmtt) REVERT: D 3 GLN cc_start: 0.7844 (pm20) cc_final: 0.7501 (pm20) REVERT: D 37 TRP cc_start: 0.8061 (m100) cc_final: 0.7273 (m100) REVERT: D 41 MET cc_start: 0.7928 (tpt) cc_final: 0.7643 (mmm) REVERT: D 49 MET cc_start: 0.8506 (mtp) cc_final: 0.8022 (mtm) REVERT: D 60 ARG cc_start: 0.8428 (ttm170) cc_final: 0.8145 (ttm-80) REVERT: D 97 CYS cc_start: 0.8058 (t) cc_final: 0.7267 (t) REVERT: G 49 MET cc_start: 0.8319 (mtm) cc_final: 0.7994 (mtp) REVERT: G 94 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6018 (tpp) REVERT: G 96 TYR cc_start: 0.8292 (m-80) cc_final: 0.7813 (m-80) REVERT: F 37 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.5708 (tp-100) REVERT: F 89 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: C 239 GLN cc_start: 0.6434 (tt0) cc_final: 0.5800 (mm-40) REVERT: C 309 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8206 (mm-30) REVERT: C 613 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: C 675 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: C 759 PHE cc_start: 0.7483 (t80) cc_final: 0.7271 (m-10) REVERT: C 811 LYS cc_start: 0.6619 (mtmm) cc_final: 0.5828 (tptp) REVERT: C 916 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8588 (tt) REVERT: C 921 LYS cc_start: 0.8829 (tttt) cc_final: 0.8056 (mppt) REVERT: C 985 ASP cc_start: 0.7429 (m-30) cc_final: 0.7110 (m-30) REVERT: B 239 GLN cc_start: 0.8420 (tt0) cc_final: 0.7940 (tt0) REVERT: B 360 ASN cc_start: 0.8400 (m-40) cc_final: 0.8105 (m-40) REVERT: B 428 ASP cc_start: 0.7848 (p0) cc_final: 0.7605 (p0) REVERT: B 465 GLU cc_start: 0.7550 (tp30) cc_final: 0.7022 (pt0) REVERT: B 529 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7839 (mmtt) REVERT: B 646 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8177 (mtp180) REVERT: B 654 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: B 814 LYS cc_start: 0.8084 (mptm) cc_final: 0.7526 (mtpt) REVERT: B 957 GLN cc_start: 0.8534 (tt0) cc_final: 0.8305 (tt0) REVERT: H 4 MET cc_start: 0.1590 (mmt) cc_final: 0.0200 (ptp) outliers start: 73 outliers final: 36 residues processed: 303 average time/residue: 0.5317 time to fit residues: 195.0127 Evaluate side-chains 289 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 216 optimal weight: 0.8980 chunk 85 optimal weight: 0.0470 chunk 118 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 324 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 68 optimal weight: 0.0670 chunk 327 optimal weight: 0.6980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN A 417 ASN A 779 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN B 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.192375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121578 restraints weight = 37358.672| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.61 r_work: 0.3153 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31004 Z= 0.103 Angle : 0.538 16.490 42260 Z= 0.271 Chirality : 0.046 0.732 4811 Planarity : 0.004 0.046 5345 Dihedral : 5.544 59.460 4862 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.64 % Allowed : 10.70 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.31 (0.13), residues: 3715 helix: 1.57 (0.20), residues: 720 sheet: 0.53 (0.16), residues: 1003 loop : -0.45 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.025 0.001 TYR B 265 PHE 0.026 0.001 PHE C 166 TRP 0.022 0.001 TRP F 96 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00222 (30921) covalent geometry : angle 0.51149 (42056) SS BOND : bond 0.00274 ( 45) SS BOND : angle 1.19102 ( 90) hydrogen bonds : bond 0.03865 ( 1232) hydrogen bonds : angle 5.64024 ( 3462) link_BETA1-4 : bond 0.00387 ( 11) link_BETA1-4 : angle 1.27754 ( 33) link_NAG-ASN : bond 0.00502 ( 27) link_NAG-ASN : angle 3.63186 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7888 (ptmt) REVERT: E 94 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7739 (t80) REVERT: A 103 ARG cc_start: 0.6969 (mtt180) cc_final: 0.6331 (mmt90) REVERT: A 119 LEU cc_start: 0.7495 (tm) cc_final: 0.7228 (tp) REVERT: A 130 LYS cc_start: 0.7748 (mppt) cc_final: 0.7448 (mptt) REVERT: A 233 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6970 (tp) REVERT: A 357 ARG cc_start: 0.8539 (ttt-90) cc_final: 0.8166 (ttt-90) REVERT: A 580 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.6487 (mp10) REVERT: A 1038 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8228 (mmtt) REVERT: D 3 GLN cc_start: 0.7958 (pm20) cc_final: 0.7595 (pm20) REVERT: D 37 TRP cc_start: 0.8173 (m100) cc_final: 0.7418 (m100) REVERT: D 41 MET cc_start: 0.7922 (tpt) cc_final: 0.7683 (mmm) REVERT: D 49 MET cc_start: 0.8445 (mtp) cc_final: 0.7945 (mtm) REVERT: D 60 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8023 (ttm-80) REVERT: D 97 CYS cc_start: 0.7863 (t) cc_final: 0.7089 (t) REVERT: G 3 GLN cc_start: 0.8157 (mt0) cc_final: 0.7612 (pt0) REVERT: G 49 MET cc_start: 0.8351 (mtm) cc_final: 0.8073 (mtp) REVERT: G 94 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6154 (tpp) REVERT: G 96 TYR cc_start: 0.8303 (m-80) cc_final: 0.7906 (m-80) REVERT: F 4 MET cc_start: 0.7513 (mtp) cc_final: 0.7275 (mmt) REVERT: F 37 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.5715 (tp-100) REVERT: F 89 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: C 198 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.3407 (t80) REVERT: C 239 GLN cc_start: 0.6462 (tt0) cc_final: 0.5781 (mm-40) REVERT: C 309 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8271 (mm-30) REVERT: C 675 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: C 921 LYS cc_start: 0.8802 (tttt) cc_final: 0.8148 (mppt) REVERT: C 985 ASP cc_start: 0.7409 (m-30) cc_final: 0.7056 (m-30) REVERT: B 100 ASN cc_start: 0.7586 (m110) cc_final: 0.6538 (p0) REVERT: B 239 GLN cc_start: 0.8391 (tt0) cc_final: 0.7928 (tt0) REVERT: B 360 ASN cc_start: 0.8423 (m-40) cc_final: 0.8166 (m-40) REVERT: B 428 ASP cc_start: 0.7880 (p0) cc_final: 0.7642 (p0) REVERT: B 465 GLU cc_start: 0.7503 (tp30) cc_final: 0.7039 (pt0) REVERT: B 498 ARG cc_start: 0.7699 (mtt-85) cc_final: 0.7461 (mtt-85) REVERT: B 654 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: B 760 CYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5150 (m) REVERT: B 957 GLN cc_start: 0.8566 (tt0) cc_final: 0.8337 (tt0) REVERT: B 994 ASP cc_start: 0.8262 (t70) cc_final: 0.7744 (t0) REVERT: B 1001 LEU cc_start: 0.8898 (tp) cc_final: 0.8632 (mt) REVERT: H 4 MET cc_start: 0.1426 (mmt) cc_final: 0.0332 (ptp) outliers start: 54 outliers final: 21 residues processed: 305 average time/residue: 0.5133 time to fit residues: 190.8321 Evaluate side-chains 274 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 136 optimal weight: 6.9990 chunk 324 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 320 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN A 417 ASN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 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 = 0.4215 r_free = 0.4215 target = 0.188120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113560 restraints weight = 35797.232| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.68 r_work: 0.3026 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 31004 Z= 0.238 Angle : 0.625 17.255 42260 Z= 0.315 Chirality : 0.050 0.820 4811 Planarity : 0.004 0.050 5345 Dihedral : 5.744 59.180 4862 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.18 % Allowed : 11.12 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % 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: 0.11 (0.13), residues: 3715 helix: 1.27 (0.19), residues: 712 sheet: 0.44 (0.16), residues: 1014 loop : -0.53 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 493 TYR 0.036 0.002 TYR D 96 PHE 0.029 0.002 PHE C 166 TRP 0.022 0.002 TRP F 96 HIS 0.007 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00566 (30921) covalent geometry : angle 0.59471 (42056) SS BOND : bond 0.00508 ( 45) SS BOND : angle 1.86796 ( 90) hydrogen bonds : bond 0.04834 ( 1232) hydrogen bonds : angle 5.88472 ( 3462) link_BETA1-4 : bond 0.00324 ( 11) link_BETA1-4 : angle 1.34908 ( 33) link_NAG-ASN : bond 0.00437 ( 27) link_NAG-ASN : angle 3.92535 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7795 (ptmt) REVERT: A 103 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6339 (mmt90) REVERT: A 119 LEU cc_start: 0.7570 (tm) cc_final: 0.7284 (tp) REVERT: A 130 LYS cc_start: 0.7696 (mppt) cc_final: 0.7376 (mptt) REVERT: A 233 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7028 (tp) REVERT: A 580 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.6624 (mp10) REVERT: A 1038 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8378 (mmtt) REVERT: D 3 GLN cc_start: 0.7890 (pm20) cc_final: 0.7509 (pm20) REVERT: D 37 TRP cc_start: 0.8175 (m100) cc_final: 0.7899 (m100) REVERT: D 49 MET cc_start: 0.8425 (mtp) cc_final: 0.7860 (mtm) REVERT: D 60 ARG cc_start: 0.8422 (ttm170) cc_final: 0.8116 (ttm-80) REVERT: D 97 CYS cc_start: 0.7787 (t) cc_final: 0.7223 (t) REVERT: G 3 GLN cc_start: 0.8229 (mt0) cc_final: 0.7593 (pt0) REVERT: G 49 MET cc_start: 0.8396 (mtm) cc_final: 0.8029 (mtp) REVERT: G 94 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6023 (tpp) REVERT: G 96 TYR cc_start: 0.8353 (m-80) cc_final: 0.8015 (m-80) REVERT: F 37 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.5599 (tp-100) REVERT: F 89 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: C 198 TYR cc_start: 0.4517 (OUTLIER) cc_final: 0.3467 (t80) REVERT: C 309 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8245 (mm-30) REVERT: C 613 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: C 675 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: C 916 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8581 (tt) REVERT: C 921 LYS cc_start: 0.8849 (tttt) cc_final: 0.8134 (mppt) REVERT: C 985 ASP cc_start: 0.7445 (m-30) cc_final: 0.7094 (m-30) REVERT: B 100 ASN cc_start: 0.7823 (m110) cc_final: 0.6864 (p0) REVERT: B 360 ASN cc_start: 0.8429 (m-40) cc_final: 0.8130 (m-40) REVERT: B 428 ASP cc_start: 0.7882 (p0) cc_final: 0.7667 (p0) REVERT: B 465 GLU cc_start: 0.7555 (tp30) cc_final: 0.7077 (pt0) REVERT: B 498 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7462 (mtt-85) REVERT: B 505 HIS cc_start: 0.7687 (m90) cc_final: 0.7400 (m90) REVERT: B 529 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7911 (mmtt) REVERT: B 654 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 760 CYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6186 (p) REVERT: B 814 LYS cc_start: 0.8147 (mptm) cc_final: 0.7581 (mtpt) REVERT: B 957 GLN cc_start: 0.8576 (tt0) cc_final: 0.8342 (tt0) REVERT: H 4 MET cc_start: 0.1517 (mmt) cc_final: 0.0267 (ptp) outliers start: 72 outliers final: 38 residues processed: 305 average time/residue: 0.5200 time to fit residues: 193.9137 Evaluate side-chains 298 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 271 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 229 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN A 55 GLN A 116 GLN A 417 ASN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.190793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115627 restraints weight = 35870.812| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.68 r_work: 0.3089 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 31004 Z= 0.121 Angle : 0.550 16.449 42260 Z= 0.276 Chirality : 0.046 0.734 4811 Planarity : 0.004 0.050 5345 Dihedral : 5.431 59.750 4862 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.52 % Allowed : 12.00 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.13), residues: 3715 helix: 1.51 (0.19), residues: 719 sheet: 0.47 (0.16), residues: 1017 loop : -0.51 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 403 TYR 0.036 0.001 TYR D 96 PHE 0.032 0.001 PHE C 166 TRP 0.027 0.001 TRP F 96 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00273 (30921) covalent geometry : angle 0.52254 (42056) SS BOND : bond 0.00396 ( 45) SS BOND : angle 1.56611 ( 90) hydrogen bonds : bond 0.03899 ( 1232) hydrogen bonds : angle 5.62888 ( 3462) link_BETA1-4 : bond 0.00353 ( 11) link_BETA1-4 : angle 1.25403 ( 33) link_NAG-ASN : bond 0.00478 ( 27) link_NAG-ASN : angle 3.57811 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7822 (ptmt) REVERT: E 94 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 103 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6306 (mmt90) REVERT: A 119 LEU cc_start: 0.7526 (tm) cc_final: 0.7282 (tp) REVERT: A 130 LYS cc_start: 0.7632 (mppt) cc_final: 0.7316 (mptt) REVERT: A 233 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.6989 (tp) REVERT: A 357 ARG cc_start: 0.8506 (ttt-90) cc_final: 0.8118 (ttt-90) REVERT: A 580 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.6400 (mp10) REVERT: A 960 ASN cc_start: 0.8477 (m-40) cc_final: 0.8010 (t0) REVERT: A 1038 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8289 (mmtt) REVERT: D 3 GLN cc_start: 0.7887 (pm20) cc_final: 0.7503 (pm20) REVERT: D 37 TRP cc_start: 0.8170 (m100) cc_final: 0.7847 (m100) REVERT: D 49 MET cc_start: 0.8350 (mtp) cc_final: 0.7889 (mtm) REVERT: D 60 ARG cc_start: 0.8396 (ttm170) cc_final: 0.7734 (ttp-110) REVERT: D 97 CYS cc_start: 0.7662 (t) cc_final: 0.7102 (t) REVERT: G 3 GLN cc_start: 0.8254 (mt0) cc_final: 0.7601 (pt0) REVERT: G 49 MET cc_start: 0.8327 (mtm) cc_final: 0.8006 (mtp) REVERT: G 94 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6019 (tpp) REVERT: G 96 TYR cc_start: 0.8301 (m-80) cc_final: 0.7878 (m-80) REVERT: F 88 CYS cc_start: 0.6388 (p) cc_final: 0.6116 (p) REVERT: F 89 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: C 198 TYR cc_start: 0.4409 (OUTLIER) cc_final: 0.3408 (t80) REVERT: C 239 GLN cc_start: 0.6325 (tt0) cc_final: 0.5673 (mp-120) REVERT: C 309 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8204 (mm-30) REVERT: C 675 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: C 811 LYS cc_start: 0.6645 (mtmm) cc_final: 0.5791 (tptp) REVERT: C 921 LYS cc_start: 0.8738 (tttt) cc_final: 0.8020 (mppt) REVERT: C 985 ASP cc_start: 0.7412 (m-30) cc_final: 0.7052 (m-30) REVERT: B 100 ASN cc_start: 0.7712 (m110) cc_final: 0.6751 (p0) REVERT: B 109 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7486 (m) REVERT: B 239 GLN cc_start: 0.8320 (tt0) cc_final: 0.7875 (tt0) REVERT: B 360 ASN cc_start: 0.8364 (m-40) cc_final: 0.8090 (m-40) REVERT: B 428 ASP cc_start: 0.7889 (p0) cc_final: 0.7681 (p0) REVERT: B 465 GLU cc_start: 0.7613 (tp30) cc_final: 0.7074 (pt0) REVERT: B 493 ARG cc_start: 0.6772 (mtt90) cc_final: 0.6413 (mtt90) REVERT: B 505 HIS cc_start: 0.7680 (m90) cc_final: 0.7392 (m90) REVERT: B 654 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: B 957 GLN cc_start: 0.8538 (tt0) cc_final: 0.8317 (tt0) REVERT: H 4 MET cc_start: 0.1577 (mmt) cc_final: 0.0319 (ptp) REVERT: I 49 MET cc_start: 0.0866 (mmm) cc_final: 0.0235 (mtp) outliers start: 50 outliers final: 26 residues processed: 293 average time/residue: 0.5173 time to fit residues: 184.3909 Evaluate side-chains 282 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 145 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 220 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 179 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 329 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.189455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112626 restraints weight = 35751.572| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.44 r_work: 0.3088 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 31004 Z= 0.166 Angle : 0.574 16.285 42260 Z= 0.288 Chirality : 0.047 0.750 4811 Planarity : 0.004 0.049 5345 Dihedral : 5.432 59.358 4862 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.76 % Allowed : 12.00 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.19 (0.13), residues: 3715 helix: 1.46 (0.19), residues: 716 sheet: 0.46 (0.16), residues: 1011 loop : -0.52 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.036 0.002 TYR D 96 PHE 0.030 0.001 PHE C 166 TRP 0.030 0.001 TRP F 96 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00388 (30921) covalent geometry : angle 0.54678 (42056) SS BOND : bond 0.00379 ( 45) SS BOND : angle 1.55826 ( 90) hydrogen bonds : bond 0.04261 ( 1232) hydrogen bonds : angle 5.66480 ( 3462) link_BETA1-4 : bond 0.00324 ( 11) link_BETA1-4 : angle 1.26710 ( 33) link_NAG-ASN : bond 0.00436 ( 27) link_NAG-ASN : angle 3.61486 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8005 (ttpt) cc_final: 0.7749 (ptmt) REVERT: E 94 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7664 (t80) REVERT: A 103 ARG cc_start: 0.6965 (mtt180) cc_final: 0.6302 (mmt90) REVERT: A 119 LEU cc_start: 0.7521 (tm) cc_final: 0.7272 (tp) REVERT: A 130 LYS cc_start: 0.7621 (mppt) cc_final: 0.7327 (mptt) REVERT: A 233 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7035 (tp) REVERT: A 357 ARG cc_start: 0.8485 (ttt-90) cc_final: 0.8092 (ttt-90) REVERT: A 580 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.6380 (mp10) REVERT: A 1038 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8322 (mmtt) REVERT: D 3 GLN cc_start: 0.7898 (pm20) cc_final: 0.7510 (pm20) REVERT: D 37 TRP cc_start: 0.8141 (m100) cc_final: 0.7831 (m100) REVERT: D 41 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7441 (mpt) REVERT: D 49 MET cc_start: 0.8361 (mtp) cc_final: 0.7888 (mtm) REVERT: D 60 ARG cc_start: 0.8385 (ttm170) cc_final: 0.7741 (ttp-110) REVERT: D 97 CYS cc_start: 0.7637 (t) cc_final: 0.7082 (t) REVERT: G 3 GLN cc_start: 0.8240 (mt0) cc_final: 0.7564 (pt0) REVERT: G 49 MET cc_start: 0.8347 (mtm) cc_final: 0.7990 (mtp) REVERT: G 94 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.5962 (tpp) REVERT: G 96 TYR cc_start: 0.8281 (m-80) cc_final: 0.7867 (m-80) REVERT: F 89 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: C 198 TYR cc_start: 0.4395 (OUTLIER) cc_final: 0.3410 (t80) REVERT: C 309 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8155 (mm-30) REVERT: C 921 LYS cc_start: 0.8743 (tttt) cc_final: 0.8013 (mppt) REVERT: C 985 ASP cc_start: 0.7436 (m-30) cc_final: 0.7064 (m-30) REVERT: B 100 ASN cc_start: 0.7834 (m110) cc_final: 0.6945 (p0) REVERT: B 109 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7455 (m) REVERT: B 239 GLN cc_start: 0.8220 (tt0) cc_final: 0.7777 (tt0) REVERT: B 360 ASN cc_start: 0.8340 (m-40) cc_final: 0.8039 (m-40) REVERT: B 428 ASP cc_start: 0.7889 (p0) cc_final: 0.7674 (p0) REVERT: B 465 GLU cc_start: 0.7578 (tp30) cc_final: 0.7040 (pt0) REVERT: B 493 ARG cc_start: 0.6754 (mtt90) cc_final: 0.6401 (mtt90) REVERT: B 505 HIS cc_start: 0.7601 (m90) cc_final: 0.7311 (m90) REVERT: B 529 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7863 (mmtt) REVERT: B 654 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: B 814 LYS cc_start: 0.8061 (mptm) cc_final: 0.7483 (mtpt) REVERT: B 957 GLN cc_start: 0.8474 (tt0) cc_final: 0.8239 (tt0) REVERT: H 4 MET cc_start: 0.1543 (mmt) cc_final: 0.0312 (ptp) REVERT: I 49 MET cc_start: 0.1319 (mmm) cc_final: 0.0627 (mtp) outliers start: 58 outliers final: 34 residues processed: 297 average time/residue: 0.5178 time to fit residues: 187.2814 Evaluate side-chains 292 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain H residue 14 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 357 optimal weight: 9.9990 chunk 322 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 327 optimal weight: 0.6980 chunk 307 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN A 116 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 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 = 0.4226 r_free = 0.4226 target = 0.189179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113963 restraints weight = 35729.875| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.54 r_work: 0.3057 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 31004 Z= 0.192 Angle : 0.598 16.799 42260 Z= 0.301 Chirality : 0.048 0.783 4811 Planarity : 0.004 0.052 5345 Dihedral : 5.495 59.408 4862 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.76 % Allowed : 12.34 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.13 (0.13), residues: 3715 helix: 1.43 (0.19), residues: 709 sheet: 0.42 (0.15), residues: 1029 loop : -0.57 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 498 TYR 0.039 0.002 TYR D 96 PHE 0.029 0.002 PHE C 166 TRP 0.036 0.002 TRP F 96 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00453 (30921) covalent geometry : angle 0.56967 (42056) SS BOND : bond 0.00390 ( 45) SS BOND : angle 1.82513 ( 90) hydrogen bonds : bond 0.04401 ( 1232) hydrogen bonds : angle 5.72020 ( 3462) link_BETA1-4 : bond 0.00306 ( 11) link_BETA1-4 : angle 1.28729 ( 33) link_NAG-ASN : bond 0.00413 ( 27) link_NAG-ASN : angle 3.73591 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7716 (ptmt) REVERT: E 94 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7657 (t80) REVERT: A 103 ARG cc_start: 0.6987 (mtt180) cc_final: 0.6319 (mmt90) REVERT: A 119 LEU cc_start: 0.7525 (tm) cc_final: 0.7279 (tp) REVERT: A 130 LYS cc_start: 0.7555 (mppt) cc_final: 0.7257 (mptt) REVERT: A 233 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7037 (tp) REVERT: A 357 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.8131 (ttt-90) REVERT: A 580 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.6533 (mp10) REVERT: A 1038 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8390 (mmtt) REVERT: D 3 GLN cc_start: 0.7920 (pm20) cc_final: 0.7532 (pm20) REVERT: D 37 TRP cc_start: 0.8135 (m100) cc_final: 0.7764 (m100) REVERT: D 49 MET cc_start: 0.8356 (mtp) cc_final: 0.7820 (mtm) REVERT: D 60 ARG cc_start: 0.8385 (ttm170) cc_final: 0.7729 (ttp-110) REVERT: D 97 CYS cc_start: 0.7649 (t) cc_final: 0.7079 (t) REVERT: G 3 GLN cc_start: 0.8263 (mt0) cc_final: 0.7615 (pt0) REVERT: G 49 MET cc_start: 0.8371 (mtm) cc_final: 0.8009 (mtp) REVERT: G 94 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.5978 (tpp) REVERT: G 96 TYR cc_start: 0.8321 (m-80) cc_final: 0.7923 (m-80) REVERT: F 89 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: C 198 TYR cc_start: 0.4528 (OUTLIER) cc_final: 0.3495 (t80) REVERT: C 205 HIS cc_start: 0.6112 (m90) cc_final: 0.5887 (t70) REVERT: C 239 GLN cc_start: 0.6298 (tt0) cc_final: 0.5638 (mp-120) REVERT: C 309 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8224 (mm-30) REVERT: C 921 LYS cc_start: 0.8805 (tttt) cc_final: 0.8075 (mppt) REVERT: C 985 ASP cc_start: 0.7438 (m-30) cc_final: 0.7061 (m-30) REVERT: B 100 ASN cc_start: 0.7930 (m110) cc_final: 0.7076 (p0) REVERT: B 109 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7541 (m) REVERT: B 360 ASN cc_start: 0.8400 (m-40) cc_final: 0.8099 (m-40) REVERT: B 428 ASP cc_start: 0.7912 (p0) cc_final: 0.7691 (p0) REVERT: B 465 GLU cc_start: 0.7612 (tp30) cc_final: 0.7058 (pt0) REVERT: B 505 HIS cc_start: 0.7716 (m90) cc_final: 0.7432 (m90) REVERT: B 529 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7944 (mmtt) REVERT: B 654 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: B 760 CYS cc_start: 0.5826 (OUTLIER) cc_final: 0.5582 (p) REVERT: B 814 LYS cc_start: 0.8080 (mptm) cc_final: 0.7508 (mtpt) REVERT: B 957 GLN cc_start: 0.8540 (tt0) cc_final: 0.8304 (tt0) REVERT: H 4 MET cc_start: 0.1449 (mmt) cc_final: 0.0196 (ptp) REVERT: I 49 MET cc_start: 0.1194 (mmm) cc_final: 0.0648 (mtp) outliers start: 58 outliers final: 36 residues processed: 289 average time/residue: 0.5252 time to fit residues: 185.4747 Evaluate side-chains 288 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 241 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain H residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 150 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.0670 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 203 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 299 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN A 116 GLN A 779 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C1125 ASN B 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.191059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116874 restraints weight = 35624.698| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.69 r_work: 0.3094 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31004 Z= 0.112 Angle : 0.544 15.848 42260 Z= 0.273 Chirality : 0.046 0.698 4811 Planarity : 0.004 0.048 5345 Dihedral : 5.229 59.822 4862 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 12.88 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.24 (0.13), residues: 3715 helix: 1.66 (0.20), residues: 717 sheet: 0.42 (0.16), residues: 1019 loop : -0.52 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 498 TYR 0.038 0.001 TYR D 96 PHE 0.029 0.001 PHE C 166 TRP 0.037 0.001 TRP F 96 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00252 (30921) covalent geometry : angle 0.51815 (42056) SS BOND : bond 0.00315 ( 45) SS BOND : angle 1.54663 ( 90) hydrogen bonds : bond 0.03717 ( 1232) hydrogen bonds : angle 5.48556 ( 3462) link_BETA1-4 : bond 0.00360 ( 11) link_BETA1-4 : angle 1.26335 ( 33) link_NAG-ASN : bond 0.00469 ( 27) link_NAG-ASN : angle 3.39414 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7713 (ptmt) REVERT: E 94 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7636 (t80) REVERT: A 103 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6320 (mmt90) REVERT: A 118 LEU cc_start: 0.6402 (mp) cc_final: 0.6151 (mt) REVERT: A 119 LEU cc_start: 0.7545 (tm) cc_final: 0.7302 (tp) REVERT: A 130 LYS cc_start: 0.7562 (mppt) cc_final: 0.7277 (mptt) REVERT: A 233 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7030 (tp) REVERT: A 357 ARG cc_start: 0.8495 (ttt-90) cc_final: 0.8135 (ttt-90) REVERT: A 580 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.6370 (mp10) REVERT: A 960 ASN cc_start: 0.8525 (m-40) cc_final: 0.8045 (t0) REVERT: A 1017 GLU cc_start: 0.8871 (tt0) cc_final: 0.8624 (tt0) REVERT: D 3 GLN cc_start: 0.7953 (pm20) cc_final: 0.7608 (pm20) REVERT: D 37 TRP cc_start: 0.8146 (m100) cc_final: 0.7809 (m100) REVERT: D 49 MET cc_start: 0.8393 (mtp) cc_final: 0.7927 (mtm) REVERT: D 60 ARG cc_start: 0.8390 (ttm170) cc_final: 0.7760 (ttp-110) REVERT: D 97 CYS cc_start: 0.7599 (t) cc_final: 0.7106 (t) REVERT: G 3 GLN cc_start: 0.8273 (mt0) cc_final: 0.7603 (pt0) REVERT: G 49 MET cc_start: 0.8366 (mtm) cc_final: 0.8089 (mtp) REVERT: G 94 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6029 (tpp) REVERT: G 96 TYR cc_start: 0.8337 (m-80) cc_final: 0.7938 (m-80) REVERT: F 3 GLN cc_start: 0.8005 (mm110) cc_final: 0.7683 (mm-40) REVERT: F 89 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: C 198 TYR cc_start: 0.4575 (OUTLIER) cc_final: 0.3565 (t80) REVERT: C 239 GLN cc_start: 0.6387 (tt0) cc_final: 0.5686 (mp10) REVERT: C 309 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8236 (mm-30) REVERT: C 921 LYS cc_start: 0.8742 (tttt) cc_final: 0.8055 (mppt) REVERT: C 985 ASP cc_start: 0.7447 (m-30) cc_final: 0.7068 (m-30) REVERT: B 100 ASN cc_start: 0.7763 (m110) cc_final: 0.7135 (p0) REVERT: B 109 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7448 (m) REVERT: B 239 GLN cc_start: 0.8242 (tt0) cc_final: 0.7845 (tt0) REVERT: B 360 ASN cc_start: 0.8355 (m-40) cc_final: 0.8082 (m-40) REVERT: B 428 ASP cc_start: 0.7913 (p0) cc_final: 0.7707 (p0) REVERT: B 465 GLU cc_start: 0.7598 (tp30) cc_final: 0.7005 (pt0) REVERT: B 493 ARG cc_start: 0.6794 (mtt90) cc_final: 0.6455 (mtt90) REVERT: B 505 HIS cc_start: 0.7724 (m90) cc_final: 0.7426 (m90) REVERT: B 760 CYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5433 (p) REVERT: B 957 GLN cc_start: 0.8547 (tt0) cc_final: 0.8331 (tt0) REVERT: H 4 MET cc_start: 0.1294 (mmt) cc_final: 0.0058 (ptp) REVERT: I 49 MET cc_start: 0.1003 (mmm) cc_final: 0.0539 (mtp) outliers start: 43 outliers final: 29 residues processed: 293 average time/residue: 0.5131 time to fit residues: 183.7437 Evaluate side-chains 290 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain H residue 14 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 66 optimal weight: 0.4980 chunk 28 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 333 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN A 116 GLN A 505 HIS A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C1125 ASN B 271 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.188303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112080 restraints weight = 35969.054| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.51 r_work: 0.3044 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 31004 Z= 0.232 Angle : 0.618 16.872 42260 Z= 0.312 Chirality : 0.049 0.795 4811 Planarity : 0.004 0.056 5345 Dihedral : 5.472 58.259 4862 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.55 % Allowed : 12.97 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.08 (0.13), residues: 3715 helix: 1.38 (0.19), residues: 702 sheet: 0.40 (0.15), residues: 1032 loop : -0.59 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 498 TYR 0.037 0.002 TYR D 96 PHE 0.024 0.002 PHE C 166 TRP 0.040 0.002 TRP F 96 HIS 0.007 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00552 (30921) covalent geometry : angle 0.59070 (42056) SS BOND : bond 0.00463 ( 45) SS BOND : angle 1.84854 ( 90) hydrogen bonds : bond 0.04638 ( 1232) hydrogen bonds : angle 5.74854 ( 3462) link_BETA1-4 : bond 0.00299 ( 11) link_BETA1-4 : angle 1.32112 ( 33) link_NAG-ASN : bond 0.00412 ( 27) link_NAG-ASN : angle 3.70720 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14274.49 seconds wall clock time: 242 minutes 39.14 seconds (14559.14 seconds total)