Starting phenix.real_space_refine on Sun May 25 16:26:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k45_36877/05_2025/8k45_36877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k45_36877/05_2025/8k45_36877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k45_36877/05_2025/8k45_36877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k45_36877/05_2025/8k45_36877.map" model { file = "/net/cci-nas-00/data/ceres_data/8k45_36877/05_2025/8k45_36877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k45_36877/05_2025/8k45_36877.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.036 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 119 5.16 5 C 17159 2.51 5 N 4412 2.21 5 O 5187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26877 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8111 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 8117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8117 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 976} 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: "C" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8003 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 966} Chain breaks: 10 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Conformer: "B" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} bond proxies already assigned to first conformer: 1003 Chain: "E" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Conformer: "B" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} bond proxies already assigned to first conformer: 1003 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: "R" 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: "T" 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: "X" 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: "a" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER D 26 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 26 " occ=0.50 residue: pdb=" N ASER E 26 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 26 " occ=0.50 Time building chain proxies: 18.25, per 1000 atoms: 0.68 Number of scatterers: 26877 At special positions: 0 Unit cell: (136.12, 146.78, 205, 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 119 16.00 O 5187 8.00 N 4412 7.00 C 17159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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 C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG X 1 " - " NAG X 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 164 " " NAG C1302 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1309 " - " ASN C 801 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.6 seconds 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6262 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 53 sheets defined 23.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.691A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.082A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.617A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.752A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.341A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.350A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.690A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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: 5.028A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.641A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.813A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.682A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.740A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.626A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.757A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.106A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.117A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.566A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.673A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.573A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.535A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.016A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.941A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.590A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 757 removed outlier: 3.608A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.716A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.505A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.058A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.636A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.280A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.766A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.582A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.559A 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 983 removed outlier: 3.915A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.860A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.071A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'E' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.789A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.871A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.610A pdb=" N ALA A 263 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.160A pdb=" N ARG A 102 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 118 Processing sheet with id=AA7, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.595A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.631A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.567A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 375 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 29 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.567A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 375 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 29 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU E 21 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.323A pdb=" N PHE A 392 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.537A pdb=" N TYR A 453 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.693A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.410A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.655A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.973A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.604A pdb=" N ALA B 263 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.562A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 104 through 107 removed outlier: 7.312A pdb=" N ILE B 105 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE B 238 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 107 " --> pdb=" O THR B 236 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 140 through 142 removed outlier: 4.033A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.801A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 327 through 328 removed outlier: 3.508A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.199A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 29 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.199A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 29 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD3, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 584 through 586 removed outlier: 6.362A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.045A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.971A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.756A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B1113 " --> pdb=" O VAL B1104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.996A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.039A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.878A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.661A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 135 through 141 removed outlier: 10.671A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 313 through 318 removed outlier: 7.045A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.861A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.913A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.957A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.957A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.140A pdb=" N GLY D 11 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP D 100 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG D 39 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 12 through 13 removed outlier: 6.370A pdb=" N MET E 35 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA E 51 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2604 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: 13.03 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6666 1.33 - 1.45: 6277 1.45 - 1.58: 14410 1.58 - 1.70: 0 1.70 - 1.83: 152 Bond restraints: 27505 Sorted by residual: bond pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" CA SER C 803 " pdb=" CB SER C 803 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.57e-02 4.06e+03 1.01e+01 bond pdb=" N ILE C 402 " pdb=" CA ILE C 402 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 9.99e+00 bond pdb=" N CYS B 131 " pdb=" CA CYS B 131 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.79e+00 bond pdb=" N THR B 167 " pdb=" CA THR B 167 " ideal model delta sigma weight residual 1.458 1.486 -0.028 9.00e-03 1.23e+04 9.69e+00 ... (remaining 27500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 36681 2.40 - 4.80: 675 4.80 - 7.19: 49 7.19 - 9.59: 6 9.59 - 11.99: 4 Bond angle restraints: 37415 Sorted by residual: angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 111.90 107.46 4.44 8.10e-01 1.52e+00 3.01e+01 angle pdb=" N GLU C 406 " pdb=" CA GLU C 406 " pdb=" C GLU C 406 " ideal model delta sigma weight residual 113.02 106.64 6.38 1.20e+00 6.94e-01 2.83e+01 angle pdb=" N THR A 604 " pdb=" CA THR A 604 " pdb=" C THR A 604 " ideal model delta sigma weight residual 114.31 108.02 6.29 1.29e+00 6.01e-01 2.38e+01 angle pdb=" N THR A 236 " pdb=" CA THR A 236 " pdb=" C THR A 236 " ideal model delta sigma weight residual 113.72 107.43 6.29 1.30e+00 5.92e-01 2.34e+01 angle pdb=" C THR A1116 " pdb=" CA THR A1116 " pdb=" CB THR A1116 " ideal model delta sigma weight residual 114.16 103.10 11.06 2.31e+00 1.87e-01 2.29e+01 ... (remaining 37410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.79: 15429 24.79 - 49.58: 1338 49.58 - 74.37: 161 74.37 - 99.16: 48 99.16 - 123.95: 3 Dihedral angle restraints: 16979 sinusoidal: 7252 harmonic: 9727 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -0.43 -85.57 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -8.69 -77.31 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 33.10 59.90 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 16976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 4301 0.172 - 0.344: 28 0.344 - 0.516: 4 0.516 - 0.688: 1 0.688 - 0.860: 2 Chirality restraints: 4336 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.24e+01 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 4333 not shown) Planarity restraints: 4798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.320 2.00e-02 2.50e+03 2.71e-01 9.19e+02 pdb=" C7 NAG C1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.471 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " -0.311 2.00e-02 2.50e+03 2.63e-01 8.65e+02 pdb=" C7 NAG B1305 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " 0.455 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " -0.294 2.00e-02 2.50e+03 2.48e-01 7.67e+02 pdb=" C7 NAG B1306 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.423 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " -0.023 2.00e-02 2.50e+03 ... (remaining 4795 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 295 2.57 - 3.15: 21825 3.15 - 3.74: 41147 3.74 - 4.32: 53779 4.32 - 4.90: 90093 Nonbonded interactions: 207139 Sorted by model distance: nonbonded pdb=" OD1 ASP B 111 " pdb=" N SER B 112 " model vdw 1.989 3.120 nonbonded pdb=" OE1 GLU A 281 " pdb=" OD1 ASN A 282 " model vdw 2.136 3.040 nonbonded pdb=" N ASN C 164 " pdb=" OD1 ASN C 164 " model vdw 2.171 3.120 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.187 3.040 nonbonded pdb=" OG SER D 1 " pdb=" OH TYR D 113 " model vdw 2.207 3.040 ... (remaining 207134 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 15 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 236 or (resid 237 and (name N o \ r name CA or name C or name O or name CB )) or resid 238 through 333 or resid 33 \ 8 through 405 or (resid 406 and (name N or name CA or name C or name O or name C \ B )) or resid 407 through 517 or resid 528 through 558 or (resid 559 and (name N \ or name CA or name C or name O or name CB )) or resid 560 through 564 or (resid \ 565 and (name N or name CA or name C or name O or name CB )) or resid 566 throu \ gh 827 or resid 853 through 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 15 through 236 or (resid 237 and (name N or name CA or nam \ e C or name O or name CB )) or resid 238 through 333 or resid 338 or (resid 339 \ and (name N or name CA or name C or name O or name CB )) or resid 340 through 40 \ 2 or (resid 403 and (name N or name CA or name C or name O or name CB )) or resi \ d 404 through 405 or (resid 406 and (name N or name CA or name C or name O or na \ me CB )) or resid 407 or (resid 408 and (name N or name CA or name C or name O o \ r name CB )) or resid 409 through 517 or resid 528 through 558 or (resid 559 and \ (name N or name CA or name C or name O or name CB )) or resid 560 through 564 o \ r (resid 565 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 66 through 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 15 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 338 or (resid 339 and (name N o \ r name CA or name C or name O or name CB )) or resid 340 through 407 or (resid 4 \ 08 and (name N or name CA or name C or name O or name CB )) or resid 409 through \ 827 or resid 853 through 1147 or resid 1301 through 1308)) } ncs_group { reference = (chain 'D' and (resid 1 through 25 or resid 27 through 124)) selection = (chain 'E' and (resid 1 through 25 or resid 27 through 124)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 66.380 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 0.005 0.057 27587 Z= 0.273 Angle : 0.729 11.990 37620 Z= 0.411 Chirality : 0.055 0.860 4336 Planarity : 0.011 0.271 4767 Dihedral : 17.547 123.946 10594 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.08 % Favored : 92.40 % Rotamer: Outliers : 2.13 % Allowed : 29.47 % Favored : 68.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 3282 helix: 1.80 (0.22), residues: 631 sheet: -0.67 (0.19), residues: 724 loop : -1.46 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.003 0.001 HIS A 505 PHE 0.019 0.001 PHE A 140 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 31) link_NAG-ASN : angle 3.11814 ( 93) link_BETA1-4 : bond 0.00380 ( 10) link_BETA1-4 : angle 1.13345 ( 30) hydrogen bonds : bond 0.14838 ( 919) hydrogen bonds : angle 6.72816 ( 2604) SS BOND : bond 0.00539 ( 41) SS BOND : angle 1.15605 ( 82) covalent geometry : bond 0.00491 (27505) covalent geometry : angle 0.71126 (37415) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 139 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6343 (mmm) cc_final: 0.5546 (mtm) REVERT: A 406 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8260 (tp30) REVERT: C 409 GLN cc_start: 0.3220 (OUTLIER) cc_final: 0.2194 (mp10) REVERT: C 978 ASN cc_start: 0.2827 (p0) cc_final: 0.2615 (p0) REVERT: D 54 TRP cc_start: 0.7707 (t-100) cc_final: 0.7506 (t-100) outliers start: 62 outliers final: 24 residues processed: 192 average time/residue: 0.3790 time to fit residues: 121.8539 Evaluate side-chains 157 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 409 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 0.6980 chunk 251 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.099082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062701 restraints weight = 88928.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.064860 restraints weight = 43710.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066191 restraints weight = 29046.512| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27587 Z= 0.140 Angle : 0.594 11.057 37620 Z= 0.296 Chirality : 0.045 0.416 4336 Planarity : 0.004 0.047 4767 Dihedral : 8.426 108.948 4640 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 3.30 % Allowed : 27.89 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3282 helix: 1.89 (0.22), residues: 650 sheet: -0.50 (0.20), residues: 685 loop : -1.38 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 37 HIS 0.004 0.001 HIS D 34 PHE 0.016 0.001 PHE B 133 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 31) link_NAG-ASN : angle 3.14935 ( 93) link_BETA1-4 : bond 0.00425 ( 10) link_BETA1-4 : angle 1.01336 ( 30) hydrogen bonds : bond 0.05259 ( 919) hydrogen bonds : angle 5.35251 ( 2604) SS BOND : bond 0.00269 ( 41) SS BOND : angle 0.88201 ( 82) covalent geometry : bond 0.00316 (27505) covalent geometry : angle 0.57222 (37415) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 140 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3533 (OUTLIER) cc_final: 0.3215 (m) REVERT: A 153 MET cc_start: 0.6590 (mmm) cc_final: 0.5720 (mtm) REVERT: A 740 MET cc_start: 0.8644 (tmm) cc_final: 0.8000 (tmm) REVERT: B 740 MET cc_start: 0.9126 (tpp) cc_final: 0.8898 (tpp) REVERT: B 869 MET cc_start: 0.8770 (ptp) cc_final: 0.8495 (mtm) REVERT: B 1107 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8444 (mtt90) REVERT: C 978 ASN cc_start: 0.2919 (p0) cc_final: 0.2522 (p0) REVERT: C 984 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8219 (tt) REVERT: D 54 TRP cc_start: 0.7830 (t-100) cc_final: 0.7468 (t-100) REVERT: E 4 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7286 (tm-30) REVERT: E 96 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5234 (m-80) outliers start: 96 outliers final: 53 residues processed: 223 average time/residue: 0.3287 time to fit residues: 123.4854 Evaluate side-chains 188 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 96 TYR Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 275 optimal weight: 0.3980 chunk 251 optimal weight: 9.9990 chunk 320 optimal weight: 7.9990 chunk 247 optimal weight: 30.0000 chunk 224 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 133 optimal weight: 30.0000 chunk 163 optimal weight: 4.9990 chunk 288 optimal weight: 0.4980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 481 ASN B1083 HIS B1135 ASN C 207 HIS C 556 ASN C 804 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 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 = 0.3776 r_free = 0.3776 target = 0.096762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.060413 restraints weight = 89488.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062471 restraints weight = 44314.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063771 restraints weight = 29588.377| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 27587 Z= 0.268 Angle : 0.657 11.955 37620 Z= 0.330 Chirality : 0.046 0.418 4336 Planarity : 0.004 0.045 4767 Dihedral : 7.895 111.240 4618 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.63 % Favored : 92.19 % Rotamer: Outliers : 5.70 % Allowed : 26.14 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3282 helix: 1.68 (0.21), residues: 656 sheet: -0.73 (0.19), residues: 714 loop : -1.48 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.006 0.001 HIS A 49 PHE 0.030 0.002 PHE D 48 TYR 0.021 0.001 TYR B 265 ARG 0.004 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 31) link_NAG-ASN : angle 3.21057 ( 93) link_BETA1-4 : bond 0.00286 ( 10) link_BETA1-4 : angle 1.24271 ( 30) hydrogen bonds : bond 0.05716 ( 919) hydrogen bonds : angle 5.33667 ( 2604) SS BOND : bond 0.00383 ( 41) SS BOND : angle 1.19140 ( 82) covalent geometry : bond 0.00623 (27505) covalent geometry : angle 0.63516 (37415) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 140 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3606 (OUTLIER) cc_final: 0.3296 (m) REVERT: A 153 MET cc_start: 0.6720 (mmm) cc_final: 0.5568 (mtm) REVERT: A 406 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: A 618 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 702 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: A 740 MET cc_start: 0.8792 (tmm) cc_final: 0.8251 (tmm) REVERT: B 646 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7938 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8429 (mtt90) REVERT: C 19 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7795 (p) REVERT: C 675 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8061 (pp30) REVERT: C 978 ASN cc_start: 0.2714 (p0) cc_final: 0.2409 (p0) REVERT: C 984 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8274 (tt) REVERT: D 54 TRP cc_start: 0.7899 (t-100) cc_final: 0.7508 (t-100) REVERT: E 4 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7389 (tm-30) outliers start: 166 outliers final: 98 residues processed: 287 average time/residue: 0.3451 time to fit residues: 164.5583 Evaluate side-chains 237 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 130 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 229 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 231 optimal weight: 0.0270 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.098118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060722 restraints weight = 86333.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062784 restraints weight = 43095.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064099 restraints weight = 29069.077| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27587 Z= 0.112 Angle : 0.566 10.993 37620 Z= 0.281 Chirality : 0.044 0.408 4336 Planarity : 0.004 0.044 4767 Dihedral : 7.241 108.800 4610 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.37 % Favored : 94.44 % Rotamer: Outliers : 3.92 % Allowed : 27.59 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3282 helix: 1.91 (0.21), residues: 653 sheet: -0.51 (0.19), residues: 711 loop : -1.33 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.005 0.001 HIS D 34 PHE 0.026 0.001 PHE A 106 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 31) link_NAG-ASN : angle 2.92517 ( 93) link_BETA1-4 : bond 0.00314 ( 10) link_BETA1-4 : angle 1.13552 ( 30) hydrogen bonds : bond 0.04768 ( 919) hydrogen bonds : angle 4.94313 ( 2604) SS BOND : bond 0.00236 ( 41) SS BOND : angle 0.83672 ( 82) covalent geometry : bond 0.00251 (27505) covalent geometry : angle 0.54619 (37415) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 148 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3953 (OUTLIER) cc_final: 0.3598 (m) REVERT: A 153 MET cc_start: 0.6699 (mmm) cc_final: 0.5853 (mtm) REVERT: A 402 ILE cc_start: 0.8854 (tp) cc_final: 0.8638 (tp) REVERT: A 406 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: A 702 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: A 740 MET cc_start: 0.8699 (tmm) cc_final: 0.8099 (tmm) REVERT: B 102 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7849 (mmt-90) REVERT: B 1107 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8471 (mtt90) REVERT: C 19 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7910 (p) REVERT: C 554 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8372 (tp30) REVERT: C 675 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7981 (pp30) REVERT: C 978 ASN cc_start: 0.2645 (p0) cc_final: 0.2385 (p0) REVERT: E 4 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7420 (tm-30) outliers start: 114 outliers final: 76 residues processed: 248 average time/residue: 0.3463 time to fit residues: 141.8439 Evaluate side-chains 221 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 137 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 242 optimal weight: 10.0000 chunk 316 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 246 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN C 61 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3779 r_free = 0.3779 target = 0.097924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060500 restraints weight = 86915.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062615 restraints weight = 42816.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063915 restraints weight = 28518.601| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27587 Z= 0.147 Angle : 0.573 11.104 37620 Z= 0.285 Chirality : 0.044 0.407 4336 Planarity : 0.004 0.044 4767 Dihedral : 6.908 108.217 4606 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.26 % Favored : 93.56 % Rotamer: Outliers : 4.50 % Allowed : 27.14 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3282 helix: 1.90 (0.21), residues: 655 sheet: -0.55 (0.20), residues: 684 loop : -1.33 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.006 0.001 HIS D 34 PHE 0.021 0.001 PHE A 106 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 31) link_NAG-ASN : angle 2.99448 ( 93) link_BETA1-4 : bond 0.00271 ( 10) link_BETA1-4 : angle 1.12143 ( 30) hydrogen bonds : bond 0.04710 ( 919) hydrogen bonds : angle 4.83669 ( 2604) SS BOND : bond 0.00251 ( 41) SS BOND : angle 1.08806 ( 82) covalent geometry : bond 0.00342 (27505) covalent geometry : angle 0.55205 (37415) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 146 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3952 (OUTLIER) cc_final: 0.3581 (m) REVERT: A 402 ILE cc_start: 0.8880 (tp) cc_final: 0.8677 (tp) REVERT: A 702 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: A 740 MET cc_start: 0.8677 (tmm) cc_final: 0.8173 (tmm) REVERT: B 646 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7890 (tmm-80) REVERT: B 1050 MET cc_start: 0.8456 (mtm) cc_final: 0.8208 (ptm) REVERT: B 1107 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8448 (mtt90) REVERT: C 19 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8009 (p) REVERT: C 675 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8009 (pp30) REVERT: E 4 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7468 (tm-30) REVERT: E 73 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7131 (tpt90) REVERT: E 107 ASN cc_start: 0.8267 (p0) cc_final: 0.8028 (p0) outliers start: 131 outliers final: 103 residues processed: 261 average time/residue: 0.3623 time to fit residues: 154.1337 Evaluate side-chains 251 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 142 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 129 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 177 optimal weight: 0.0170 chunk 176 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 263 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.097645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061629 restraints weight = 87996.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063717 restraints weight = 43226.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065015 restraints weight = 28628.051| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 27587 Z= 0.104 Angle : 0.559 11.180 37620 Z= 0.275 Chirality : 0.044 0.398 4336 Planarity : 0.004 0.045 4767 Dihedral : 6.588 106.656 4606 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.31 % Favored : 94.51 % Rotamer: Outliers : 3.85 % Allowed : 27.79 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3282 helix: 1.97 (0.21), residues: 651 sheet: -0.38 (0.20), residues: 680 loop : -1.25 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.006 0.001 HIS D 34 PHE 0.021 0.001 PHE A 106 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 31) link_NAG-ASN : angle 2.88415 ( 93) link_BETA1-4 : bond 0.00297 ( 10) link_BETA1-4 : angle 1.08697 ( 30) hydrogen bonds : bond 0.04270 ( 919) hydrogen bonds : angle 4.67099 ( 2604) SS BOND : bond 0.00219 ( 41) SS BOND : angle 0.81958 ( 82) covalent geometry : bond 0.00236 (27505) covalent geometry : angle 0.53948 (37415) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 154 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3904 (OUTLIER) cc_final: 0.3547 (m) REVERT: A 153 MET cc_start: 0.6488 (mmm) cc_final: 0.5741 (mtm) REVERT: A 702 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: A 740 MET cc_start: 0.8583 (tmm) cc_final: 0.8078 (tmm) REVERT: B 96 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: B 102 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7954 (mmt-90) REVERT: B 646 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7844 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8441 (mtt90) REVERT: C 19 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7981 (p) REVERT: C 554 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: C 675 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7958 (pp30) REVERT: C 983 ARG cc_start: 0.8571 (tmm-80) cc_final: 0.8221 (ttp80) REVERT: E 4 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7527 (tm-30) REVERT: E 73 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7147 (tpt90) outliers start: 112 outliers final: 84 residues processed: 249 average time/residue: 0.3649 time to fit residues: 148.7962 Evaluate side-chains 237 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 144 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 247 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.097284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.061527 restraints weight = 86218.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063595 restraints weight = 42444.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064913 restraints weight = 28065.187| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27587 Z= 0.118 Angle : 0.557 10.656 37620 Z= 0.275 Chirality : 0.044 0.395 4336 Planarity : 0.004 0.046 4767 Dihedral : 6.305 105.894 4602 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 4.19 % Allowed : 27.69 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3282 helix: 2.01 (0.21), residues: 651 sheet: -0.44 (0.20), residues: 666 loop : -1.22 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.006 0.001 HIS D 34 PHE 0.020 0.001 PHE A 106 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 31) link_NAG-ASN : angle 2.87567 ( 93) link_BETA1-4 : bond 0.00280 ( 10) link_BETA1-4 : angle 1.07904 ( 30) hydrogen bonds : bond 0.04219 ( 919) hydrogen bonds : angle 4.59232 ( 2604) SS BOND : bond 0.00218 ( 41) SS BOND : angle 0.81343 ( 82) covalent geometry : bond 0.00275 (27505) covalent geometry : angle 0.53752 (37415) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 151 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3842 (OUTLIER) cc_final: 0.3498 (m) REVERT: A 153 MET cc_start: 0.6567 (mmm) cc_final: 0.5853 (mtt) REVERT: A 702 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8493 (tm-30) REVERT: A 740 MET cc_start: 0.8584 (tmm) cc_final: 0.8109 (tmm) REVERT: B 357 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7309 (tmm-80) REVERT: B 646 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7848 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8413 (mtt90) REVERT: C 19 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7930 (p) REVERT: C 675 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7948 (pp30) REVERT: C 983 ARG cc_start: 0.8595 (tmm-80) cc_final: 0.8213 (ttp80) REVERT: E 4 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 37 TRP cc_start: 0.6856 (m100) cc_final: 0.6650 (m100) outliers start: 122 outliers final: 101 residues processed: 257 average time/residue: 0.3445 time to fit residues: 145.5394 Evaluate side-chains 253 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 145 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain E residue 101 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 177 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 323 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.097829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061683 restraints weight = 88049.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063796 restraints weight = 43444.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065019 restraints weight = 28792.882| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 27587 Z= 0.106 Angle : 0.549 10.472 37620 Z= 0.270 Chirality : 0.044 0.390 4336 Planarity : 0.004 0.046 4767 Dihedral : 6.128 104.799 4602 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.22 % Favored : 94.63 % Rotamer: Outliers : 4.29 % Allowed : 27.59 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3282 helix: 2.07 (0.22), residues: 645 sheet: -0.45 (0.20), residues: 682 loop : -1.18 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.007 0.001 HIS D 34 PHE 0.019 0.001 PHE A 106 TYR 0.018 0.001 TYR B1067 ARG 0.009 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 31) link_NAG-ASN : angle 2.79510 ( 93) link_BETA1-4 : bond 0.00310 ( 10) link_BETA1-4 : angle 1.05418 ( 30) hydrogen bonds : bond 0.04045 ( 919) hydrogen bonds : angle 4.50226 ( 2604) SS BOND : bond 0.00219 ( 41) SS BOND : angle 0.74378 ( 82) covalent geometry : bond 0.00247 (27505) covalent geometry : angle 0.53084 (37415) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 151 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7400 (t70) REVERT: A 131 CYS cc_start: 0.3940 (OUTLIER) cc_final: 0.3547 (m) REVERT: A 153 MET cc_start: 0.6447 (mmm) cc_final: 0.5893 (mtt) REVERT: A 702 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: A 740 MET cc_start: 0.8543 (tmm) cc_final: 0.8057 (tmm) REVERT: A 774 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8012 (mm-40) REVERT: B 96 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6912 (tt0) REVERT: B 102 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8005 (mmt-90) REVERT: B 357 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7379 (tmm-80) REVERT: B 646 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7843 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8413 (mtt90) REVERT: C 19 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8059 (p) REVERT: C 554 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8402 (tp30) REVERT: C 675 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7955 (pp30) REVERT: C 983 ARG cc_start: 0.8546 (tmm-80) cc_final: 0.8164 (ttp80) REVERT: D 30 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 53 ASP cc_start: 0.7573 (m-30) cc_final: 0.7133 (p0) REVERT: E 4 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7616 (tm-30) REVERT: E 21 LEU cc_start: 0.6819 (mt) cc_final: 0.6376 (mt) REVERT: E 37 TRP cc_start: 0.6920 (m100) cc_final: 0.6663 (m100) outliers start: 125 outliers final: 91 residues processed: 258 average time/residue: 0.3628 time to fit residues: 154.4733 Evaluate side-chains 245 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 143 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 242 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 245 optimal weight: 50.0000 chunk 10 optimal weight: 0.0470 chunk 142 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.096544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060511 restraints weight = 89141.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.062573 restraints weight = 43462.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.063871 restraints weight = 28767.707| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27587 Z= 0.179 Angle : 0.598 10.918 37620 Z= 0.297 Chirality : 0.044 0.396 4336 Planarity : 0.004 0.048 4767 Dihedral : 6.244 105.467 4602 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.44 % Rotamer: Outliers : 4.26 % Allowed : 27.55 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3282 helix: 1.92 (0.21), residues: 654 sheet: -0.51 (0.20), residues: 687 loop : -1.27 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.005 0.001 HIS D 34 PHE 0.020 0.001 PHE A 562 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 31) link_NAG-ASN : angle 2.91481 ( 93) link_BETA1-4 : bond 0.00296 ( 10) link_BETA1-4 : angle 1.10293 ( 30) hydrogen bonds : bond 0.04664 ( 919) hydrogen bonds : angle 4.68011 ( 2604) SS BOND : bond 0.00262 ( 41) SS BOND : angle 0.93864 ( 82) covalent geometry : bond 0.00419 (27505) covalent geometry : angle 0.57922 (37415) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 143 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7243 (t-90) REVERT: A 131 CYS cc_start: 0.3934 (OUTLIER) cc_final: 0.3583 (m) REVERT: A 153 MET cc_start: 0.6507 (mmm) cc_final: 0.5981 (mtt) REVERT: A 702 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: A 740 MET cc_start: 0.8662 (tmm) cc_final: 0.8151 (tmm) REVERT: B 357 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7477 (tmm-80) REVERT: B 646 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7887 (tmm-80) REVERT: B 902 MET cc_start: 0.9081 (tpp) cc_final: 0.8651 (tpt) REVERT: B 1107 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8360 (mtt90) REVERT: C 19 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8067 (p) REVERT: C 675 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7908 (pp30) REVERT: C 983 ARG cc_start: 0.8636 (tmm-80) cc_final: 0.8236 (ttp80) REVERT: D 53 ASP cc_start: 0.7612 (m-30) cc_final: 0.7119 (p0) REVERT: E 4 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7646 (tm-30) outliers start: 124 outliers final: 105 residues processed: 252 average time/residue: 0.3436 time to fit residues: 142.9928 Evaluate side-chains 248 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 135 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 225 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 308 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.097499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.060303 restraints weight = 86198.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062310 restraints weight = 42709.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063604 restraints weight = 28707.911| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27587 Z= 0.175 Angle : 0.602 10.763 37620 Z= 0.299 Chirality : 0.045 0.396 4336 Planarity : 0.004 0.048 4767 Dihedral : 6.270 105.080 4602 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 3.95 % Allowed : 28.00 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3282 helix: 1.91 (0.21), residues: 653 sheet: -0.57 (0.20), residues: 687 loop : -1.28 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP E 37 HIS 0.007 0.001 HIS D 34 PHE 0.022 0.001 PHE A 562 TYR 0.019 0.001 TYR B1067 ARG 0.008 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 31) link_NAG-ASN : angle 2.89178 ( 93) link_BETA1-4 : bond 0.00266 ( 10) link_BETA1-4 : angle 1.07628 ( 30) hydrogen bonds : bond 0.04667 ( 919) hydrogen bonds : angle 4.69880 ( 2604) SS BOND : bond 0.00287 ( 41) SS BOND : angle 0.94909 ( 82) covalent geometry : bond 0.00411 (27505) covalent geometry : angle 0.58344 (37415) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 136 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: A 131 CYS cc_start: 0.4026 (OUTLIER) cc_final: 0.3666 (m) REVERT: A 153 MET cc_start: 0.6537 (mmm) cc_final: 0.5957 (mtt) REVERT: A 702 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: A 740 MET cc_start: 0.8648 (tmm) cc_final: 0.8099 (tmm) REVERT: B 96 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: B 646 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7892 (tmm-80) REVERT: B 902 MET cc_start: 0.9079 (tpp) cc_final: 0.8651 (tpt) REVERT: B 1107 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8388 (mtt90) REVERT: C 675 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7918 (pp30) REVERT: C 983 ARG cc_start: 0.8619 (tmm-80) cc_final: 0.8219 (ttp80) REVERT: D 53 ASP cc_start: 0.7606 (m-30) cc_final: 0.7002 (p0) REVERT: D 56 ASP cc_start: 0.8889 (t0) cc_final: 0.8615 (t0) REVERT: E 4 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7664 (tm-30) outliers start: 115 outliers final: 105 residues processed: 237 average time/residue: 0.3586 time to fit residues: 140.1063 Evaluate side-chains 248 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 136 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1146 ASP Chi-restraints excluded: chain D residue 100 TRP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 101 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 109 optimal weight: 0.7980 chunk 201 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 230 optimal weight: 0.0370 chunk 278 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 250 optimal weight: 20.0000 chunk 281 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062156 restraints weight = 87570.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064292 restraints weight = 42871.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.065628 restraints weight = 28298.077| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 27587 Z= 0.101 Angle : 0.570 11.777 37620 Z= 0.280 Chirality : 0.044 0.380 4336 Planarity : 0.004 0.047 4767 Dihedral : 5.968 102.746 4602 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 94.99 % Rotamer: Outliers : 3.09 % Allowed : 28.86 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3282 helix: 2.16 (0.22), residues: 635 sheet: -0.48 (0.20), residues: 701 loop : -1.16 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP E 37 HIS 0.007 0.001 HIS D 34 PHE 0.019 0.001 PHE A 562 TYR 0.017 0.001 TYR A1067 ARG 0.008 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 31) link_NAG-ASN : angle 2.69849 ( 93) link_BETA1-4 : bond 0.00356 ( 10) link_BETA1-4 : angle 1.01951 ( 30) hydrogen bonds : bond 0.03910 ( 919) hydrogen bonds : angle 4.44707 ( 2604) SS BOND : bond 0.00220 ( 41) SS BOND : angle 0.75995 ( 82) covalent geometry : bond 0.00232 (27505) covalent geometry : angle 0.55319 (37415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11812.73 seconds wall clock time: 206 minutes 42.95 seconds (12402.95 seconds total)