Starting phenix.real_space_refine on Fri Jun 20 13:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpf_43407/06_2025/8vpf_43407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpf_43407/06_2025/8vpf_43407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vpf_43407/06_2025/8vpf_43407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpf_43407/06_2025/8vpf_43407.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpf_43407/06_2025/8vpf_43407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpf_43407/06_2025/8vpf_43407.cif" } resolution = 3.2 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 15120 2.51 5 N 3921 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23832 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6011 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 37, 'TRANS': 738} Chain breaks: 8 Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 787 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6011 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 37, 'TRANS': 738} Chain breaks: 8 Chain: "D" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "F" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 787 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 6011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6011 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 37, 'TRANS': 738} Chain breaks: 8 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "G" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 787 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 15.56, per 1000 atoms: 0.65 Number of scatterers: 23832 At special positions: 0 Unit cell: (148.39, 160.93, 138.985, 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 111 16.00 O 4680 8.00 N 3921 7.00 C 15120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.12 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.05 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.09 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.12 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.05 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.09 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.12 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.05 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.09 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.02 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A 691 " " NAG A1303 " - " ASN A1056 " " NAG A1304 " - " ASN A 602 " " NAG A1305 " - " ASN A 269 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B 691 " " NAG B1303 " - " ASN B1056 " " NAG B1304 " - " ASN B 602 " " NAG B1305 " - " ASN B 269 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C 691 " " NAG C1303 " - " ASN C1056 " " NAG C1304 " - " ASN C 602 " " NAG C1305 " - " ASN C 269 " " NAG H 1 " - " ASN A1080 " " NAG I 1 " - " ASN A1116 " " NAG J 1 " - " ASN A 783 " " NAG K 1 " - " ASN A 699 " " NAG L 1 " - " ASN B1080 " " NAG O 1 " - " ASN B1116 " " NAG P 1 " - " ASN B 783 " " NAG Q 1 " - " ASN B 699 " " NAG R 1 " - " ASN C1080 " " NAG S 1 " - " ASN C1116 " " NAG T 1 " - " ASN C 783 " " NAG U 1 " - " ASN C 699 " Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 2.9 seconds 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5568 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 57 sheets defined 23.5% alpha, 36.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 736 through 739 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.803A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.752A pdb=" N ALA A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.283A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 Processing helix chain 'A' and resid 927 through 947 removed outlier: 4.142A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.934A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 736 through 739 Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.802A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 761 " --> pdb=" O ASP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.752A pdb=" N ALA B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 872 Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.283A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.142A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.935A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 736 through 739 Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.802A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 761 " --> pdb=" O ASP C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.753A pdb=" N ALA C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 872 Processing helix chain 'C' and resid 879 through 889 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.283A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 927 through 947 removed outlier: 4.142A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.934A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 7.368A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 5.721A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 removed outlier: 7.358A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 104 removed outlier: 3.875A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.593A pdb=" N SER M 108 " --> pdb=" O TYR M 104 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL M 33 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.593A pdb=" N SER M 108 " --> pdb=" O TYR M 104 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL M 117 " --> pdb=" O ARG M 98 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU M 100 " --> pdb=" O MET M 115 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N MET M 115 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 306 removed outlier: 5.292A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 6.751A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.306A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.063A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 693 through 709 removed outlier: 6.632A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 709 removed outlier: 6.632A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN A1088 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER A1093 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB6, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB7, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 4.574A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 3 through 6 removed outlier: 6.783A pdb=" N VAL M 18 " --> pdb=" O THR M 84 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR M 84 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL M 20 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU M 82 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS M 22 " --> pdb=" O TYR M 80 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR M 80 " --> pdb=" O CYS M 22 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA M 24 " --> pdb=" O ILE M 78 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE M 78 " --> pdb=" O ALA M 24 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.551A pdb=" N ALA N 10 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 9 through 11 removed outlier: 6.551A pdb=" N ALA N 10 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE N 93 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL N 101 " --> pdb=" O PHE N 93 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY N 95 " --> pdb=" O PHE N 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AC4, first strand: chain 'B' and resid 31 through 34 removed outlier: 7.367A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 51 through 59 removed outlier: 7.358A pdb=" N THR B 261 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP B 277 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET B 263 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 275 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS B 265 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 98 through 104 removed outlier: 3.875A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.594A pdb=" N SER D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL D 33 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.594A pdb=" N SER D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D 117 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D 100 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N MET D 115 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 298 through 306 removed outlier: 5.292A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 312 through 314 removed outlier: 6.752A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.306A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.062A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 693 through 709 removed outlier: 6.631A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 693 through 709 removed outlier: 6.631A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN B1088 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER B1093 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD7, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD8, first strand: chain 'B' and resid 1063 through 1065 removed outlier: 4.574A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.783A pdb=" N VAL D 18 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR D 84 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL D 20 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU D 82 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS D 22 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR D 80 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA D 24 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 78 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AE2, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.551A pdb=" N ALA F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.551A pdb=" N ALA F 10 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE F 93 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL F 101 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY F 95 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.368A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 51 through 59 removed outlier: 7.358A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 98 through 104 removed outlier: 3.875A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 212 through 214 removed outlier: 6.594A pdb=" N SER E 108 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL E 33 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 212 through 214 removed outlier: 6.594A pdb=" N SER E 108 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU E 100 " --> pdb=" O MET E 115 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N MET E 115 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 298 through 306 removed outlier: 5.293A pdb=" N ILE C 299 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR C 585 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLN C 301 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 583 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.306A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 693 through 709 removed outlier: 6.632A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 693 through 709 removed outlier: 6.632A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN C1088 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER C1093 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AF6, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF7, first strand: chain 'C' and resid 1063 through 1065 removed outlier: 4.574A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 6 removed outlier: 6.783A pdb=" N VAL E 18 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR E 84 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL E 20 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU E 82 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS E 22 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA E 24 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 78 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AG1, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.551A pdb=" N ALA G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.551A pdb=" N ALA G 10 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N PHE G 93 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL G 101 " --> pdb=" O PHE G 93 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY G 95 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 18 through 23 1069 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.20 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5538 1.32 - 1.47: 8350 1.47 - 1.61: 10238 1.61 - 1.75: 63 1.75 - 1.89: 135 Bond restraints: 24324 Sorted by residual: bond pdb=" CB ASN B 896 " pdb=" CG ASN B 896 " ideal model delta sigma weight residual 1.516 1.345 0.171 2.50e-02 1.60e+03 4.66e+01 bond pdb=" CB ASN A 896 " pdb=" CG ASN A 896 " ideal model delta sigma weight residual 1.516 1.345 0.171 2.50e-02 1.60e+03 4.66e+01 bond pdb=" CB ASN C 896 " pdb=" CG ASN C 896 " ideal model delta sigma weight residual 1.516 1.346 0.170 2.50e-02 1.60e+03 4.64e+01 bond pdb=" CB LEU A 831 " pdb=" CG LEU A 831 " ideal model delta sigma weight residual 1.530 1.646 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" CB LEU B 831 " pdb=" CG LEU B 831 " ideal model delta sigma weight residual 1.530 1.646 -0.116 2.00e-02 2.50e+03 3.34e+01 ... (remaining 24319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.99: 32916 6.99 - 13.99: 129 13.99 - 20.98: 0 20.98 - 27.98: 0 27.98 - 34.97: 3 Bond angle restraints: 33048 Sorted by residual: angle pdb=" C2 NAG U 2 " pdb=" N2 NAG U 2 " pdb=" C7 NAG U 2 " ideal model delta sigma weight residual 124.56 159.53 -34.97 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C2 NAG Q 2 " pdb=" N2 NAG Q 2 " pdb=" C7 NAG Q 2 " ideal model delta sigma weight residual 124.56 159.52 -34.96 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C2 NAG K 2 " pdb=" N2 NAG K 2 " pdb=" C7 NAG K 2 " ideal model delta sigma weight residual 124.56 159.51 -34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N GLY N 95 " pdb=" CA GLY N 95 " pdb=" C GLY N 95 " ideal model delta sigma weight residual 111.95 102.58 9.37 9.50e-01 1.11e+00 9.72e+01 angle pdb=" N GLY F 95 " pdb=" CA GLY F 95 " pdb=" C GLY F 95 " ideal model delta sigma weight residual 111.95 102.59 9.36 9.50e-01 1.11e+00 9.71e+01 ... (remaining 33043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.11: 14482 21.11 - 42.23: 323 42.23 - 63.34: 111 63.34 - 84.45: 39 84.45 - 105.57: 21 Dihedral angle restraints: 14976 sinusoidal: 6285 harmonic: 8691 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS A 635 " pdb=" CB CYS A 635 " ideal model delta sinusoidal sigma weight residual 93.00 33.77 59.23 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS B 603 " pdb=" SG CYS B 603 " pdb=" SG CYS B 635 " pdb=" CB CYS B 635 " ideal model delta sinusoidal sigma weight residual 93.00 33.77 59.23 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" CB CYS C 603 " pdb=" SG CYS C 603 " pdb=" SG CYS C 635 " pdb=" CB CYS C 635 " ideal model delta sinusoidal sigma weight residual 93.00 33.79 59.21 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 14973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2750 0.104 - 0.208: 855 0.208 - 0.312: 182 0.312 - 0.416: 70 0.416 - 0.519: 43 Chirality restraints: 3900 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 ... (remaining 3897 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 691 " -0.056 2.00e-02 2.50e+03 6.10e-02 4.65e+01 pdb=" CG ASN A 691 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 691 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 691 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 691 " -0.056 2.00e-02 2.50e+03 6.08e-02 4.62e+01 pdb=" CG ASN C 691 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 691 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 691 " 0.097 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 691 " -0.056 2.00e-02 2.50e+03 6.07e-02 4.61e+01 pdb=" CG ASN B 691 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 691 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 691 " 0.096 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.073 2.00e-02 2.50e+03 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9468 2.89 - 3.40: 21607 3.40 - 3.90: 40466 3.90 - 4.40: 47578 4.40 - 4.90: 77579 Nonbonded interactions: 196698 Sorted by model distance: nonbonded pdb=" N SER M 76 " pdb=" N ASN M 77 " model vdw 2.393 2.560 nonbonded pdb=" N SER E 76 " pdb=" N ASN E 77 " model vdw 2.393 2.560 nonbonded pdb=" N SER D 76 " pdb=" N ASN D 77 " model vdw 2.394 2.560 nonbonded pdb=" N ASN G 27 " pdb=" O ASN G 27 " model vdw 2.395 2.496 nonbonded pdb=" N ASN F 27 " pdb=" O ASN F 27 " model vdw 2.395 2.496 ... (remaining 196693 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 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: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 61.920 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.240 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:3.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 : 0.022 0.171 24399 Z= 1.128 Angle : 1.829 34.974 33240 Z= 1.208 Chirality : 0.119 0.519 3900 Planarity : 0.008 0.031 4197 Dihedral : 11.381 105.568 9309 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.53 % 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: 0.43 (0.14), residues: 2961 helix: -0.35 (0.18), residues: 624 sheet: 0.75 (0.20), residues: 627 loop : 0.51 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.011 TRP G 37 HIS 0.007 0.002 HIS C1030 PHE 0.036 0.006 PHE B 83 TYR 0.048 0.008 TYR C 778 ARG 0.006 0.001 ARG C 183 Details of bonding type rmsd link_NAG-ASN : bond 0.08185 ( 27) link_NAG-ASN : angle 2.39491 ( 81) link_BETA1-4 : bond 0.07303 ( 15) link_BETA1-4 : angle 4.51117 ( 45) hydrogen bonds : bond 0.15233 ( 1012) hydrogen bonds : angle 8.05400 ( 2856) SS BOND : bond 0.03293 ( 33) SS BOND : angle 2.78362 ( 66) covalent geometry : bond 0.02143 (24324) covalent geometry : angle 1.81880 (33048) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 623 time to evaluate : 2.524 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 67 THR cc_start: 0.8062 (m) cc_final: 0.7673 (p) REVERT: A 768 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7945 (mttp) REVERT: A 1082 THR cc_start: 0.8111 (m) cc_final: 0.7848 (p) REVERT: M 45 LEU cc_start: 0.8094 (pp) cc_final: 0.7636 (pp) REVERT: N 26 TYR cc_start: 0.7689 (m-80) cc_final: 0.7117 (m-80) REVERT: B 67 THR cc_start: 0.8050 (m) cc_final: 0.7605 (p) REVERT: B 722 MET cc_start: 0.8442 (tpp) cc_final: 0.8156 (tpt) REVERT: B 768 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7892 (mtmt) REVERT: B 1082 THR cc_start: 0.8013 (m) cc_final: 0.7769 (p) REVERT: C 67 THR cc_start: 0.7939 (m) cc_final: 0.7494 (p) REVERT: C 768 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7927 (mttp) REVERT: C 1082 THR cc_start: 0.7943 (m) cc_final: 0.7735 (p) REVERT: G 26 TYR cc_start: 0.7708 (m-80) cc_final: 0.7095 (m-80) outliers start: 6 outliers final: 0 residues processed: 626 average time/residue: 0.3621 time to fit residues: 350.0152 Evaluate side-chains 348 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 269 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 214 ASN A 661 HIS ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1088 GLN N 71 ASN B 78 ASN B 214 ASN B 661 HIS B 786 GLN B 838 ASN B 951 ASN B 992 GLN B1088 GLN C 78 ASN C 214 ASN C 661 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1088 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128017 restraints weight = 30845.871| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.84 r_work: 0.3292 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24399 Z= 0.184 Angle : 0.730 15.392 33240 Z= 0.379 Chirality : 0.048 0.171 3900 Planarity : 0.005 0.041 4197 Dihedral : 7.809 71.927 4104 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 8.19 % Favored : 89.67 % 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: 0.50 (0.15), residues: 2961 helix: 1.45 (0.20), residues: 603 sheet: 0.46 (0.17), residues: 822 loop : -0.11 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 36 HIS 0.006 0.001 HIS M 32 PHE 0.026 0.002 PHE A 83 TYR 0.026 0.002 TYR E 94 ARG 0.004 0.001 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00785 ( 27) link_NAG-ASN : angle 2.53217 ( 81) link_BETA1-4 : bond 0.00676 ( 15) link_BETA1-4 : angle 3.09508 ( 45) hydrogen bonds : bond 0.05305 ( 1012) hydrogen bonds : angle 6.25891 ( 2856) SS BOND : bond 0.00381 ( 33) SS BOND : angle 1.60590 ( 66) covalent geometry : bond 0.00423 (24324) covalent geometry : angle 0.70836 (33048) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 419 time to evaluate : 2.408 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 274 ASP cc_start: 0.7886 (t0) cc_final: 0.7562 (m-30) REVERT: A 768 LYS cc_start: 0.8478 (mmtt) cc_final: 0.7883 (mtmm) REVERT: A 1104 VAL cc_start: 0.8384 (t) cc_final: 0.8142 (p) REVERT: N 26 TYR cc_start: 0.7975 (m-80) cc_final: 0.7055 (m-80) REVERT: N 47 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7754 (mtpp) REVERT: N 80 LEU cc_start: 0.7308 (mt) cc_final: 0.7038 (tt) REVERT: B 50 ASP cc_start: 0.7930 (t0) cc_final: 0.7559 (t0) REVERT: B 183 ARG cc_start: 0.7374 (mtt90) cc_final: 0.7097 (mpt180) REVERT: B 274 ASP cc_start: 0.7987 (t0) cc_final: 0.7495 (m-30) REVERT: B 289 SER cc_start: 0.8813 (t) cc_final: 0.8597 (p) REVERT: B 558 PHE cc_start: 0.5841 (m-80) cc_final: 0.5632 (m-80) REVERT: B 632 GLN cc_start: 0.8167 (mp10) cc_final: 0.7918 (mp10) REVERT: B 720 CYS cc_start: 0.7219 (t) cc_final: 0.6948 (t) REVERT: B 730 GLU cc_start: 0.7817 (mp0) cc_final: 0.7107 (mp0) REVERT: B 768 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7899 (mtmt) REVERT: B 951 ASN cc_start: 0.8488 (m-40) cc_final: 0.8245 (m-40) REVERT: D 22 CYS cc_start: 0.6191 (m) cc_final: 0.5892 (m) REVERT: D 60 TYR cc_start: 0.7496 (m-80) cc_final: 0.7167 (m-80) REVERT: F 62 ASP cc_start: 0.7728 (t0) cc_final: 0.7308 (t0) REVERT: F 85 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6761 (mm-30) REVERT: F 101 VAL cc_start: 0.9049 (p) cc_final: 0.8841 (m) REVERT: C 50 ASP cc_start: 0.8062 (t0) cc_final: 0.7687 (t0) REVERT: C 183 ARG cc_start: 0.7184 (mtt90) cc_final: 0.6879 (mpt180) REVERT: C 289 SER cc_start: 0.8854 (t) cc_final: 0.8638 (p) REVERT: C 733 ASN cc_start: 0.8258 (m-40) cc_final: 0.7986 (m110) REVERT: C 768 LYS cc_start: 0.8487 (mmtt) cc_final: 0.7949 (pttm) REVERT: E 60 TYR cc_start: 0.7427 (m-80) cc_final: 0.7216 (m-10) REVERT: G 17 SER cc_start: 0.7405 (OUTLIER) cc_final: 0.7174 (p) REVERT: G 80 LEU cc_start: 0.7380 (mt) cc_final: 0.7124 (tt) outliers start: 55 outliers final: 27 residues processed: 450 average time/residue: 0.3602 time to fit residues: 250.2270 Evaluate side-chains 358 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 330 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 51 PHE Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 53 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 66 optimal weight: 0.2980 chunk 131 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 289 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 895 GLN A 987 GLN A 992 GLN N 39 GLN N 71 ASN B 214 ASN B 992 GLN F 39 GLN C 214 ASN C 895 GLN C 987 GLN C 992 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126773 restraints weight = 30740.553| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.86 r_work: 0.3255 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24399 Z= 0.148 Angle : 0.625 18.262 33240 Z= 0.323 Chirality : 0.046 0.191 3900 Planarity : 0.004 0.039 4197 Dihedral : 6.317 53.780 4104 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.91 % Allowed : 11.03 % Favored : 87.06 % 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: 0.41 (0.15), residues: 2961 helix: 1.87 (0.21), residues: 606 sheet: 0.23 (0.18), residues: 741 loop : -0.28 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 36 HIS 0.004 0.001 HIS B1046 PHE 0.016 0.002 PHE C 83 TYR 0.024 0.002 TYR C1049 ARG 0.006 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 27) link_NAG-ASN : angle 2.00653 ( 81) link_BETA1-4 : bond 0.00703 ( 15) link_BETA1-4 : angle 2.21591 ( 45) hydrogen bonds : bond 0.04381 ( 1012) hydrogen bonds : angle 5.69266 ( 2856) SS BOND : bond 0.00364 ( 33) SS BOND : angle 1.37384 ( 66) covalent geometry : bond 0.00338 (24324) covalent geometry : angle 0.61048 (33048) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 376 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7450 (mtt90) cc_final: 0.7071 (mpt180) REVERT: A 274 ASP cc_start: 0.7985 (t0) cc_final: 0.7616 (m-30) REVERT: A 768 LYS cc_start: 0.8609 (mmtt) cc_final: 0.7934 (mtmm) REVERT: A 877 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: A 1104 VAL cc_start: 0.8346 (t) cc_final: 0.8064 (p) REVERT: M 57 ARG cc_start: 0.6619 (ttp-170) cc_final: 0.6402 (ttp-170) REVERT: M 59 ASN cc_start: 0.7613 (t0) cc_final: 0.7300 (m-40) REVERT: M 81 MET cc_start: 0.6563 (ttp) cc_final: 0.6145 (ttp) REVERT: M 90 ASP cc_start: 0.6944 (m-30) cc_final: 0.6176 (t0) REVERT: N 26 TYR cc_start: 0.7836 (m-80) cc_final: 0.6854 (m-80) REVERT: N 47 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7686 (mtpp) REVERT: N 80 LEU cc_start: 0.7377 (mt) cc_final: 0.7044 (tt) REVERT: N 85 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6324 (pt0) REVERT: B 183 ARG cc_start: 0.7479 (mtt90) cc_final: 0.7268 (mpt180) REVERT: B 185 PHE cc_start: 0.7820 (m-80) cc_final: 0.7618 (m-80) REVERT: B 274 ASP cc_start: 0.7989 (t0) cc_final: 0.7420 (m-30) REVERT: B 301 GLN cc_start: 0.9162 (tt0) cc_final: 0.8881 (tt0) REVERT: B 632 GLN cc_start: 0.8219 (mp10) cc_final: 0.7944 (mp10) REVERT: B 720 CYS cc_start: 0.7318 (t) cc_final: 0.7009 (t) REVERT: B 730 GLU cc_start: 0.7702 (mp0) cc_final: 0.7400 (mp0) REVERT: B 768 LYS cc_start: 0.8406 (mmtt) cc_final: 0.7856 (mtmm) REVERT: B 951 ASN cc_start: 0.8603 (m-40) cc_final: 0.8380 (m-40) REVERT: D 59 ASN cc_start: 0.7474 (m110) cc_final: 0.7169 (t0) REVERT: D 90 ASP cc_start: 0.6994 (m-30) cc_final: 0.6225 (t0) REVERT: D 98 ARG cc_start: 0.7212 (ttp-170) cc_final: 0.6794 (ttp-110) REVERT: F 92 SER cc_start: 0.8628 (p) cc_final: 0.7934 (t) REVERT: C 45 GLU cc_start: 0.8101 (pm20) cc_final: 0.7839 (pm20) REVERT: C 50 ASP cc_start: 0.8176 (t0) cc_final: 0.7938 (t0) REVERT: C 183 ARG cc_start: 0.7310 (mtt90) cc_final: 0.6929 (mpt180) REVERT: C 263 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8642 (ttp) REVERT: C 720 CYS cc_start: 0.7180 (t) cc_final: 0.6934 (t) REVERT: C 733 ASN cc_start: 0.8306 (m-40) cc_final: 0.7944 (m110) REVERT: C 768 LYS cc_start: 0.8621 (mmtt) cc_final: 0.7918 (mtmm) REVERT: C 877 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: E 36 TRP cc_start: 0.7693 (m100) cc_final: 0.7345 (m100) REVERT: G 26 TYR cc_start: 0.8009 (m-80) cc_final: 0.7009 (m-80) REVERT: G 55 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7134 (mttt) REVERT: G 80 LEU cc_start: 0.7597 (mt) cc_final: 0.7224 (tt) REVERT: G 85 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6423 (pt0) outliers start: 49 outliers final: 38 residues processed: 409 average time/residue: 0.3862 time to fit residues: 245.4461 Evaluate side-chains 386 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 51 PHE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 53 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 263 optimal weight: 0.6980 chunk 252 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 199 optimal weight: 0.0000 chunk 172 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 992 GLN B 626 ASN B 992 GLN C 214 ASN C 737 GLN C 992 GLN C 993 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126556 restraints weight = 31142.830| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.96 r_work: 0.3260 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24399 Z= 0.133 Angle : 0.579 14.805 33240 Z= 0.300 Chirality : 0.045 0.191 3900 Planarity : 0.004 0.037 4197 Dihedral : 5.538 53.206 4104 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.53 % Allowed : 11.42 % Favored : 86.04 % 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: 0.33 (0.15), residues: 2961 helix: 2.01 (0.21), residues: 603 sheet: 0.05 (0.18), residues: 768 loop : -0.34 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 36 HIS 0.003 0.001 HIS B1046 PHE 0.013 0.001 PHE B1024 TYR 0.021 0.002 TYR B1049 ARG 0.006 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 27) link_NAG-ASN : angle 1.87615 ( 81) link_BETA1-4 : bond 0.00594 ( 15) link_BETA1-4 : angle 1.86260 ( 45) hydrogen bonds : bond 0.03979 ( 1012) hydrogen bonds : angle 5.44764 ( 2856) SS BOND : bond 0.00368 ( 33) SS BOND : angle 1.35188 ( 66) covalent geometry : bond 0.00307 (24324) covalent geometry : angle 0.56548 (33048) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 370 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7429 (mtt90) cc_final: 0.7066 (mpt180) REVERT: A 274 ASP cc_start: 0.7862 (t0) cc_final: 0.7519 (m-30) REVERT: A 720 CYS cc_start: 0.7372 (t) cc_final: 0.7098 (t) REVERT: A 768 LYS cc_start: 0.8620 (mmtt) cc_final: 0.7921 (mttp) REVERT: A 877 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: A 996 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8497 (ttm-80) REVERT: A 1104 VAL cc_start: 0.8335 (t) cc_final: 0.8059 (p) REVERT: M 90 ASP cc_start: 0.6879 (m-30) cc_final: 0.6292 (t0) REVERT: M 94 TYR cc_start: 0.7811 (m-80) cc_final: 0.6832 (m-80) REVERT: N 26 TYR cc_start: 0.7808 (m-80) cc_final: 0.6787 (m-80) REVERT: N 47 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7671 (mtpp) REVERT: N 80 LEU cc_start: 0.7415 (mt) cc_final: 0.6967 (tt) REVERT: N 85 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6227 (pt0) REVERT: B 183 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7267 (mpt180) REVERT: B 221 LYS cc_start: 0.8066 (tttt) cc_final: 0.7558 (mmtm) REVERT: B 274 ASP cc_start: 0.7944 (t0) cc_final: 0.7384 (m-30) REVERT: B 301 GLN cc_start: 0.9160 (tt0) cc_final: 0.8868 (tt0) REVERT: B 632 GLN cc_start: 0.8232 (mp10) cc_final: 0.7951 (mp10) REVERT: B 720 CYS cc_start: 0.7350 (t) cc_final: 0.7055 (t) REVERT: B 768 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7877 (mtmm) REVERT: B 877 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: B 884 MET cc_start: 0.8233 (tpp) cc_final: 0.7880 (tpt) REVERT: D 59 ASN cc_start: 0.7539 (m110) cc_final: 0.7131 (t0) REVERT: D 90 ASP cc_start: 0.6948 (m-30) cc_final: 0.6236 (t0) REVERT: D 98 ARG cc_start: 0.7287 (ttp-170) cc_final: 0.7085 (ttp-110) REVERT: F 5 THR cc_start: 0.8499 (m) cc_final: 0.8129 (p) REVERT: F 50 ILE cc_start: 0.8868 (mt) cc_final: 0.8615 (tp) REVERT: F 71 ASN cc_start: 0.8090 (m-40) cc_final: 0.7834 (m110) REVERT: F 85 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6401 (pt0) REVERT: F 92 SER cc_start: 0.8483 (p) cc_final: 0.7746 (t) REVERT: C 45 GLU cc_start: 0.8136 (pm20) cc_final: 0.7893 (pm20) REVERT: C 183 ARG cc_start: 0.7349 (mtt90) cc_final: 0.7035 (mpt180) REVERT: C 263 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8583 (ttp) REVERT: C 558 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5551 (t80) REVERT: C 720 CYS cc_start: 0.7170 (t) cc_final: 0.6908 (t) REVERT: C 768 LYS cc_start: 0.8603 (mmtt) cc_final: 0.7909 (mtmm) REVERT: C 877 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: E 36 TRP cc_start: 0.7706 (m100) cc_final: 0.7278 (m100) REVERT: E 60 TYR cc_start: 0.7671 (m-10) cc_final: 0.7299 (m-10) REVERT: E 90 ASP cc_start: 0.7009 (m-30) cc_final: 0.6091 (t70) REVERT: G 26 TYR cc_start: 0.8031 (m-80) cc_final: 0.6972 (m-80) REVERT: G 55 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7289 (mttt) REVERT: G 71 ASN cc_start: 0.8174 (m110) cc_final: 0.7777 (m-40) REVERT: G 80 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7188 (tp) REVERT: G 85 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6400 (pt0) outliers start: 65 outliers final: 43 residues processed: 412 average time/residue: 0.3640 time to fit residues: 234.6159 Evaluate side-chains 387 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 338 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 206 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 105 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 171 optimal weight: 0.0970 chunk 178 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 744 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 214 ASN B 523 GLN B 737 GLN B 992 GLN D 39 GLN F 40 GLN C 214 ASN C 523 GLN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN E 39 GLN G 40 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120607 restraints weight = 31635.972| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.09 r_work: 0.3163 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 24399 Z= 0.266 Angle : 0.660 13.333 33240 Z= 0.344 Chirality : 0.049 0.218 3900 Planarity : 0.004 0.039 4197 Dihedral : 5.579 52.432 4104 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.31 % Allowed : 11.89 % Favored : 84.80 % 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: -0.04 (0.15), residues: 2961 helix: 1.63 (0.21), residues: 603 sheet: -0.20 (0.17), residues: 789 loop : -0.54 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 36 HIS 0.007 0.001 HIS B1046 PHE 0.034 0.002 PHE C 213 TYR 0.025 0.002 TYR B1049 ARG 0.008 0.001 ARG A 553 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 27) link_NAG-ASN : angle 1.92013 ( 81) link_BETA1-4 : bond 0.00559 ( 15) link_BETA1-4 : angle 1.64765 ( 45) hydrogen bonds : bond 0.04609 ( 1012) hydrogen bonds : angle 5.67379 ( 2856) SS BOND : bond 0.00579 ( 33) SS BOND : angle 1.71122 ( 66) covalent geometry : bond 0.00646 (24324) covalent geometry : angle 0.64795 (33048) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 356 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7211 (mpt180) REVERT: A 221 LYS cc_start: 0.8092 (tttt) cc_final: 0.7701 (mmtm) REVERT: A 274 ASP cc_start: 0.7858 (t0) cc_final: 0.7554 (m-30) REVERT: A 560 ASP cc_start: 0.8032 (t0) cc_final: 0.7540 (m-30) REVERT: A 720 CYS cc_start: 0.7349 (t) cc_final: 0.6966 (t) REVERT: A 768 LYS cc_start: 0.8720 (mmtt) cc_final: 0.7981 (mttp) REVERT: A 1104 VAL cc_start: 0.8526 (t) cc_final: 0.8300 (p) REVERT: M 90 ASP cc_start: 0.6926 (m-30) cc_final: 0.6192 (t0) REVERT: N 26 TYR cc_start: 0.8003 (m-80) cc_final: 0.6690 (m-80) REVERT: N 49 MET cc_start: 0.9078 (mmm) cc_final: 0.8516 (mmm) REVERT: N 50 ILE cc_start: 0.8961 (mt) cc_final: 0.8684 (tp) REVERT: N 80 LEU cc_start: 0.7486 (mt) cc_final: 0.6964 (tt) REVERT: N 85 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6206 (pt0) REVERT: B 183 ARG cc_start: 0.7702 (mtt90) cc_final: 0.7400 (mpt180) REVERT: B 221 LYS cc_start: 0.8131 (tttt) cc_final: 0.7731 (mmtm) REVERT: B 274 ASP cc_start: 0.7984 (t0) cc_final: 0.7416 (m-30) REVERT: B 301 GLN cc_start: 0.9199 (tt0) cc_final: 0.8911 (tt0) REVERT: B 632 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: B 720 CYS cc_start: 0.7460 (t) cc_final: 0.7174 (t) REVERT: B 768 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7978 (mtmt) REVERT: B 877 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: B 886 TYR cc_start: 0.8312 (t80) cc_final: 0.7723 (t80) REVERT: D 59 ASN cc_start: 0.7514 (m110) cc_final: 0.7109 (t0) REVERT: D 90 ASP cc_start: 0.7015 (m-30) cc_final: 0.6341 (t0) REVERT: F 71 ASN cc_start: 0.8350 (m-40) cc_final: 0.8040 (m110) REVERT: F 85 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6411 (pt0) REVERT: C 183 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7073 (mpt180) REVERT: C 558 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5571 (t80) REVERT: C 720 CYS cc_start: 0.7334 (t) cc_final: 0.7058 (t) REVERT: C 768 LYS cc_start: 0.8634 (mmtt) cc_final: 0.7964 (mttp) REVERT: C 877 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: C 886 TYR cc_start: 0.8279 (t80) cc_final: 0.7778 (t80) REVERT: E 36 TRP cc_start: 0.7835 (m100) cc_final: 0.7305 (m100) REVERT: E 90 ASP cc_start: 0.6971 (m-30) cc_final: 0.6087 (t70) REVERT: G 26 TYR cc_start: 0.8213 (m-80) cc_final: 0.6952 (m-80) REVERT: G 71 ASN cc_start: 0.8393 (m110) cc_final: 0.8150 (m-40) REVERT: G 80 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7169 (tp) outliers start: 85 outliers final: 72 residues processed: 406 average time/residue: 0.3428 time to fit residues: 218.3259 Evaluate side-chains 409 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 332 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 51 PHE Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 92 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 180 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 233 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 248 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 214 ASN B 992 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124358 restraints weight = 31071.137| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.97 r_work: 0.3236 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24399 Z= 0.127 Angle : 0.559 12.556 33240 Z= 0.288 Chirality : 0.045 0.203 3900 Planarity : 0.004 0.036 4197 Dihedral : 5.265 53.183 4104 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.38 % Allowed : 13.45 % Favored : 84.17 % 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: 0.07 (0.15), residues: 2961 helix: 1.91 (0.21), residues: 603 sheet: -0.12 (0.18), residues: 762 loop : -0.56 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 36 HIS 0.003 0.001 HIS B1046 PHE 0.017 0.001 PHE B 185 TYR 0.024 0.001 TYR M 95 ARG 0.005 0.000 ARG M 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 27) link_NAG-ASN : angle 1.83019 ( 81) link_BETA1-4 : bond 0.00524 ( 15) link_BETA1-4 : angle 1.38764 ( 45) hydrogen bonds : bond 0.03730 ( 1012) hydrogen bonds : angle 5.34136 ( 2856) SS BOND : bond 0.00442 ( 33) SS BOND : angle 1.55986 ( 66) covalent geometry : bond 0.00293 (24324) covalent geometry : angle 0.54679 (33048) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 369 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7190 (mpt180) REVERT: A 221 LYS cc_start: 0.8035 (tttt) cc_final: 0.7620 (mmtm) REVERT: A 274 ASP cc_start: 0.7829 (t0) cc_final: 0.7483 (m-30) REVERT: A 560 ASP cc_start: 0.8045 (t0) cc_final: 0.7639 (m-30) REVERT: A 604 THR cc_start: 0.8499 (m) cc_final: 0.8262 (p) REVERT: A 720 CYS cc_start: 0.7321 (t) cc_final: 0.6960 (t) REVERT: A 768 LYS cc_start: 0.8669 (mmtt) cc_final: 0.7949 (mttp) REVERT: A 964 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 1104 VAL cc_start: 0.8297 (t) cc_final: 0.8068 (p) REVERT: M 90 ASP cc_start: 0.6955 (m-30) cc_final: 0.6354 (t0) REVERT: M 94 TYR cc_start: 0.7936 (m-80) cc_final: 0.6938 (m-80) REVERT: N 5 THR cc_start: 0.8597 (m) cc_final: 0.8197 (p) REVERT: N 26 TYR cc_start: 0.7777 (m-80) cc_final: 0.6558 (m-80) REVERT: N 50 ILE cc_start: 0.8861 (mt) cc_final: 0.8607 (tp) REVERT: N 80 LEU cc_start: 0.7466 (mt) cc_final: 0.6890 (tt) REVERT: N 85 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6187 (pt0) REVERT: B 50 ASP cc_start: 0.7996 (t0) cc_final: 0.7730 (t0) REVERT: B 183 ARG cc_start: 0.7631 (mtt90) cc_final: 0.7340 (mpt180) REVERT: B 221 LYS cc_start: 0.8091 (tttt) cc_final: 0.7703 (mmtm) REVERT: B 274 ASP cc_start: 0.7861 (t0) cc_final: 0.7251 (m-30) REVERT: B 301 GLN cc_start: 0.9144 (tt0) cc_final: 0.8854 (tt0) REVERT: B 604 THR cc_start: 0.8628 (m) cc_final: 0.8334 (p) REVERT: B 720 CYS cc_start: 0.7349 (t) cc_final: 0.7052 (t) REVERT: B 768 LYS cc_start: 0.8538 (mmtt) cc_final: 0.7908 (mtmt) REVERT: B 877 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7918 (pt0) REVERT: B 1104 VAL cc_start: 0.8383 (t) cc_final: 0.8145 (p) REVERT: D 59 ASN cc_start: 0.7481 (m110) cc_final: 0.7159 (t0) REVERT: D 90 ASP cc_start: 0.6982 (m-30) cc_final: 0.6337 (t70) REVERT: D 98 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7408 (ttp-110) REVERT: F 5 THR cc_start: 0.8634 (m) cc_final: 0.8394 (p) REVERT: F 50 ILE cc_start: 0.8827 (mt) cc_final: 0.8539 (tp) REVERT: F 71 ASN cc_start: 0.8203 (m-40) cc_final: 0.7993 (m110) REVERT: F 85 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6224 (pt0) REVERT: C 183 ARG cc_start: 0.7406 (mtt90) cc_final: 0.7077 (mpt180) REVERT: C 221 LYS cc_start: 0.8093 (tttt) cc_final: 0.7671 (mmtm) REVERT: C 306 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7577 (mtp180) REVERT: C 558 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5512 (t80) REVERT: C 720 CYS cc_start: 0.7206 (t) cc_final: 0.6929 (t) REVERT: C 768 LYS cc_start: 0.8613 (mmtt) cc_final: 0.7940 (mtmm) REVERT: C 877 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: E 36 TRP cc_start: 0.7833 (m100) cc_final: 0.7413 (m100) REVERT: E 90 ASP cc_start: 0.6832 (m-30) cc_final: 0.6074 (t70) REVERT: G 26 TYR cc_start: 0.7982 (m-80) cc_final: 0.6803 (m-80) REVERT: G 50 ILE cc_start: 0.8772 (mt) cc_final: 0.8309 (tp) REVERT: G 71 ASN cc_start: 0.8325 (m110) cc_final: 0.8119 (m-40) REVERT: G 80 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7121 (tp) REVERT: G 85 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6384 (pt0) outliers start: 61 outliers final: 45 residues processed: 409 average time/residue: 0.3627 time to fit residues: 230.9670 Evaluate side-chains 386 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 242 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 292 optimal weight: 0.0170 chunk 18 optimal weight: 2.9990 chunk 188 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN N 40 GLN B 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124733 restraints weight = 31249.144| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.90 r_work: 0.3246 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24399 Z= 0.121 Angle : 0.561 12.458 33240 Z= 0.287 Chirality : 0.045 0.225 3900 Planarity : 0.004 0.036 4197 Dihedral : 5.208 59.652 4104 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.38 % Allowed : 14.39 % Favored : 83.24 % 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: 0.11 (0.15), residues: 2961 helix: 1.98 (0.21), residues: 603 sheet: -0.14 (0.18), residues: 762 loop : -0.53 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 36 HIS 0.003 0.000 HIS B1046 PHE 0.017 0.001 PHE C 185 TYR 0.023 0.001 TYR E 95 ARG 0.008 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 27) link_NAG-ASN : angle 1.73939 ( 81) link_BETA1-4 : bond 0.00505 ( 15) link_BETA1-4 : angle 1.33301 ( 45) hydrogen bonds : bond 0.03637 ( 1012) hydrogen bonds : angle 5.21575 ( 2856) SS BOND : bond 0.00372 ( 33) SS BOND : angle 1.81491 ( 66) covalent geometry : bond 0.00278 (24324) covalent geometry : angle 0.54807 (33048) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 349 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7467 (mtt90) cc_final: 0.7202 (mpt180) REVERT: A 185 PHE cc_start: 0.7668 (m-80) cc_final: 0.7424 (m-80) REVERT: A 221 LYS cc_start: 0.8112 (tttt) cc_final: 0.7737 (mmtm) REVERT: A 263 MET cc_start: 0.8910 (ttp) cc_final: 0.8706 (ttp) REVERT: A 274 ASP cc_start: 0.7802 (t0) cc_final: 0.7438 (m-30) REVERT: A 560 ASP cc_start: 0.8060 (t0) cc_final: 0.7656 (m-30) REVERT: A 604 THR cc_start: 0.8489 (m) cc_final: 0.8262 (p) REVERT: A 720 CYS cc_start: 0.7316 (t) cc_final: 0.6960 (t) REVERT: A 768 LYS cc_start: 0.8689 (mmtt) cc_final: 0.7978 (mttp) REVERT: A 1104 VAL cc_start: 0.8262 (t) cc_final: 0.8032 (p) REVERT: M 57 ARG cc_start: 0.6535 (ttp-170) cc_final: 0.5898 (ptt180) REVERT: M 90 ASP cc_start: 0.6934 (m-30) cc_final: 0.6380 (t0) REVERT: N 5 THR cc_start: 0.8354 (m) cc_final: 0.7955 (p) REVERT: N 26 TYR cc_start: 0.7730 (m-80) cc_final: 0.6486 (m-80) REVERT: N 49 MET cc_start: 0.8756 (mmp) cc_final: 0.8340 (mmm) REVERT: N 50 ILE cc_start: 0.8800 (mt) cc_final: 0.8573 (tp) REVERT: N 80 LEU cc_start: 0.7466 (mt) cc_final: 0.6829 (tp) REVERT: N 85 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6105 (pt0) REVERT: B 50 ASP cc_start: 0.8002 (t0) cc_final: 0.7776 (t0) REVERT: B 183 ARG cc_start: 0.7620 (mtt90) cc_final: 0.7354 (mpt180) REVERT: B 221 LYS cc_start: 0.8068 (tttt) cc_final: 0.7701 (mmtm) REVERT: B 274 ASP cc_start: 0.7861 (t0) cc_final: 0.7290 (m-30) REVERT: B 301 GLN cc_start: 0.9124 (tt0) cc_final: 0.8848 (tt0) REVERT: B 560 ASP cc_start: 0.8142 (t0) cc_final: 0.7522 (m-30) REVERT: B 604 THR cc_start: 0.8611 (m) cc_final: 0.8326 (p) REVERT: B 720 CYS cc_start: 0.7338 (t) cc_final: 0.7052 (t) REVERT: B 768 LYS cc_start: 0.8554 (mmtt) cc_final: 0.7912 (mtmt) REVERT: B 877 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: B 1104 VAL cc_start: 0.8368 (t) cc_final: 0.8152 (p) REVERT: D 59 ASN cc_start: 0.7479 (m110) cc_final: 0.7160 (t0) REVERT: D 90 ASP cc_start: 0.6947 (m-30) cc_final: 0.6324 (t70) REVERT: D 98 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7355 (ttp-110) REVERT: F 5 THR cc_start: 0.8571 (m) cc_final: 0.8326 (p) REVERT: F 50 ILE cc_start: 0.8749 (mt) cc_final: 0.8459 (tp) REVERT: F 85 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6118 (pt0) REVERT: C 45 GLU cc_start: 0.8145 (pm20) cc_final: 0.7773 (pm20) REVERT: C 183 ARG cc_start: 0.7421 (mtt90) cc_final: 0.7093 (mpt180) REVERT: C 221 LYS cc_start: 0.8039 (tttt) cc_final: 0.7552 (mmtm) REVERT: C 306 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7624 (mtp180) REVERT: C 558 PHE cc_start: 0.5889 (OUTLIER) cc_final: 0.5437 (t80) REVERT: C 720 CYS cc_start: 0.7150 (t) cc_final: 0.6889 (t) REVERT: C 768 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7955 (mtmm) REVERT: C 877 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: E 36 TRP cc_start: 0.7850 (m100) cc_final: 0.7310 (m100) REVERT: E 90 ASP cc_start: 0.6868 (m-30) cc_final: 0.6019 (t70) REVERT: G 4 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5362 (tt) REVERT: G 26 TYR cc_start: 0.7848 (m-80) cc_final: 0.6677 (m-80) REVERT: G 50 ILE cc_start: 0.8646 (mt) cc_final: 0.8208 (tp) REVERT: G 71 ASN cc_start: 0.8306 (m110) cc_final: 0.8087 (m-40) REVERT: G 80 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7080 (tp) REVERT: G 85 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6266 (pt0) outliers start: 61 outliers final: 46 residues processed: 389 average time/residue: 0.3535 time to fit residues: 214.3235 Evaluate side-chains 384 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 333 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 40 GLN Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 92 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 25 optimal weight: 3.9990 chunk 247 optimal weight: 0.1980 chunk 177 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN B 992 GLN F 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122451 restraints weight = 31345.747| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.05 r_work: 0.3185 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24399 Z= 0.184 Angle : 0.589 12.548 33240 Z= 0.303 Chirality : 0.046 0.245 3900 Planarity : 0.004 0.046 4197 Dihedral : 5.162 52.993 4104 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.77 % Allowed : 14.58 % Favored : 82.65 % 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: 0.03 (0.15), residues: 2961 helix: 1.78 (0.21), residues: 606 sheet: -0.13 (0.18), residues: 783 loop : -0.57 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 36 HIS 0.018 0.001 HIS N 41 PHE 0.015 0.002 PHE B 213 TYR 0.023 0.002 TYR A1049 ARG 0.008 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 27) link_NAG-ASN : angle 1.75070 ( 81) link_BETA1-4 : bond 0.00520 ( 15) link_BETA1-4 : angle 1.30642 ( 45) hydrogen bonds : bond 0.03933 ( 1012) hydrogen bonds : angle 5.33973 ( 2856) SS BOND : bond 0.00432 ( 33) SS BOND : angle 1.66782 ( 66) covalent geometry : bond 0.00446 (24324) covalent geometry : angle 0.57732 (33048) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 346 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8207 (pm20) cc_final: 0.7914 (pm20) REVERT: A 183 ARG cc_start: 0.7546 (mtt90) cc_final: 0.7247 (mpt180) REVERT: A 185 PHE cc_start: 0.7829 (m-80) cc_final: 0.7620 (m-80) REVERT: A 221 LYS cc_start: 0.8163 (tttt) cc_final: 0.7753 (mmtm) REVERT: A 274 ASP cc_start: 0.7885 (t0) cc_final: 0.7545 (m-30) REVERT: A 560 ASP cc_start: 0.8055 (t0) cc_final: 0.7605 (m-30) REVERT: A 604 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8286 (p) REVERT: A 720 CYS cc_start: 0.7331 (t) cc_final: 0.6942 (t) REVERT: A 768 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8034 (mttp) REVERT: A 1104 VAL cc_start: 0.8395 (t) cc_final: 0.8173 (p) REVERT: M 90 ASP cc_start: 0.6910 (m-30) cc_final: 0.6431 (t0) REVERT: N 26 TYR cc_start: 0.7788 (m-80) cc_final: 0.6464 (m-80) REVERT: N 49 MET cc_start: 0.8822 (mmp) cc_final: 0.8576 (mmm) REVERT: N 50 ILE cc_start: 0.8902 (mt) cc_final: 0.8645 (tp) REVERT: N 80 LEU cc_start: 0.7457 (mt) cc_final: 0.6786 (tp) REVERT: N 85 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6146 (pt0) REVERT: B 183 ARG cc_start: 0.7723 (mtt90) cc_final: 0.7379 (mpt180) REVERT: B 221 LYS cc_start: 0.8143 (tttt) cc_final: 0.7761 (mmtm) REVERT: B 274 ASP cc_start: 0.7917 (t0) cc_final: 0.7344 (m-30) REVERT: B 301 GLN cc_start: 0.9190 (tt0) cc_final: 0.8921 (tt0) REVERT: B 306 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7645 (ttt180) REVERT: B 558 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5714 (t80) REVERT: B 560 ASP cc_start: 0.8185 (t0) cc_final: 0.7577 (m-30) REVERT: B 604 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8333 (p) REVERT: B 720 CYS cc_start: 0.7441 (t) cc_final: 0.7176 (t) REVERT: B 768 LYS cc_start: 0.8611 (mmtt) cc_final: 0.7904 (mttp) REVERT: B 877 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: B 884 MET cc_start: 0.8349 (tpt) cc_final: 0.7980 (mmt) REVERT: B 886 TYR cc_start: 0.8261 (t80) cc_final: 0.7668 (t80) REVERT: B 1104 VAL cc_start: 0.8470 (t) cc_final: 0.8253 (p) REVERT: D 59 ASN cc_start: 0.7550 (m110) cc_final: 0.7185 (t0) REVERT: D 90 ASP cc_start: 0.6941 (m-30) cc_final: 0.6425 (t70) REVERT: F 5 THR cc_start: 0.8555 (m) cc_final: 0.8208 (p) REVERT: F 50 ILE cc_start: 0.8759 (mt) cc_final: 0.8288 (tp) REVERT: F 85 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6131 (pt0) REVERT: C 183 ARG cc_start: 0.7495 (mtt90) cc_final: 0.7149 (mpt180) REVERT: C 221 LYS cc_start: 0.8115 (tttt) cc_final: 0.7702 (mmtm) REVERT: C 306 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7666 (mtp180) REVERT: C 720 CYS cc_start: 0.7313 (t) cc_final: 0.7058 (t) REVERT: C 768 LYS cc_start: 0.8705 (mmtt) cc_final: 0.7996 (mttp) REVERT: C 837 PHE cc_start: 0.8455 (m-80) cc_final: 0.8227 (m-80) REVERT: C 877 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: E 36 TRP cc_start: 0.7869 (m100) cc_final: 0.7239 (m100) REVERT: E 81 MET cc_start: 0.6452 (ttp) cc_final: 0.6077 (ttp) REVERT: E 90 ASP cc_start: 0.6899 (m-30) cc_final: 0.6141 (t70) REVERT: G 4 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5378 (tt) REVERT: G 26 TYR cc_start: 0.7983 (m-80) cc_final: 0.6720 (m-80) REVERT: G 50 ILE cc_start: 0.8787 (mt) cc_final: 0.8337 (tp) REVERT: G 80 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7055 (tp) REVERT: G 85 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6277 (pt0) outliers start: 71 outliers final: 55 residues processed: 392 average time/residue: 0.3562 time to fit residues: 217.4221 Evaluate side-chains 397 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 335 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 92 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 282 optimal weight: 10.0000 chunk 12 optimal weight: 0.4980 chunk 177 optimal weight: 10.0000 chunk 240 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 208 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN M 39 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN B 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124401 restraints weight = 31326.992| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.96 r_work: 0.3227 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24399 Z= 0.128 Angle : 0.553 13.136 33240 Z= 0.282 Chirality : 0.045 0.226 3900 Planarity : 0.004 0.038 4197 Dihedral : 4.978 53.160 4104 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.26 % Allowed : 15.52 % Favored : 82.22 % 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: 0.09 (0.15), residues: 2961 helix: 1.89 (0.21), residues: 606 sheet: -0.09 (0.18), residues: 783 loop : -0.55 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 36 HIS 0.002 0.000 HIS C1046 PHE 0.014 0.001 PHE C1024 TYR 0.025 0.001 TYR E 95 ARG 0.007 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 27) link_NAG-ASN : angle 1.66754 ( 81) link_BETA1-4 : bond 0.00493 ( 15) link_BETA1-4 : angle 1.22711 ( 45) hydrogen bonds : bond 0.03599 ( 1012) hydrogen bonds : angle 5.18422 ( 2856) SS BOND : bond 0.00385 ( 33) SS BOND : angle 1.53261 ( 66) covalent geometry : bond 0.00302 (24324) covalent geometry : angle 0.54178 (33048) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 344 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7529 (mtt90) cc_final: 0.7239 (mpt180) REVERT: A 185 PHE cc_start: 0.7840 (m-80) cc_final: 0.7627 (m-80) REVERT: A 221 LYS cc_start: 0.8137 (tttt) cc_final: 0.7747 (mmtm) REVERT: A 274 ASP cc_start: 0.7840 (t0) cc_final: 0.7499 (m-30) REVERT: A 306 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7386 (mtp85) REVERT: A 560 ASP cc_start: 0.8002 (t0) cc_final: 0.7571 (m-30) REVERT: A 720 CYS cc_start: 0.7290 (t) cc_final: 0.6908 (t) REVERT: A 768 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8019 (mttp) REVERT: A 1104 VAL cc_start: 0.8339 (t) cc_final: 0.8105 (p) REVERT: M 57 ARG cc_start: 0.6364 (ttp-170) cc_final: 0.5816 (ptt180) REVERT: M 90 ASP cc_start: 0.6949 (m-30) cc_final: 0.6399 (t0) REVERT: N 5 THR cc_start: 0.8361 (m) cc_final: 0.7963 (p) REVERT: N 26 TYR cc_start: 0.7646 (m-80) cc_final: 0.6365 (m-80) REVERT: N 49 MET cc_start: 0.8779 (mmp) cc_final: 0.8541 (mmm) REVERT: N 50 ILE cc_start: 0.8758 (mt) cc_final: 0.8521 (tp) REVERT: N 80 LEU cc_start: 0.7302 (mt) cc_final: 0.6791 (tp) REVERT: N 85 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6046 (pt0) REVERT: B 50 ASP cc_start: 0.7897 (t0) cc_final: 0.7690 (t0) REVERT: B 183 ARG cc_start: 0.7695 (mtt90) cc_final: 0.7352 (mpt180) REVERT: B 274 ASP cc_start: 0.7612 (t0) cc_final: 0.6972 (m-30) REVERT: B 301 GLN cc_start: 0.9160 (tt0) cc_final: 0.8884 (tt0) REVERT: B 306 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7558 (ttt180) REVERT: B 558 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5714 (t80) REVERT: B 560 ASP cc_start: 0.8129 (t0) cc_final: 0.7525 (m-30) REVERT: B 604 THR cc_start: 0.8579 (m) cc_final: 0.8364 (p) REVERT: B 720 CYS cc_start: 0.7396 (t) cc_final: 0.7125 (t) REVERT: B 768 LYS cc_start: 0.8565 (mmtt) cc_final: 0.7879 (mttp) REVERT: B 877 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7986 (pt0) REVERT: B 1104 VAL cc_start: 0.8376 (t) cc_final: 0.8149 (p) REVERT: D 59 ASN cc_start: 0.7634 (m110) cc_final: 0.7180 (t0) REVERT: D 90 ASP cc_start: 0.6967 (m-30) cc_final: 0.6478 (t70) REVERT: F 5 THR cc_start: 0.8475 (m) cc_final: 0.8132 (p) REVERT: F 50 ILE cc_start: 0.8494 (mt) cc_final: 0.8060 (tp) REVERT: F 85 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6091 (pt0) REVERT: C 183 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7154 (mpt180) REVERT: C 221 LYS cc_start: 0.8095 (tttt) cc_final: 0.7627 (mmtm) REVERT: C 306 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7694 (mtp180) REVERT: C 720 CYS cc_start: 0.7214 (t) cc_final: 0.6960 (t) REVERT: C 768 LYS cc_start: 0.8680 (mmtt) cc_final: 0.7974 (mttp) REVERT: C 837 PHE cc_start: 0.8385 (m-80) cc_final: 0.8147 (m-80) REVERT: C 877 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: E 36 TRP cc_start: 0.7868 (m100) cc_final: 0.7152 (m100) REVERT: E 81 MET cc_start: 0.6468 (ttp) cc_final: 0.5901 (ttp) REVERT: E 90 ASP cc_start: 0.6875 (m-30) cc_final: 0.6212 (t70) REVERT: G 4 LEU cc_start: 0.5640 (OUTLIER) cc_final: 0.5412 (tt) REVERT: G 5 THR cc_start: 0.8589 (m) cc_final: 0.8341 (p) REVERT: G 26 TYR cc_start: 0.7934 (m-80) cc_final: 0.6661 (m-80) REVERT: G 50 ILE cc_start: 0.8600 (mt) cc_final: 0.8200 (tp) REVERT: G 55 LYS cc_start: 0.7843 (mtpt) cc_final: 0.7179 (mttt) REVERT: G 80 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7042 (tp) REVERT: G 85 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6206 (pt0) outliers start: 58 outliers final: 49 residues processed: 383 average time/residue: 0.3707 time to fit residues: 220.7972 Evaluate side-chains 386 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 92 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 251 optimal weight: 0.5980 chunk 282 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 265 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 737 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124336 restraints weight = 31543.875| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.97 r_work: 0.3215 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24399 Z= 0.131 Angle : 0.554 13.858 33240 Z= 0.282 Chirality : 0.045 0.237 3900 Planarity : 0.004 0.038 4197 Dihedral : 4.905 53.299 4104 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.26 % Allowed : 15.63 % Favored : 82.11 % 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: 0.10 (0.15), residues: 2961 helix: 1.90 (0.21), residues: 606 sheet: -0.07 (0.18), residues: 792 loop : -0.55 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP M 36 HIS 0.003 0.001 HIS B1046 PHE 0.013 0.001 PHE B1024 TYR 0.021 0.001 TYR A1049 ARG 0.005 0.000 ARG F 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 27) link_NAG-ASN : angle 1.61713 ( 81) link_BETA1-4 : bond 0.00485 ( 15) link_BETA1-4 : angle 1.19933 ( 45) hydrogen bonds : bond 0.03571 ( 1012) hydrogen bonds : angle 5.16569 ( 2856) SS BOND : bond 0.00375 ( 33) SS BOND : angle 1.37331 ( 66) covalent geometry : bond 0.00311 (24324) covalent geometry : angle 0.54509 (33048) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 345 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7515 (mtt90) cc_final: 0.7246 (mpt180) REVERT: A 185 PHE cc_start: 0.7879 (m-80) cc_final: 0.7648 (m-80) REVERT: A 221 LYS cc_start: 0.8122 (tttt) cc_final: 0.7742 (mmtm) REVERT: A 274 ASP cc_start: 0.7820 (t0) cc_final: 0.7477 (m-30) REVERT: A 560 ASP cc_start: 0.7948 (t0) cc_final: 0.7512 (m-30) REVERT: A 720 CYS cc_start: 0.7289 (t) cc_final: 0.6904 (t) REVERT: A 768 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8003 (mttp) REVERT: A 1104 VAL cc_start: 0.8329 (t) cc_final: 0.8098 (p) REVERT: M 57 ARG cc_start: 0.6427 (ttp-170) cc_final: 0.5832 (ptt180) REVERT: M 90 ASP cc_start: 0.6897 (m-30) cc_final: 0.6499 (t0) REVERT: N 26 TYR cc_start: 0.7694 (m-80) cc_final: 0.6261 (m-80) REVERT: N 80 LEU cc_start: 0.7300 (mt) cc_final: 0.6786 (tp) REVERT: N 85 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6044 (pt0) REVERT: B 183 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7347 (mpt180) REVERT: B 274 ASP cc_start: 0.7611 (t0) cc_final: 0.6982 (m-30) REVERT: B 301 GLN cc_start: 0.9165 (tt0) cc_final: 0.8890 (tt0) REVERT: B 306 ARG cc_start: 0.8010 (ttt180) cc_final: 0.7503 (ttt180) REVERT: B 558 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5637 (t80) REVERT: B 604 THR cc_start: 0.8556 (m) cc_final: 0.8356 (p) REVERT: B 720 CYS cc_start: 0.7373 (t) cc_final: 0.7110 (t) REVERT: B 768 LYS cc_start: 0.8557 (mmtt) cc_final: 0.7874 (mttp) REVERT: B 877 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: B 1104 VAL cc_start: 0.8397 (t) cc_final: 0.8159 (p) REVERT: D 59 ASN cc_start: 0.7713 (m110) cc_final: 0.7271 (t0) REVERT: D 90 ASP cc_start: 0.6983 (m-30) cc_final: 0.6530 (t70) REVERT: F 5 THR cc_start: 0.8482 (m) cc_final: 0.8151 (p) REVERT: F 50 ILE cc_start: 0.8550 (mt) cc_final: 0.8142 (tp) REVERT: F 55 LYS cc_start: 0.8635 (ptpp) cc_final: 0.8108 (ptpt) REVERT: F 85 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6092 (pt0) REVERT: C 183 ARG cc_start: 0.7502 (mtt90) cc_final: 0.7162 (mpt180) REVERT: C 221 LYS cc_start: 0.8037 (tttt) cc_final: 0.7740 (mmtm) REVERT: C 720 CYS cc_start: 0.7234 (t) cc_final: 0.6977 (t) REVERT: C 768 LYS cc_start: 0.8681 (mmtt) cc_final: 0.7962 (mttp) REVERT: C 877 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: E 36 TRP cc_start: 0.7849 (m100) cc_final: 0.7225 (m100) REVERT: E 73 ASP cc_start: 0.7703 (t70) cc_final: 0.7442 (t70) REVERT: E 90 ASP cc_start: 0.6868 (m-30) cc_final: 0.6184 (t70) REVERT: G 4 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5359 (tt) REVERT: G 5 THR cc_start: 0.8591 (m) cc_final: 0.8341 (p) REVERT: G 26 TYR cc_start: 0.7926 (m-80) cc_final: 0.6568 (m-80) REVERT: G 50 ILE cc_start: 0.8516 (mt) cc_final: 0.8115 (tp) REVERT: G 55 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7186 (mttt) REVERT: G 80 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7089 (tp) REVERT: G 85 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6149 (pt0) outliers start: 58 outliers final: 49 residues processed: 383 average time/residue: 0.3775 time to fit residues: 224.8552 Evaluate side-chains 389 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 92 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 PHE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain F residue 92 SER Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.0270 chunk 36 optimal weight: 0.4980 chunk 238 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 835 GLN A 992 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124227 restraints weight = 31251.403| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.91 r_work: 0.3241 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24399 Z= 0.131 Angle : 0.555 13.044 33240 Z= 0.283 Chirality : 0.045 0.236 3900 Planarity : 0.004 0.046 4197 Dihedral : 4.870 53.252 4104 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.30 % Allowed : 16.02 % Favored : 81.68 % 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: 0.16 (0.15), residues: 2961 helix: 1.91 (0.21), residues: 606 sheet: 0.14 (0.19), residues: 756 loop : -0.59 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP N 37 HIS 0.003 0.001 HIS M 32 PHE 0.016 0.001 PHE F 64 TYR 0.023 0.001 TYR E 95 ARG 0.008 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 27) link_NAG-ASN : angle 1.58443 ( 81) link_BETA1-4 : bond 0.00489 ( 15) link_BETA1-4 : angle 1.18949 ( 45) hydrogen bonds : bond 0.03548 ( 1012) hydrogen bonds : angle 5.15121 ( 2856) SS BOND : bond 0.00361 ( 33) SS BOND : angle 1.35508 ( 66) covalent geometry : bond 0.00310 (24324) covalent geometry : angle 0.54624 (33048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11603.98 seconds wall clock time: 199 minutes 41.89 seconds (11981.89 seconds total)