Starting phenix.real_space_refine on Mon Jun 23 10:17:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k45_36877/06_2025/8k45_36877.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k45_36877/06_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_36877/06_2025/8k45_36877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k45_36877/06_2025/8k45_36877.map" model { file = "/net/cci-nas-00/data/ceres_data/8k45_36877/06_2025/8k45_36877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k45_36877/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.60, per 1000 atoms: 0.65 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: 7.45 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: 4.05 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: 11.86 Time building geometry restraints manager: 8.06 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: 11.310 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: 1.140 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 64.290 Find NCS groups from input model: 1.690 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.990 ------------------------------------------------------------------------------- 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 : 3.292 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: 0.3912 time to fit residues: 125.8267 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 : 2.987 ------------------------------------------------------------------------------- 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 = 0.062689 restraints weight = 88928.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064875 restraints weight = 43778.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066191 restraints weight = 29017.435| |-----------------------------------------------------------------------------| 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: 0.8418 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 : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3540 (OUTLIER) cc_final: 0.3221 (m) REVERT: A 153 MET cc_start: 0.6587 (mmm) cc_final: 0.5717 (mtm) REVERT: A 740 MET cc_start: 0.8644 (tmm) cc_final: 0.8001 (tmm) REVERT: B 740 MET cc_start: 0.9126 (tpp) cc_final: 0.8898 (tpp) REVERT: B 869 MET cc_start: 0.8769 (ptp) cc_final: 0.8494 (mtm) REVERT: B 1107 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8444 (mtt90) REVERT: C 978 ASN cc_start: 0.2918 (p0) cc_final: 0.2523 (p0) REVERT: C 984 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8215 (tt) REVERT: D 54 TRP cc_start: 0.7824 (t-100) cc_final: 0.7464 (t-100) REVERT: E 4 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7283 (tm-30) REVERT: E 96 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5251 (m-80) outliers start: 96 outliers final: 53 residues processed: 223 average time/residue: 0.3654 time to fit residues: 136.9403 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 : 5.351 ------------------------------------------------------------------------------- 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: 0.0170 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: 7.9990 chunk 253 optimal weight: 4.9990 chunk 305 optimal weight: 0.8980 chunk 133 optimal weight: 30.0000 chunk 163 optimal weight: 4.9990 chunk 288 optimal weight: 0.6980 overall best weight: 2.3222 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.097264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.059824 restraints weight = 86662.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061855 restraints weight = 43386.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063063 restraints weight = 29129.557| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 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 = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27587 Z= 0.202 Angle : 0.605 11.590 37620 Z= 0.303 Chirality : 0.045 0.412 4336 Planarity : 0.004 0.045 4767 Dihedral : 7.741 111.152 4618 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.05 % Favored : 92.77 % Rotamer: Outliers : 5.32 % Allowed : 26.00 % Favored : 68.67 % 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: -0.79 (0.15), residues: 3282 helix: 1.78 (0.21), residues: 657 sheet: -0.53 (0.20), residues: 694 loop : -1.41 (0.14), residues: 1931 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 0.034 0.001 PHE D 48 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 31) link_NAG-ASN : angle 3.06387 ( 93) link_BETA1-4 : bond 0.00223 ( 10) link_BETA1-4 : angle 1.18411 ( 30) hydrogen bonds : bond 0.05291 ( 919) hydrogen bonds : angle 5.15212 ( 2604) SS BOND : bond 0.00293 ( 41) SS BOND : angle 1.02991 ( 82) covalent geometry : bond 0.00470 (27505) covalent geometry : angle 0.58444 (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 296 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 141 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3927 (OUTLIER) cc_final: 0.3563 (m) REVERT: A 153 MET cc_start: 0.6707 (mmm) cc_final: 0.5634 (mtm) REVERT: A 406 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: A 702 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: A 740 MET cc_start: 0.8767 (tmm) cc_final: 0.8135 (tmm) REVERT: B 740 MET cc_start: 0.9239 (tpp) cc_final: 0.9000 (tpp) REVERT: B 1107 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (mtt90) REVERT: C 19 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7977 (p) REVERT: C 675 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8017 (pp30) REVERT: C 978 ASN cc_start: 0.2730 (p0) cc_final: 0.2415 (p0) REVERT: C 984 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8109 (tt) REVERT: D 48 PHE cc_start: 0.4604 (t80) cc_final: 0.4290 (t80) REVERT: D 54 TRP cc_start: 0.7849 (t-100) cc_final: 0.7494 (t-100) REVERT: E 4 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7271 (tm-30) outliers start: 155 outliers final: 88 residues processed: 278 average time/residue: 0.4608 time to fit residues: 217.5902 Evaluate side-chains 228 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 133 time to evaluate : 3.112 ------------------------------------------------------------------------------- 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 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 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 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 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 316 SER 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 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 961 THR Chi-restraints excluded: chain B residue 963 VAL 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 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 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 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: 0.9990 chunk 118 optimal weight: 0.6980 chunk 208 optimal weight: 0.6980 chunk 231 optimal weight: 0.0070 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 207 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.097788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061745 restraints weight = 87511.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063864 restraints weight = 42965.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065188 restraints weight = 28364.621| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 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 = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1221 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 : 0.552 10.830 37620 Z= 0.273 Chirality : 0.044 0.403 4336 Planarity : 0.004 0.042 4767 Dihedral : 6.993 107.391 4610 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.19 % Favored : 94.63 % Rotamer: Outliers : 3.61 % Allowed : 27.65 % Favored : 68.74 % 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: -0.59 (0.15), residues: 3282 helix: 1.96 (0.21), residues: 654 sheet: -0.47 (0.19), residues: 704 loop : -1.25 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.005 0.001 HIS D 34 PHE 0.024 0.001 PHE A 106 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 31) link_NAG-ASN : angle 2.86122 ( 93) link_BETA1-4 : bond 0.00332 ( 10) link_BETA1-4 : angle 1.09663 ( 30) hydrogen bonds : bond 0.04356 ( 919) hydrogen bonds : angle 4.79881 ( 2604) SS BOND : bond 0.00204 ( 41) SS BOND : angle 0.77094 ( 82) covalent geometry : bond 0.00231 (27505) covalent geometry : angle 0.53237 (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: 105 poor density : 157 time to evaluate : 2.952 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: 0.3791 (OUTLIER) cc_final: 0.3477 (m) REVERT: A 153 MET cc_start: 0.6690 (mmm) cc_final: 0.5873 (mtm) REVERT: A 233 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6637 (tt) REVERT: A 402 ILE cc_start: 0.8821 (tp) cc_final: 0.8599 (tp) REVERT: A 406 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7369 (tp30) REVERT: A 702 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8803 (tp30) REVERT: A 740 MET cc_start: 0.8682 (tmm) cc_final: 0.8036 (tmm) REVERT: B 646 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7833 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8343 (mtt90) REVERT: C 19 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7864 (p) REVERT: C 675 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7990 (pp30) REVERT: C 1029 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.7375 (ttp) REVERT: E 4 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7436 (tm-30) REVERT: E 73 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7137 (tpt90) outliers start: 105 outliers final: 63 residues processed: 243 average time/residue: 0.3652 time to fit residues: 144.5916 Evaluate side-chains 216 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 144 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE 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 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 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 751 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 96 GLU 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 551 VAL Chi-restraints excluded: chain B residue 565 PHE 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 697 MET 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 226 LEU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 VAL 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 912 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 994 ASP 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 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 242 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 257 optimal weight: 0.0070 chunk 27 optimal weight: 0.7980 chunk 246 optimal weight: 0.0870 chunk 141 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 overall best weight: 1.5780 ------------------------------------------------------------------------------- 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** ** 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 = 0.3786 r_free = 0.3786 target = 0.098255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060622 restraints weight = 87291.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062660 restraints weight = 43551.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063991 restraints weight = 29167.942| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 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 = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1291 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= 0.148 Angle : 0.565 11.050 37620 Z= 0.280 Chirality : 0.044 0.404 4336 Planarity : 0.004 0.044 4767 Dihedral : 6.688 107.474 4604 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.17 % Favored : 93.65 % Rotamer: Outliers : 3.95 % Allowed : 27.52 % Favored : 68.53 % 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: -0.59 (0.15), residues: 3282 helix: 2.00 (0.21), residues: 653 sheet: -0.49 (0.20), residues: 686 loop : -1.25 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.007 0.001 HIS D 34 PHE 0.021 0.001 PHE A 106 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 31) link_NAG-ASN : angle 2.96919 ( 93) link_BETA1-4 : bond 0.00227 ( 10) link_BETA1-4 : angle 1.11325 ( 30) hydrogen bonds : bond 0.04579 ( 919) hydrogen bonds : angle 4.75763 ( 2604) SS BOND : bond 0.00234 ( 41) SS BOND : angle 0.84918 ( 82) covalent geometry : bond 0.00345 (27505) covalent geometry : angle 0.54492 (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 265 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 150 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3958 (OUTLIER) cc_final: 0.3579 (m) REVERT: A 402 ILE cc_start: 0.8873 (tp) cc_final: 0.8672 (tp) REVERT: A 702 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: A 740 MET cc_start: 0.8735 (tmm) cc_final: 0.8160 (tmm) REVERT: B 646 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7836 (tmm-80) REVERT: B 1050 MET cc_start: 0.8444 (mtm) cc_final: 0.8192 (ptm) REVERT: B 1107 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8395 (mtt90) REVERT: C 19 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8037 (p) REVERT: C 675 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7986 (pp30) REVERT: C 965 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8763 (tp40) REVERT: C 980 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8032 (tt) REVERT: E 4 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7430 (tm-30) REVERT: E 73 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7116 (tpt90) REVERT: E 107 ASN cc_start: 0.8251 (p0) cc_final: 0.7989 (p0) outliers start: 115 outliers final: 82 residues processed: 249 average time/residue: 0.3550 time to fit residues: 145.2490 Evaluate side-chains 233 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 143 time to evaluate : 2.883 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 202 LYS 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 574 ASP 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 900 MET Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE 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 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 305 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 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 581 THR 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 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 1115 ILE Chi-restraints excluded: chain B residue 1118 ASP 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 402 ILE 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 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 980 ILE 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 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 Chi-restraints excluded: chain E residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 129 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 61 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 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 = 0.3781 r_free = 0.3781 target = 0.097052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061156 restraints weight = 87589.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063178 restraints weight = 42998.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064478 restraints weight = 28494.978| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 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 = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1389 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= 0.132 Angle : 0.565 10.820 37620 Z= 0.279 Chirality : 0.044 0.400 4336 Planarity : 0.004 0.046 4767 Dihedral : 6.525 106.749 4604 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.74 % Favored : 94.08 % Rotamer: Outliers : 4.53 % Allowed : 26.86 % Favored : 68.60 % 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: 2.03 (0.21), residues: 651 sheet: -0.47 (0.20), residues: 686 loop : -1.23 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.005 0.001 HIS D 34 PHE 0.020 0.001 PHE A 106 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 31) link_NAG-ASN : angle 2.92251 ( 93) link_BETA1-4 : bond 0.00261 ( 10) link_BETA1-4 : angle 1.10065 ( 30) hydrogen bonds : bond 0.04444 ( 919) hydrogen bonds : angle 4.70578 ( 2604) SS BOND : bond 0.00240 ( 41) SS BOND : angle 1.09269 ( 82) covalent geometry : bond 0.00306 (27505) covalent geometry : angle 0.54458 (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 284 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 152 time to evaluate : 3.390 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: 0.3851 (OUTLIER) cc_final: 0.3483 (m) REVERT: A 153 MET cc_start: 0.6542 (mmm) cc_final: 0.5833 (mtt) REVERT: A 402 ILE cc_start: 0.8872 (tp) cc_final: 0.8665 (tp) REVERT: A 702 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8494 (tm-30) REVERT: A 740 MET cc_start: 0.8636 (tmm) cc_final: 0.8114 (tmm) REVERT: B 646 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7842 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8414 (mtt90) REVERT: C 19 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7952 (p) REVERT: C 554 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (tp30) REVERT: C 675 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7965 (pp30) REVERT: C 980 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7984 (tt) REVERT: E 4 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 107 ASN cc_start: 0.8234 (p0) cc_final: 0.8033 (p0) outliers start: 132 outliers final: 104 residues processed: 266 average time/residue: 0.3626 time to fit residues: 159.8782 Evaluate side-chains 257 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 145 time to evaluate : 3.112 ------------------------------------------------------------------------------- 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 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 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 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 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 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 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 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 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 15 CYS Chi-restraints excluded: chain C residue 19 THR 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 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 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 742 ILE 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 974 SER Chi-restraints excluded: chain C residue 980 ILE 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 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 35 MET Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 105 LEU 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: 6.9990 chunk 269 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 255 optimal weight: 0.0040 overall best weight: 1.5798 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.098126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060745 restraints weight = 86419.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062852 restraints weight = 42662.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064155 restraints weight = 28420.224| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 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 = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27587 Z= 0.147 Angle : 0.570 10.807 37620 Z= 0.282 Chirality : 0.044 0.398 4336 Planarity : 0.004 0.047 4767 Dihedral : 6.384 106.309 4602 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.04 % Favored : 93.77 % Rotamer: Outliers : 4.64 % Allowed : 26.79 % Favored : 68.57 % 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: -0.59 (0.15), residues: 3282 helix: 2.02 (0.22), residues: 649 sheet: -0.49 (0.20), residues: 686 loop : -1.24 (0.14), residues: 1947 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 0.019 0.001 TYR B1067 ARG 0.011 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 31) link_NAG-ASN : angle 2.92423 ( 93) link_BETA1-4 : bond 0.00227 ( 10) link_BETA1-4 : angle 1.10258 ( 30) hydrogen bonds : bond 0.04501 ( 919) hydrogen bonds : angle 4.68914 ( 2604) SS BOND : bond 0.00247 ( 41) SS BOND : angle 0.97416 ( 82) covalent geometry : bond 0.00345 (27505) covalent geometry : angle 0.54953 (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 284 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 149 time to evaluate : 2.967 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: 0.3907 (OUTLIER) cc_final: 0.3539 (m) REVERT: A 153 MET cc_start: 0.6565 (mmm) cc_final: 0.5860 (mtt) REVERT: A 402 ILE cc_start: 0.8882 (tp) cc_final: 0.8663 (tp) REVERT: A 702 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: A 740 MET cc_start: 0.8556 (tmm) cc_final: 0.8029 (tmm) REVERT: B 646 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7877 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8404 (mtt90) REVERT: C 19 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8040 (p) REVERT: C 675 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7986 (pp30) REVERT: C 978 ASN cc_start: 0.2491 (p0) cc_final: 0.2211 (p0) REVERT: E 4 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7465 (tm-30) outliers start: 135 outliers final: 110 residues processed: 266 average time/residue: 0.4472 time to fit residues: 197.9840 Evaluate side-chains 258 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 142 time to evaluate : 6.312 ------------------------------------------------------------------------------- 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 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 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 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 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 305 SER 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 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 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 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 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 1115 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 56 LEU 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 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 859 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE 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 35 MET 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 111 VAL 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: 0.9980 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 127 optimal weight: 0.0470 chunk 18 optimal weight: 0.0060 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 overall best weight: 0.5294 ------------------------------------------------------------------------------- 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 ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.062173 restraints weight = 87493.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064246 restraints weight = 42780.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.065591 restraints weight = 28247.991| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- 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: 0.1618 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= 0.097 Angle : 0.552 10.245 37620 Z= 0.272 Chirality : 0.044 0.388 4336 Planarity : 0.004 0.047 4767 Dihedral : 6.142 104.841 4602 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.91 % Favored : 94.90 % Rotamer: Outliers : 3.68 % Allowed : 27.69 % Favored : 68.64 % 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: -0.46 (0.15), residues: 3282 helix: 2.10 (0.22), residues: 647 sheet: -0.43 (0.19), residues: 720 loop : -1.14 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.007 0.001 HIS D 34 PHE 0.025 0.001 PHE B 133 TYR 0.018 0.001 TYR A1067 ARG 0.010 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 31) link_NAG-ASN : angle 2.77289 ( 93) link_BETA1-4 : bond 0.00364 ( 10) link_BETA1-4 : angle 1.06624 ( 30) hydrogen bonds : bond 0.04005 ( 919) hydrogen bonds : angle 4.51102 ( 2604) SS BOND : bond 0.00212 ( 41) SS BOND : angle 0.72316 ( 82) covalent geometry : bond 0.00219 (27505) covalent geometry : angle 0.53454 (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 262 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 155 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3853 (OUTLIER) cc_final: 0.3496 (m) REVERT: A 153 MET cc_start: 0.6354 (mmm) cc_final: 0.5814 (mtt) REVERT: A 402 ILE cc_start: 0.8864 (tp) cc_final: 0.8661 (tp) REVERT: A 702 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: A 740 MET cc_start: 0.8460 (tmm) cc_final: 0.7973 (tmm) REVERT: A 774 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8049 (mm-40) REVERT: B 357 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7537 (tmm-80) REVERT: B 646 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7837 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8437 (mtt90) REVERT: C 19 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (p) REVERT: C 554 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8360 (tp30) REVERT: C 675 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7967 (pp30) REVERT: C 978 ASN cc_start: 0.2723 (p0) cc_final: 0.2431 (p0) REVERT: D 30 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7402 (tm-30) REVERT: D 53 ASP cc_start: 0.7595 (m-30) cc_final: 0.7158 (p0) REVERT: E 4 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7539 (tm-30) outliers start: 107 outliers final: 77 residues processed: 246 average time/residue: 0.3672 time to fit residues: 148.4961 Evaluate side-chains 231 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 146 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 233 ILE 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 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL 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 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 67 VAL 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 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 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 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 813 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 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 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 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 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 981 PHE 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 8 SER 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 Chi-restraints excluded: chain E residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 242 optimal weight: 7.9990 chunk 120 optimal weight: 0.3980 chunk 245 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.096609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.060651 restraints weight = 88437.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062711 restraints weight = 43658.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063922 restraints weight = 29054.661| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 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 = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.063 | | 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: 0.8383 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27587 Z= 0.165 Angle : 0.584 10.722 37620 Z= 0.290 Chirality : 0.044 0.394 4336 Planarity : 0.004 0.048 4767 Dihedral : 6.185 105.115 4602 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.83 % Rotamer: Outliers : 3.92 % Allowed : 27.69 % Favored : 68.40 % 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: -0.53 (0.15), residues: 3282 helix: 2.07 (0.22), residues: 647 sheet: -0.55 (0.20), residues: 704 loop : -1.16 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP E 37 HIS 0.007 0.001 HIS D 34 PHE 0.022 0.001 PHE B 133 TYR 0.018 0.001 TYR B1067 ARG 0.010 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 31) link_NAG-ASN : angle 2.87691 ( 93) link_BETA1-4 : bond 0.00213 ( 10) link_BETA1-4 : angle 1.08292 ( 30) hydrogen bonds : bond 0.04433 ( 919) hydrogen bonds : angle 4.62041 ( 2604) SS BOND : bond 0.00246 ( 41) SS BOND : angle 1.02645 ( 82) covalent geometry : bond 0.00386 (27505) covalent geometry : angle 0.56531 (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 258 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 144 time to evaluate : 2.944 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: 0.3921 (OUTLIER) cc_final: 0.3552 (m) REVERT: A 153 MET cc_start: 0.6477 (mmm) cc_final: 0.5968 (mtp) REVERT: A 402 ILE cc_start: 0.8922 (tp) cc_final: 0.8695 (tp) REVERT: A 406 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7463 (tp30) REVERT: A 702 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8512 (tm-30) REVERT: A 740 MET cc_start: 0.8543 (tmm) cc_final: 0.8019 (tmm) REVERT: B 96 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: B 357 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7634 (tmm-80) REVERT: B 646 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7850 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8383 (mtt90) REVERT: C 19 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8080 (p) REVERT: C 554 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: C 675 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7943 (pp30) REVERT: C 978 ASN cc_start: 0.2808 (p0) cc_final: 0.2563 (p0) REVERT: D 53 ASP cc_start: 0.7622 (m-30) cc_final: 0.7129 (p0) REVERT: E 4 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7551 (tm-30) REVERT: E 21 LEU cc_start: 0.7016 (mt) cc_final: 0.6601 (mm) REVERT: E 107 ASN cc_start: 0.8343 (p0) cc_final: 0.8106 (p0) outliers start: 114 outliers final: 96 residues processed: 243 average time/residue: 0.3882 time to fit residues: 154.9435 Evaluate side-chains 247 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 141 time to evaluate : 3.376 ------------------------------------------------------------------------------- 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 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 349 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 406 GLU 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 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 973 ILE Chi-restraints excluded: chain A residue 1083 HIS 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 67 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 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 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 763 LEU 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 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 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 951 VAL 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 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 35 MET 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 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 225 optimal weight: 0.0470 chunk 298 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 308 optimal weight: 6.9990 chunk 329 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.097167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.061315 restraints weight = 87246.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063383 restraints weight = 43054.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.064696 restraints weight = 28634.872| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 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 = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1697 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= 0.126 Angle : 0.572 10.457 37620 Z= 0.283 Chirality : 0.044 0.389 4336 Planarity : 0.004 0.048 4767 Dihedral : 6.094 104.383 4602 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.31 % Favored : 94.54 % Rotamer: Outliers : 3.64 % Allowed : 28.03 % Favored : 68.33 % 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: -0.52 (0.15), residues: 3282 helix: 2.07 (0.22), residues: 647 sheet: -0.56 (0.20), residues: 709 loop : -1.15 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP E 37 HIS 0.006 0.001 HIS D 34 PHE 0.026 0.001 PHE B 133 TYR 0.018 0.001 TYR B1067 ARG 0.008 0.000 ARG D 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 31) link_NAG-ASN : angle 2.79513 ( 93) link_BETA1-4 : bond 0.00289 ( 10) link_BETA1-4 : angle 1.05104 ( 30) hydrogen bonds : bond 0.04229 ( 919) hydrogen bonds : angle 4.54086 ( 2604) SS BOND : bond 0.00235 ( 41) SS BOND : angle 0.89690 ( 82) covalent geometry : bond 0.00294 (27505) covalent geometry : angle 0.55447 (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 252 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 146 time to evaluate : 3.774 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: 0.3790 (OUTLIER) cc_final: 0.3429 (m) REVERT: A 153 MET cc_start: 0.6513 (mmm) cc_final: 0.5974 (mtp) REVERT: A 402 ILE cc_start: 0.8901 (tp) cc_final: 0.8671 (tp) REVERT: A 406 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: A 702 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: A 740 MET cc_start: 0.8515 (tmm) cc_final: 0.7950 (tmm) REVERT: B 357 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7716 (tmm-80) REVERT: B 646 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7856 (tmm-80) REVERT: B 1107 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8415 (mtt90) REVERT: C 554 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8377 (tp30) REVERT: C 675 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: D 53 ASP cc_start: 0.7612 (m-30) cc_final: 0.7137 (p0) REVERT: D 56 ASP cc_start: 0.8937 (t0) cc_final: 0.8693 (t0) REVERT: E 4 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7609 (tm-30) REVERT: E 21 LEU cc_start: 0.6898 (mt) cc_final: 0.6493 (mm) outliers start: 106 outliers final: 91 residues processed: 237 average time/residue: 0.4914 time to fit residues: 197.3050 Evaluate side-chains 240 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 141 time to evaluate : 5.491 ------------------------------------------------------------------------------- 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 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 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 406 GLU 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 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 973 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 67 VAL 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 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 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 813 SER Chi-restraints excluded: chain B residue 959 LEU 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 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 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 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 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 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 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 Chi-restraints excluded: chain E residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 109 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 230 optimal weight: 0.6980 chunk 278 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 250 optimal weight: 30.0000 chunk 281 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.097811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.061754 restraints weight = 87872.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063843 restraints weight = 43338.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065065 restraints weight = 28702.953| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 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 = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1783 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= 0.107 Angle : 0.566 10.412 37620 Z= 0.279 Chirality : 0.044 0.386 4336 Planarity : 0.004 0.048 4767 Dihedral : 5.940 103.288 4602 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.95 % Favored : 94.90 % Rotamer: Outliers : 3.64 % Allowed : 27.96 % Favored : 68.40 % 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: -0.45 (0.15), residues: 3282 helix: 2.17 (0.22), residues: 639 sheet: -0.53 (0.20), residues: 708 loop : -1.09 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP E 37 HIS 0.006 0.001 HIS D 34 PHE 0.024 0.001 PHE B 133 TYR 0.018 0.001 TYR A1067 ARG 0.009 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 31) link_NAG-ASN : angle 2.73991 ( 93) link_BETA1-4 : bond 0.00316 ( 10) link_BETA1-4 : angle 1.03802 ( 30) hydrogen bonds : bond 0.04006 ( 919) hydrogen bonds : angle 4.44670 ( 2604) SS BOND : bond 0.00205 ( 41) SS BOND : angle 0.80273 ( 82) covalent geometry : bond 0.00249 (27505) covalent geometry : angle 0.54856 (37415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13947.09 seconds wall clock time: 250 minutes 38.27 seconds (15038.27 seconds total)