Starting phenix.real_space_refine on Fri May 23 04:41:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpf_43407/05_2025/8vpf_43407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpf_43407/05_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_43407/05_2025/8vpf_43407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpf_43407/05_2025/8vpf_43407.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpf_43407/05_2025/8vpf_43407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpf_43407/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 13.95, per 1000 atoms: 0.59 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: 6.05 Conformation dependent library (CDL) restraints added in 2.8 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: 4.09 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: 10.11 Time building geometry restraints manager: 7.04 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: 0.15 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: 3.070 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: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 54.950 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.330 ------------------------------------------------------------------------------- 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 : 2.512 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: 0.3627 time to fit residues: 349.5297 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 : 2.562 ------------------------------------------------------------------------------- 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: 3.20 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 2.822 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: 0.7882 (mtmm) REVERT: A 1104 VAL cc_start: 0.8385 (t) cc_final: 0.8143 (p) REVERT: N 26 TYR cc_start: 0.7975 (m-80) cc_final: 0.7057 (m-80) REVERT: N 47 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7753 (mtpp) REVERT: N 80 LEU cc_start: 0.7310 (mt) cc_final: 0.7039 (tt) REVERT: B 50 ASP cc_start: 0.7929 (t0) cc_final: 0.7559 (t0) REVERT: B 183 ARG cc_start: 0.7373 (mtt90) cc_final: 0.7099 (mpt180) REVERT: B 274 ASP cc_start: 0.7986 (t0) cc_final: 0.7497 (m-30) REVERT: B 289 SER cc_start: 0.8813 (t) cc_final: 0.8599 (p) REVERT: B 558 PHE cc_start: 0.5839 (m-80) cc_final: 0.5629 (m-80) REVERT: B 632 GLN cc_start: 0.8166 (mp10) cc_final: 0.7918 (mp10) REVERT: B 720 CYS cc_start: 0.7219 (t) cc_final: 0.6947 (t) REVERT: B 730 GLU cc_start: 0.7822 (mp0) cc_final: 0.7110 (mp0) REVERT: B 768 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7901 (mtmt) REVERT: B 951 ASN cc_start: 0.8488 (m-40) cc_final: 0.8244 (m-40) REVERT: D 22 CYS cc_start: 0.6187 (m) cc_final: 0.5887 (m) REVERT: D 60 TYR cc_start: 0.7496 (m-80) cc_final: 0.7168 (m-80) REVERT: F 62 ASP cc_start: 0.7729 (t0) cc_final: 0.7308 (t0) REVERT: F 85 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6759 (mm-30) REVERT: F 101 VAL cc_start: 0.9049 (p) cc_final: 0.8841 (m) REVERT: C 50 ASP cc_start: 0.8061 (t0) cc_final: 0.7686 (t0) REVERT: C 183 ARG cc_start: 0.7185 (mtt90) cc_final: 0.6882 (mpt180) REVERT: C 289 SER cc_start: 0.8854 (t) cc_final: 0.8639 (p) REVERT: C 733 ASN cc_start: 0.8260 (m-40) cc_final: 0.7986 (m110) REVERT: C 768 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7948 (pttm) REVERT: E 60 TYR cc_start: 0.7426 (m-80) cc_final: 0.7216 (m-10) REVERT: G 17 SER cc_start: 0.7404 (OUTLIER) cc_final: 0.7172 (p) REVERT: G 80 LEU cc_start: 0.7382 (mt) cc_final: 0.7123 (tt) outliers start: 55 outliers final: 27 residues processed: 450 average time/residue: 0.3707 time to fit residues: 257.8218 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 : 2.726 ------------------------------------------------------------------------------- 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: 0.1980 chunk 131 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 289 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.159059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126232 restraints weight = 30772.341| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.87 r_work: 0.3249 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3186 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= 0.153 Angle : 0.626 18.518 33240 Z= 0.324 Chirality : 0.047 0.194 3900 Planarity : 0.004 0.045 4197 Dihedral : 6.206 53.763 4104 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.22 % Allowed : 10.60 % Favored : 87.17 % 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: 0.37 (0.15), residues: 2961 helix: 1.85 (0.21), residues: 606 sheet: 0.17 (0.18), residues: 747 loop : -0.28 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 36 HIS 0.004 0.001 HIS B1046 PHE 0.016 0.002 PHE C 83 TYR 0.026 0.002 TYR C1049 ARG 0.006 0.001 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 27) link_NAG-ASN : angle 1.95028 ( 81) link_BETA1-4 : bond 0.00703 ( 15) link_BETA1-4 : angle 2.12958 ( 45) hydrogen bonds : bond 0.04352 ( 1012) hydrogen bonds : angle 5.66734 ( 2856) SS BOND : bond 0.00444 ( 33) SS BOND : angle 1.40284 ( 66) covalent geometry : bond 0.00356 (24324) covalent geometry : angle 0.61248 (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 432 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 375 time to evaluate : 2.607 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: 0.7451 (mtt90) cc_final: 0.7097 (mpt180) REVERT: A 274 ASP cc_start: 0.7979 (t0) cc_final: 0.7610 (m-30) REVERT: A 768 LYS cc_start: 0.8623 (mmtt) cc_final: 0.7945 (mttp) REVERT: A 877 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: A 1104 VAL cc_start: 0.8360 (t) cc_final: 0.8081 (p) REVERT: M 59 ASN cc_start: 0.7653 (t0) cc_final: 0.7360 (m-40) REVERT: M 81 MET cc_start: 0.6607 (ttp) cc_final: 0.6226 (ttp) REVERT: M 90 ASP cc_start: 0.6919 (m-30) cc_final: 0.6109 (t0) REVERT: N 26 TYR cc_start: 0.7865 (m-80) cc_final: 0.6858 (m-80) REVERT: N 47 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7684 (mtpp) REVERT: N 80 LEU cc_start: 0.7395 (mt) cc_final: 0.7045 (tt) REVERT: N 85 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6269 (pt0) REVERT: B 183 ARG cc_start: 0.7519 (mtt90) cc_final: 0.7287 (mpt180) REVERT: B 274 ASP cc_start: 0.7989 (t0) cc_final: 0.7418 (m-30) REVERT: B 301 GLN cc_start: 0.9180 (tt0) cc_final: 0.8894 (tt0) REVERT: B 632 GLN cc_start: 0.8214 (mp10) cc_final: 0.7928 (mp10) REVERT: B 720 CYS cc_start: 0.7317 (t) cc_final: 0.7010 (t) REVERT: B 730 GLU cc_start: 0.7707 (mp0) cc_final: 0.7407 (mp0) REVERT: B 733 ASN cc_start: 0.8201 (p0) cc_final: 0.7968 (p0) REVERT: B 768 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7860 (mtmm) REVERT: D 22 CYS cc_start: 0.6062 (m) cc_final: 0.5849 (m) REVERT: D 59 ASN cc_start: 0.7503 (m110) cc_final: 0.7177 (t0) REVERT: D 90 ASP cc_start: 0.7002 (m-30) cc_final: 0.6251 (t0) REVERT: D 98 ARG cc_start: 0.7242 (ttp-170) cc_final: 0.6836 (ttp-110) REVERT: F 26 TYR cc_start: 0.8088 (m-80) cc_final: 0.7839 (m-80) REVERT: F 92 SER cc_start: 0.8626 (p) cc_final: 0.7936 (t) REVERT: C 45 GLU cc_start: 0.8120 (pm20) cc_final: 0.7856 (pm20) REVERT: C 50 ASP cc_start: 0.8089 (t0) cc_final: 0.7867 (t0) REVERT: C 183 ARG cc_start: 0.7303 (mtt90) cc_final: 0.6958 (mpt180) REVERT: C 263 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8627 (ttp) REVERT: C 720 CYS cc_start: 0.7231 (t) cc_final: 0.6968 (t) REVERT: C 768 LYS cc_start: 0.8595 (mmtt) cc_final: 0.7916 (mtmm) REVERT: C 877 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: E 36 TRP cc_start: 0.7695 (m100) cc_final: 0.7325 (m100) REVERT: G 26 TYR cc_start: 0.8060 (m-80) cc_final: 0.7016 (m-80) REVERT: G 55 LYS cc_start: 0.7506 (mtpt) cc_final: 0.7142 (mttt) REVERT: G 80 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7219 (tp) REVERT: G 85 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6428 (pt0) outliers start: 57 outliers final: 42 residues processed: 412 average time/residue: 0.3836 time to fit residues: 245.0861 Evaluate side-chains 387 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 341 time to evaluate : 2.880 ------------------------------------------------------------------------------- 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 841 THR 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 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 70 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 717 SER 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 918 GLU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU 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: 0.6980 chunk 111 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 199 optimal weight: 0.0970 chunk 172 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 214 ASN B 523 GLN B 992 GLN C 214 ASN C 737 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 = 0.3947 r_free = 0.3947 target = 0.159185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126192 restraints weight = 31144.283| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.97 r_work: 0.3260 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3471 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= 0.134 Angle : 0.580 14.467 33240 Z= 0.299 Chirality : 0.045 0.192 3900 Planarity : 0.004 0.037 4197 Dihedral : 5.548 53.157 4104 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.34 % Allowed : 11.77 % Favored : 85.89 % 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: 0.32 (0.15), residues: 2961 helix: 2.01 (0.21), residues: 603 sheet: 0.04 (0.18), residues: 768 loop : -0.36 (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 C1049 ARG 0.006 0.000 ARG F 56 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 27) link_NAG-ASN : angle 1.87930 ( 81) link_BETA1-4 : bond 0.00536 ( 15) link_BETA1-4 : angle 1.85269 ( 45) hydrogen bonds : bond 0.03982 ( 1012) hydrogen bonds : angle 5.44457 ( 2856) SS BOND : bond 0.00561 ( 33) SS BOND : angle 1.32819 ( 66) covalent geometry : bond 0.00308 (24324) covalent geometry : angle 0.56653 (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 432 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 372 time to evaluate : 2.827 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: 0.7430 (mtt90) cc_final: 0.7067 (mpt180) REVERT: A 274 ASP cc_start: 0.7858 (t0) cc_final: 0.7511 (m-30) REVERT: A 720 CYS cc_start: 0.7370 (t) cc_final: 0.7101 (t) REVERT: A 768 LYS cc_start: 0.8625 (mmtt) cc_final: 0.7922 (mttp) REVERT: A 877 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: A 1104 VAL cc_start: 0.8344 (t) cc_final: 0.8073 (p) REVERT: M 90 ASP cc_start: 0.6871 (m-30) cc_final: 0.6312 (t0) REVERT: M 94 TYR cc_start: 0.7833 (m-80) cc_final: 0.6868 (m-80) REVERT: N 26 TYR cc_start: 0.7808 (m-80) cc_final: 0.6768 (m-80) REVERT: N 47 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7674 (mtpp) REVERT: N 80 LEU cc_start: 0.7415 (mt) cc_final: 0.6952 (tt) REVERT: N 85 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6212 (pt0) REVERT: B 183 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7359 (mpt180) REVERT: B 221 LYS cc_start: 0.8034 (tttt) cc_final: 0.7520 (mmtm) REVERT: B 274 ASP cc_start: 0.7943 (t0) cc_final: 0.7383 (m-30) REVERT: B 301 GLN cc_start: 0.9151 (tt0) cc_final: 0.8861 (tt0) REVERT: B 632 GLN cc_start: 0.8232 (mp10) cc_final: 0.7951 (mp10) REVERT: B 720 CYS cc_start: 0.7322 (t) cc_final: 0.7014 (t) REVERT: B 768 LYS cc_start: 0.8501 (mmtt) cc_final: 0.7889 (mtmm) REVERT: B 877 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8074 (pt0) REVERT: B 884 MET cc_start: 0.8191 (tpp) cc_final: 0.7872 (tpt) REVERT: D 59 ASN cc_start: 0.7520 (m110) cc_final: 0.7120 (t0) REVERT: D 90 ASP cc_start: 0.6948 (m-30) cc_final: 0.6236 (t0) REVERT: D 98 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.6935 (ttp-110) REVERT: F 5 THR cc_start: 0.8535 (m) cc_final: 0.8164 (p) REVERT: F 26 TYR cc_start: 0.8075 (m-80) cc_final: 0.7874 (m-80) REVERT: F 85 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6474 (pt0) REVERT: F 92 SER cc_start: 0.8502 (p) cc_final: 0.7770 (t) REVERT: C 45 GLU cc_start: 0.8137 (pm20) cc_final: 0.7896 (pm20) REVERT: C 183 ARG cc_start: 0.7339 (mtt90) cc_final: 0.7041 (mpt180) REVERT: C 263 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8581 (ttp) REVERT: C 720 CYS cc_start: 0.7153 (t) cc_final: 0.6889 (t) REVERT: C 768 LYS cc_start: 0.8609 (mmtt) cc_final: 0.7918 (mtmm) REVERT: C 877 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: C 996 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8248 (mtt90) REVERT: E 36 TRP cc_start: 0.7707 (m100) cc_final: 0.7323 (m100) REVERT: E 59 ASN cc_start: 0.7533 (t0) cc_final: 0.7295 (m110) REVERT: E 60 TYR cc_start: 0.7652 (m-10) cc_final: 0.7288 (m-10) REVERT: E 90 ASP cc_start: 0.6965 (m-30) cc_final: 0.6053 (t70) REVERT: G 26 TYR cc_start: 0.8049 (m-80) cc_final: 0.6985 (m-80) REVERT: G 55 LYS cc_start: 0.7645 (mtpt) cc_final: 0.7281 (mttt) REVERT: G 71 ASN cc_start: 0.8184 (m110) cc_final: 0.7782 (m-40) REVERT: G 80 LEU cc_start: 0.7665 (mt) cc_final: 0.7174 (tp) REVERT: G 85 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6410 (pt0) outliers start: 60 outliers final: 41 residues processed: 412 average time/residue: 0.3690 time to fit residues: 238.6461 Evaluate side-chains 380 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 335 time to evaluate : 2.860 ------------------------------------------------------------------------------- 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 539 THR Chi-restraints excluded: chain A residue 558 PHE 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 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 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 289 SER Chi-restraints excluded: chain B residue 556 SER 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 877 GLN Chi-restraints excluded: chain B residue 983 LEU 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 589 ASN 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 1118 THR Chi-restraints excluded: chain E residue 45 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: 0.5980 chunk 105 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 737 GLN B 992 GLN D 39 GLN F 40 GLN F 71 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN G 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120324 restraints weight = 31636.895| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.99 r_work: 0.3162 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 24399 Z= 0.271 Angle : 0.665 13.352 33240 Z= 0.348 Chirality : 0.049 0.197 3900 Planarity : 0.004 0.039 4197 Dihedral : 5.625 52.431 4104 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.35 % Allowed : 11.66 % Favored : 84.99 % 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: -0.08 (0.15), residues: 2961 helix: 1.59 (0.21), residues: 600 sheet: -0.23 (0.17), residues: 798 loop : -0.56 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 36 HIS 0.007 0.001 HIS B1046 PHE 0.039 0.002 PHE C 213 TYR 0.025 0.002 TYR B1049 ARG 0.006 0.001 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 27) link_NAG-ASN : angle 1.94303 ( 81) link_BETA1-4 : bond 0.00506 ( 15) link_BETA1-4 : angle 1.62259 ( 45) hydrogen bonds : bond 0.04672 ( 1012) hydrogen bonds : angle 5.69984 ( 2856) SS BOND : bond 0.00563 ( 33) SS BOND : angle 1.70318 ( 66) covalent geometry : bond 0.00659 (24324) covalent geometry : angle 0.65237 (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 440 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 354 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7193 (mpt180) REVERT: A 221 LYS cc_start: 0.8074 (tttt) cc_final: 0.7696 (mmtm) REVERT: A 274 ASP cc_start: 0.7863 (t0) cc_final: 0.7548 (m-30) REVERT: A 720 CYS cc_start: 0.7364 (t) cc_final: 0.6971 (t) REVERT: A 768 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8000 (mttp) REVERT: A 886 TYR cc_start: 0.8344 (t80) cc_final: 0.7798 (t80) REVERT: A 1104 VAL cc_start: 0.8534 (t) cc_final: 0.8314 (p) REVERT: M 90 ASP cc_start: 0.6989 (m-30) cc_final: 0.6256 (t0) REVERT: N 26 TYR cc_start: 0.7925 (m-80) cc_final: 0.6584 (m-80) REVERT: N 49 MET cc_start: 0.9052 (mmm) cc_final: 0.8558 (mmm) REVERT: N 50 ILE cc_start: 0.8999 (mt) cc_final: 0.8715 (tp) REVERT: N 80 LEU cc_start: 0.7488 (mt) cc_final: 0.6970 (tt) REVERT: N 85 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6185 (pt0) REVERT: B 183 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7409 (mpt180) REVERT: B 221 LYS cc_start: 0.8109 (tttt) cc_final: 0.7728 (mmtm) REVERT: B 274 ASP cc_start: 0.7977 (t0) cc_final: 0.7403 (m-30) REVERT: B 301 GLN cc_start: 0.9182 (tt0) cc_final: 0.8895 (tt0) REVERT: B 632 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: B 720 CYS cc_start: 0.7453 (t) cc_final: 0.7163 (t) REVERT: B 768 LYS cc_start: 0.8642 (mmtt) cc_final: 0.7940 (mttp) REVERT: B 877 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7935 (pt0) REVERT: B 886 TYR cc_start: 0.8299 (t80) cc_final: 0.7724 (t80) REVERT: D 22 CYS cc_start: 0.5979 (m) cc_final: 0.5766 (m) REVERT: D 59 ASN cc_start: 0.7516 (m110) cc_final: 0.7187 (t0) REVERT: D 90 ASP cc_start: 0.7030 (m-30) cc_final: 0.6367 (t0) REVERT: F 85 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6418 (pt0) REVERT: C 183 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7087 (mpt180) REVERT: C 720 CYS cc_start: 0.7329 (t) cc_final: 0.7053 (t) REVERT: C 768 LYS cc_start: 0.8650 (mmtt) cc_final: 0.7985 (mttp) REVERT: C 877 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: C 886 TYR cc_start: 0.8281 (t80) cc_final: 0.7798 (t80) REVERT: E 36 TRP cc_start: 0.7899 (m100) cc_final: 0.7490 (m100) REVERT: E 57 ARG cc_start: 0.6791 (ttp-170) cc_final: 0.6086 (ptt90) REVERT: E 59 ASN cc_start: 0.7721 (t0) cc_final: 0.7373 (m110) REVERT: E 60 TYR cc_start: 0.7675 (m-10) cc_final: 0.7255 (m-10) REVERT: E 90 ASP cc_start: 0.7006 (m-30) cc_final: 0.6222 (t70) REVERT: G 26 TYR cc_start: 0.8233 (m-80) cc_final: 0.6945 (m-80) REVERT: G 71 ASN cc_start: 0.8436 (m110) cc_final: 0.8201 (m-40) REVERT: G 80 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7184 (tt) outliers start: 86 outliers final: 70 residues processed: 410 average time/residue: 0.3458 time to fit residues: 221.1834 Evaluate side-chains 407 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 333 time to evaluate : 2.450 ------------------------------------------------------------------------------- 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 215 THR 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 717 SER Chi-restraints excluded: chain A residue 837 PHE 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 962 ILE 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 87 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 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 589 ASN 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 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 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: 0.6980 chunk 233 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 992 GLN C 214 ASN C 737 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123247 restraints weight = 31145.257| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.92 r_work: 0.3225 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24399 Z= 0.142 Angle : 0.565 12.145 33240 Z= 0.293 Chirality : 0.045 0.202 3900 Planarity : 0.004 0.037 4197 Dihedral : 5.319 53.131 4104 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.22 % Allowed : 13.88 % Favored : 83.90 % 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: 1.82 (0.21), residues: 603 sheet: -0.12 (0.18), residues: 783 loop : -0.58 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 36 HIS 0.002 0.001 HIS C1046 PHE 0.015 0.001 PHE A1024 TYR 0.023 0.002 TYR D 95 ARG 0.007 0.000 ARG C 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 27) link_NAG-ASN : angle 1.84263 ( 81) link_BETA1-4 : bond 0.00511 ( 15) link_BETA1-4 : angle 1.37906 ( 45) hydrogen bonds : bond 0.03829 ( 1012) hydrogen bonds : angle 5.40905 ( 2856) SS BOND : bond 0.00406 ( 33) SS BOND : angle 1.56202 ( 66) covalent geometry : bond 0.00337 (24324) covalent geometry : angle 0.55270 (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 422 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 365 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7183 (mpt180) REVERT: A 221 LYS cc_start: 0.8003 (tttt) cc_final: 0.7645 (mmtm) REVERT: A 274 ASP cc_start: 0.7831 (t0) cc_final: 0.7480 (m-30) REVERT: A 604 THR cc_start: 0.8524 (m) cc_final: 0.8293 (p) REVERT: A 720 CYS cc_start: 0.7245 (t) cc_final: 0.6839 (t) REVERT: A 768 LYS cc_start: 0.8694 (mmtt) cc_final: 0.7991 (mttp) REVERT: A 1104 VAL cc_start: 0.8329 (t) cc_final: 0.8105 (p) REVERT: M 57 ARG cc_start: 0.6252 (ttp-170) cc_final: 0.5877 (ptt180) REVERT: M 90 ASP cc_start: 0.6973 (m-30) cc_final: 0.6374 (t0) REVERT: M 94 TYR cc_start: 0.7972 (m-80) cc_final: 0.7027 (m-80) REVERT: N 5 THR cc_start: 0.8628 (m) cc_final: 0.8232 (p) REVERT: N 26 TYR cc_start: 0.7847 (m-80) cc_final: 0.6557 (m-80) REVERT: N 49 MET cc_start: 0.9014 (mmm) cc_final: 0.8502 (mmm) REVERT: N 50 ILE cc_start: 0.8901 (mt) cc_final: 0.8624 (tp) REVERT: N 80 LEU cc_start: 0.7494 (mt) cc_final: 0.6927 (tp) REVERT: N 85 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6119 (pt0) REVERT: B 50 ASP cc_start: 0.8031 (t0) cc_final: 0.7784 (t0) REVERT: B 183 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7345 (mpt180) REVERT: B 221 LYS cc_start: 0.8068 (tttt) cc_final: 0.7701 (mmtm) REVERT: B 274 ASP cc_start: 0.7860 (t0) cc_final: 0.7250 (m-30) REVERT: B 301 GLN cc_start: 0.9145 (tt0) cc_final: 0.8859 (tt0) REVERT: B 604 THR cc_start: 0.8636 (m) cc_final: 0.8338 (p) REVERT: B 720 CYS cc_start: 0.7297 (t) cc_final: 0.7004 (t) REVERT: B 722 MET cc_start: 0.8848 (tpt) cc_final: 0.8628 (tpt) REVERT: B 768 LYS cc_start: 0.8571 (mmtt) cc_final: 0.7927 (mtmt) REVERT: B 877 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: B 1104 VAL cc_start: 0.8380 (t) cc_final: 0.8145 (p) REVERT: D 59 ASN cc_start: 0.7485 (m110) cc_final: 0.7161 (t0) REVERT: D 90 ASP cc_start: 0.6997 (m-30) cc_final: 0.6382 (t70) REVERT: F 5 THR cc_start: 0.8648 (m) cc_final: 0.8348 (p) REVERT: F 26 TYR cc_start: 0.8143 (m-80) cc_final: 0.7729 (m-80) REVERT: F 50 ILE cc_start: 0.8863 (mt) cc_final: 0.8494 (tp) REVERT: F 85 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6340 (pt0) REVERT: C 50 ASP cc_start: 0.7951 (t0) cc_final: 0.7680 (t0) REVERT: C 183 ARG cc_start: 0.7429 (mtt90) cc_final: 0.7090 (mpt180) REVERT: C 221 LYS cc_start: 0.8102 (tttt) cc_final: 0.7681 (mmtm) REVERT: C 720 CYS cc_start: 0.7194 (t) cc_final: 0.6916 (t) REVERT: C 768 LYS cc_start: 0.8624 (mmtt) cc_final: 0.7955 (mttp) REVERT: C 877 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: E 36 TRP cc_start: 0.7870 (m100) cc_final: 0.7317 (m100) REVERT: E 60 TYR cc_start: 0.7636 (m-10) cc_final: 0.7342 (m-10) REVERT: E 90 ASP cc_start: 0.6876 (m-30) cc_final: 0.6224 (t70) REVERT: G 26 TYR cc_start: 0.8040 (m-80) cc_final: 0.6825 (m-80) REVERT: G 50 ILE cc_start: 0.8918 (mt) cc_final: 0.8495 (tp) REVERT: G 80 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7133 (tp) REVERT: G 85 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6427 (pt0) outliers start: 57 outliers final: 44 residues processed: 405 average time/residue: 0.3568 time to fit residues: 224.5571 Evaluate side-chains 387 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 340 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 558 PHE Chi-restraints excluded: chain A residue 717 SER 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 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 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 556 SER Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 717 SER 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 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 296 ASP Chi-restraints excluded: chain C residue 589 ASN 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 1118 THR Chi-restraints excluded: chain E residue 18 VAL 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: 0.0370 chunk 18 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN N 40 GLN B 992 GLN E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.124341 restraints weight = 31275.271| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.92 r_work: 0.3220 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24399 Z= 0.127 Angle : 0.549 11.572 33240 Z= 0.283 Chirality : 0.045 0.191 3900 Planarity : 0.004 0.037 4197 Dihedral : 5.205 59.732 4104 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.46 % Allowed : 14.54 % Favored : 83.00 % 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: 0.08 (0.15), residues: 2961 helix: 1.89 (0.21), residues: 603 sheet: -0.11 (0.18), residues: 783 loop : -0.55 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 36 HIS 0.003 0.000 HIS B1046 PHE 0.014 0.001 PHE C 185 TYR 0.027 0.001 TYR E 95 ARG 0.009 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 27) link_NAG-ASN : angle 1.72046 ( 81) link_BETA1-4 : bond 0.00489 ( 15) link_BETA1-4 : angle 1.28970 ( 45) hydrogen bonds : bond 0.03660 ( 1012) hydrogen bonds : angle 5.23408 ( 2856) SS BOND : bond 0.00423 ( 33) SS BOND : angle 1.38490 ( 66) covalent geometry : bond 0.00298 (24324) covalent geometry : angle 0.53815 (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 416 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 353 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7510 (mtt90) cc_final: 0.7234 (mpt180) REVERT: A 185 PHE cc_start: 0.7788 (m-80) cc_final: 0.7555 (m-80) REVERT: A 221 LYS cc_start: 0.8088 (tttt) cc_final: 0.7736 (mmtm) REVERT: A 274 ASP cc_start: 0.7833 (t0) cc_final: 0.7497 (m-30) REVERT: A 604 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 720 CYS cc_start: 0.7303 (t) cc_final: 0.6900 (t) REVERT: A 768 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8023 (mttp) REVERT: A 1104 VAL cc_start: 0.8314 (t) cc_final: 0.8085 (p) REVERT: M 90 ASP cc_start: 0.6922 (m-30) cc_final: 0.6396 (t0) REVERT: N 5 THR cc_start: 0.8500 (m) cc_final: 0.8106 (p) REVERT: N 26 TYR cc_start: 0.7726 (m-80) cc_final: 0.6448 (m-80) REVERT: N 50 ILE cc_start: 0.8846 (mt) cc_final: 0.8613 (tp) REVERT: N 80 LEU cc_start: 0.7493 (mt) cc_final: 0.6851 (tp) REVERT: N 85 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6038 (pt0) REVERT: B 183 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7350 (mpt180) REVERT: B 221 LYS cc_start: 0.8027 (tttt) cc_final: 0.7680 (mmtm) REVERT: B 274 ASP cc_start: 0.7879 (t0) cc_final: 0.7294 (m-30) REVERT: B 301 GLN cc_start: 0.9174 (tt0) cc_final: 0.8901 (tt0) REVERT: B 604 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8364 (p) REVERT: B 720 CYS cc_start: 0.7433 (t) cc_final: 0.7159 (t) REVERT: B 722 MET cc_start: 0.8837 (tpt) cc_final: 0.8614 (tpt) REVERT: B 768 LYS cc_start: 0.8612 (mmtt) cc_final: 0.7916 (mttp) REVERT: B 877 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: B 976 ASP cc_start: 0.8180 (m-30) cc_final: 0.7980 (m-30) REVERT: B 1104 VAL cc_start: 0.8377 (t) cc_final: 0.8141 (p) REVERT: D 59 ASN cc_start: 0.7542 (m110) cc_final: 0.7193 (t0) REVERT: D 90 ASP cc_start: 0.6881 (m-30) cc_final: 0.6310 (t70) REVERT: F 5 THR cc_start: 0.8543 (m) cc_final: 0.8251 (p) REVERT: F 26 TYR cc_start: 0.8046 (m-80) cc_final: 0.7557 (m-80) REVERT: F 50 ILE cc_start: 0.8799 (mt) cc_final: 0.8491 (tp) REVERT: F 85 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6125 (pt0) REVERT: C 50 ASP cc_start: 0.7958 (t0) cc_final: 0.7725 (t0) REVERT: C 183 ARG cc_start: 0.7488 (mtt90) cc_final: 0.7143 (mpt180) REVERT: C 221 LYS cc_start: 0.8078 (tttt) cc_final: 0.7594 (mmtm) REVERT: C 720 CYS cc_start: 0.7185 (t) cc_final: 0.6919 (t) REVERT: C 768 LYS cc_start: 0.8674 (mmtt) cc_final: 0.7968 (mttp) REVERT: C 877 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: E 36 TRP cc_start: 0.7838 (m100) cc_final: 0.7318 (m100) REVERT: E 57 ARG cc_start: 0.6865 (ttp-170) cc_final: 0.6541 (ptt90) REVERT: E 90 ASP cc_start: 0.6863 (m-30) cc_final: 0.6188 (t70) REVERT: G 4 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.5383 (tt) REVERT: G 26 TYR cc_start: 0.7921 (m-80) cc_final: 0.6690 (m-80) REVERT: G 32 TYR cc_start: 0.8764 (m-80) cc_final: 0.8452 (m-80) REVERT: G 50 ILE cc_start: 0.8769 (mt) cc_final: 0.8376 (tp) REVERT: G 80 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7075 (tp) REVERT: G 85 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6233 (pt0) outliers start: 63 outliers final: 46 residues processed: 395 average time/residue: 0.3734 time to fit residues: 229.6518 Evaluate side-chains 383 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 214 ASN Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 877 GLN 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 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 556 SER 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 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 69 THR Chi-restraints excluded: chain D residue 84 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 215 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 601 VAL 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 916 ILE Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 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: 1.9990 chunk 247 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN N 40 GLN B 214 ASN B 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121369 restraints weight = 31323.534| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.12 r_work: 0.3188 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24399 Z= 0.191 Angle : 0.586 11.562 33240 Z= 0.302 Chirality : 0.046 0.192 3900 Planarity : 0.004 0.038 4197 Dihedral : 5.186 53.023 4104 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.92 % Allowed : 14.62 % Favored : 82.46 % 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: -0.06 (0.15), residues: 2961 helix: 1.69 (0.21), residues: 606 sheet: -0.18 (0.18), residues: 804 loop : -0.62 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 36 HIS 0.004 0.001 HIS C1046 PHE 0.016 0.002 PHE A 103 TYR 0.024 0.002 TYR A1049 ARG 0.008 0.000 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 27) link_NAG-ASN : angle 1.75083 ( 81) link_BETA1-4 : bond 0.00502 ( 15) link_BETA1-4 : angle 1.27107 ( 45) hydrogen bonds : bond 0.03964 ( 1012) hydrogen bonds : angle 5.34635 ( 2856) SS BOND : bond 0.00442 ( 33) SS BOND : angle 1.36806 ( 66) covalent geometry : bond 0.00462 (24324) covalent geometry : angle 0.57586 (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 415 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 340 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7515 (mtt90) cc_final: 0.7133 (mpt180) REVERT: A 185 PHE cc_start: 0.7770 (m-80) cc_final: 0.7555 (m-80) REVERT: A 221 LYS cc_start: 0.8194 (tttt) cc_final: 0.7760 (mmtm) REVERT: A 274 ASP cc_start: 0.7850 (t0) cc_final: 0.7451 (m-30) REVERT: A 604 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 720 CYS cc_start: 0.7327 (t) cc_final: 0.6930 (t) REVERT: A 768 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8011 (mttp) REVERT: A 1104 VAL cc_start: 0.8437 (t) cc_final: 0.8196 (p) REVERT: M 90 ASP cc_start: 0.6859 (m-30) cc_final: 0.6405 (t0) REVERT: N 5 THR cc_start: 0.8554 (m) cc_final: 0.8124 (p) REVERT: N 26 TYR cc_start: 0.7702 (m-80) cc_final: 0.6344 (m-80) REVERT: N 49 MET cc_start: 0.9049 (mmm) cc_final: 0.8542 (mmm) REVERT: N 50 ILE cc_start: 0.8938 (mt) cc_final: 0.8581 (tp) REVERT: N 80 LEU cc_start: 0.7465 (mt) cc_final: 0.6760 (tp) REVERT: N 85 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6019 (pt0) REVERT: B 183 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7255 (mpt180) REVERT: B 221 LYS cc_start: 0.8102 (tttt) cc_final: 0.7714 (mmtm) REVERT: B 274 ASP cc_start: 0.7882 (t0) cc_final: 0.7232 (m-30) REVERT: B 301 GLN cc_start: 0.9218 (tt0) cc_final: 0.8933 (tt0) REVERT: B 604 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 720 CYS cc_start: 0.7420 (t) cc_final: 0.7148 (t) REVERT: B 768 LYS cc_start: 0.8650 (mmtt) cc_final: 0.7887 (mttp) REVERT: B 877 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: B 886 TYR cc_start: 0.8245 (t80) cc_final: 0.7617 (t80) REVERT: B 976 ASP cc_start: 0.8202 (m-30) cc_final: 0.7992 (m-30) REVERT: B 1104 VAL cc_start: 0.8481 (t) cc_final: 0.8240 (p) REVERT: D 59 ASN cc_start: 0.7557 (m110) cc_final: 0.7163 (t0) REVERT: D 90 ASP cc_start: 0.6815 (m-30) cc_final: 0.6335 (t70) REVERT: F 5 THR cc_start: 0.8583 (m) cc_final: 0.8201 (p) REVERT: F 26 TYR cc_start: 0.8115 (m-80) cc_final: 0.7572 (m-80) REVERT: F 50 ILE cc_start: 0.8802 (mt) cc_final: 0.8348 (tp) REVERT: F 85 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6099 (pt0) REVERT: C 50 ASP cc_start: 0.8016 (t0) cc_final: 0.7806 (t0) REVERT: C 183 ARG cc_start: 0.7462 (mtt90) cc_final: 0.7036 (mpt180) REVERT: C 221 LYS cc_start: 0.8184 (tttt) cc_final: 0.7723 (mmtm) REVERT: C 306 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7750 (mtp180) REVERT: C 720 CYS cc_start: 0.7277 (t) cc_final: 0.7019 (t) REVERT: C 768 LYS cc_start: 0.8731 (mmtt) cc_final: 0.7965 (mttp) REVERT: C 877 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: E 36 TRP cc_start: 0.7846 (m100) cc_final: 0.7120 (m100) REVERT: E 57 ARG cc_start: 0.6909 (ttp-170) cc_final: 0.6350 (ptt90) REVERT: E 90 ASP cc_start: 0.6882 (m-30) cc_final: 0.6136 (t70) REVERT: G 4 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5228 (tt) REVERT: G 26 TYR cc_start: 0.7940 (m-80) cc_final: 0.6642 (m-80) REVERT: G 32 TYR cc_start: 0.8801 (m-80) cc_final: 0.8476 (m-80) REVERT: G 80 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7013 (tp) REVERT: G 85 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6150 (pt0) outliers start: 75 outliers final: 61 residues processed: 392 average time/residue: 0.3775 time to fit residues: 229.8857 Evaluate side-chains 400 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 333 time to evaluate : 2.656 ------------------------------------------------------------------------------- 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 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 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 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 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 214 ASN 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 589 ASN Chi-restraints excluded: chain B residue 604 THR 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 984 GLN 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 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 D residue 125 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 215 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 601 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 240 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 208 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 992 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN B 214 ASN B 614 GLN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121223 restraints weight = 31545.186| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.02 r_work: 0.3169 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24399 Z= 0.233 Angle : 0.622 12.003 33240 Z= 0.322 Chirality : 0.047 0.201 3900 Planarity : 0.004 0.042 4197 Dihedral : 5.304 52.726 4104 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.92 % Allowed : 14.46 % Favored : 82.61 % 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: -0.20 (0.15), residues: 2961 helix: 1.51 (0.21), residues: 606 sheet: -0.25 (0.18), residues: 804 loop : -0.69 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 36 HIS 0.005 0.001 HIS C1046 PHE 0.017 0.002 PHE C1024 TYR 0.024 0.002 TYR B1049 ARG 0.009 0.001 ARG B 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 27) link_NAG-ASN : angle 1.80923 ( 81) link_BETA1-4 : bond 0.00498 ( 15) link_BETA1-4 : angle 1.25879 ( 45) hydrogen bonds : bond 0.04188 ( 1012) hydrogen bonds : angle 5.48404 ( 2856) SS BOND : bond 0.00530 ( 33) SS BOND : angle 1.67966 ( 66) covalent geometry : bond 0.00569 (24324) covalent geometry : angle 0.61067 (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 413 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 338 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7246 (mpt180) REVERT: A 185 PHE cc_start: 0.7880 (m-80) cc_final: 0.7669 (m-80) REVERT: A 221 LYS cc_start: 0.8165 (tttt) cc_final: 0.7777 (mmtm) REVERT: A 274 ASP cc_start: 0.7901 (t0) cc_final: 0.7573 (m-30) REVERT: A 604 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 720 CYS cc_start: 0.7330 (t) cc_final: 0.6945 (t) REVERT: A 768 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8019 (mttp) REVERT: A 1104 VAL cc_start: 0.8474 (t) cc_final: 0.8261 (p) REVERT: M 90 ASP cc_start: 0.6949 (m-30) cc_final: 0.6392 (t0) REVERT: N 5 THR cc_start: 0.8617 (m) cc_final: 0.8219 (p) REVERT: N 26 TYR cc_start: 0.7811 (m-80) cc_final: 0.6279 (m-80) REVERT: N 49 MET cc_start: 0.9068 (mmm) cc_final: 0.8593 (mmm) REVERT: N 50 ILE cc_start: 0.8967 (mt) cc_final: 0.8664 (tp) REVERT: N 80 LEU cc_start: 0.7254 (mt) cc_final: 0.6859 (tp) REVERT: N 85 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6125 (pt0) REVERT: B 183 ARG cc_start: 0.7700 (mtt90) cc_final: 0.7367 (mpt180) REVERT: B 221 LYS cc_start: 0.8064 (tttt) cc_final: 0.7730 (mmtm) REVERT: B 301 GLN cc_start: 0.9186 (tt0) cc_final: 0.8911 (tt0) REVERT: B 604 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 720 CYS cc_start: 0.7369 (t) cc_final: 0.7074 (t) REVERT: B 737 GLN cc_start: 0.7595 (mm110) cc_final: 0.7371 (mm-40) REVERT: B 768 LYS cc_start: 0.8654 (mmtt) cc_final: 0.7938 (mttp) REVERT: B 877 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: B 886 TYR cc_start: 0.8266 (t80) cc_final: 0.7677 (t80) REVERT: B 1104 VAL cc_start: 0.8485 (t) cc_final: 0.8254 (p) REVERT: D 59 ASN cc_start: 0.7555 (m110) cc_final: 0.7252 (t0) REVERT: D 90 ASP cc_start: 0.6984 (m-30) cc_final: 0.6494 (t70) REVERT: F 5 THR cc_start: 0.8586 (m) cc_final: 0.8231 (p) REVERT: F 26 TYR cc_start: 0.8213 (m-80) cc_final: 0.7850 (m-80) REVERT: F 50 ILE cc_start: 0.8811 (mt) cc_final: 0.8294 (tp) REVERT: F 85 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6150 (pt0) REVERT: C 50 ASP cc_start: 0.8055 (t0) cc_final: 0.7840 (t0) REVERT: C 183 ARG cc_start: 0.7591 (mtt90) cc_final: 0.7187 (mpt180) REVERT: C 221 LYS cc_start: 0.8129 (tttt) cc_final: 0.7710 (mmtm) REVERT: C 720 CYS cc_start: 0.7257 (t) cc_final: 0.6997 (t) REVERT: C 768 LYS cc_start: 0.8701 (mmtt) cc_final: 0.7997 (mttp) REVERT: C 877 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: C 886 TYR cc_start: 0.8235 (t80) cc_final: 0.7771 (t80) REVERT: E 36 TRP cc_start: 0.7876 (m100) cc_final: 0.7324 (m100) REVERT: E 57 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6439 (ptt90) REVERT: E 90 ASP cc_start: 0.6949 (m-30) cc_final: 0.6330 (t70) REVERT: G 4 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5535 (tt) REVERT: G 26 TYR cc_start: 0.8111 (m-80) cc_final: 0.6695 (m-80) REVERT: G 32 TYR cc_start: 0.8731 (m-80) cc_final: 0.8509 (m-80) REVERT: G 80 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7055 (tp) REVERT: G 85 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6284 (pt0) outliers start: 75 outliers final: 62 residues processed: 389 average time/residue: 0.3711 time to fit residues: 223.9932 Evaluate side-chains 399 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 331 time to evaluate : 2.943 ------------------------------------------------------------------------------- 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 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 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 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 589 ASN Chi-restraints excluded: chain B residue 604 THR 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 984 GLN 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 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 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 214 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 ASN Chi-restraints excluded: chain C residue 601 VAL 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 976 ASP 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: 10.0000 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 265 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN A 992 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122927 restraints weight = 31588.605| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.03 r_work: 0.3203 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4395 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= 0.139 Angle : 0.571 12.553 33240 Z= 0.293 Chirality : 0.045 0.196 3900 Planarity : 0.004 0.056 4197 Dihedral : 5.141 53.053 4104 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.30 % Allowed : 15.09 % Favored : 82.61 % 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: 1.75 (0.21), residues: 606 sheet: -0.22 (0.18), residues: 804 loop : -0.63 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 36 HIS 0.003 0.000 HIS M 32 PHE 0.014 0.001 PHE C1024 TYR 0.021 0.002 TYR B1049 ARG 0.009 0.001 ARG M 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 27) link_NAG-ASN : angle 1.71828 ( 81) link_BETA1-4 : bond 0.00480 ( 15) link_BETA1-4 : angle 1.18522 ( 45) hydrogen bonds : bond 0.03742 ( 1012) hydrogen bonds : angle 5.31268 ( 2856) SS BOND : bond 0.00432 ( 33) SS BOND : angle 1.74130 ( 66) covalent geometry : bond 0.00330 (24324) covalent geometry : angle 0.55902 (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 402 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 343 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7582 (mtt90) cc_final: 0.7236 (mpt180) REVERT: A 185 PHE cc_start: 0.7869 (m-80) cc_final: 0.7650 (m-80) REVERT: A 221 LYS cc_start: 0.8188 (tttt) cc_final: 0.7819 (mmtm) REVERT: A 274 ASP cc_start: 0.7845 (t0) cc_final: 0.7492 (m-30) REVERT: A 604 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 720 CYS cc_start: 0.7309 (t) cc_final: 0.6926 (t) REVERT: A 768 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8033 (mttp) REVERT: A 1104 VAL cc_start: 0.8403 (t) cc_final: 0.8172 (p) REVERT: M 90 ASP cc_start: 0.6906 (m-30) cc_final: 0.6380 (t0) REVERT: N 5 THR cc_start: 0.8586 (m) cc_final: 0.8172 (p) REVERT: N 26 TYR cc_start: 0.7779 (m-80) cc_final: 0.6307 (m-80) REVERT: N 49 MET cc_start: 0.9004 (mmm) cc_final: 0.8524 (mmm) REVERT: N 50 ILE cc_start: 0.8929 (mt) cc_final: 0.8599 (tp) REVERT: N 80 LEU cc_start: 0.7339 (mt) cc_final: 0.6830 (tp) REVERT: N 85 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6073 (pt0) REVERT: B 183 ARG cc_start: 0.7668 (mtt90) cc_final: 0.7322 (mpt180) REVERT: B 232 ARG cc_start: 0.7123 (ptm160) cc_final: 0.6851 (ptm160) REVERT: B 274 ASP cc_start: 0.7731 (t0) cc_final: 0.7089 (m-30) REVERT: B 301 GLN cc_start: 0.9170 (tt0) cc_final: 0.8900 (tt0) REVERT: B 558 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5753 (t80) REVERT: B 604 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8366 (p) REVERT: B 720 CYS cc_start: 0.7400 (t) cc_final: 0.7119 (t) REVERT: B 768 LYS cc_start: 0.8612 (mmtt) cc_final: 0.7904 (mttp) REVERT: B 877 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: B 1104 VAL cc_start: 0.8405 (t) cc_final: 0.8161 (p) REVERT: D 59 ASN cc_start: 0.7612 (m110) cc_final: 0.7263 (t0) REVERT: D 90 ASP cc_start: 0.6943 (m-30) cc_final: 0.6454 (t70) REVERT: F 5 THR cc_start: 0.8544 (m) cc_final: 0.8179 (p) REVERT: F 26 TYR cc_start: 0.8097 (m-80) cc_final: 0.7524 (m-80) REVERT: F 50 ILE cc_start: 0.8634 (mt) cc_final: 0.8144 (tp) REVERT: F 55 LYS cc_start: 0.7537 (mtpt) cc_final: 0.7002 (mttt) REVERT: F 85 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6128 (pt0) REVERT: C 183 ARG cc_start: 0.7542 (mtt90) cc_final: 0.7151 (mpt180) REVERT: C 221 LYS cc_start: 0.8053 (tttt) cc_final: 0.7607 (mmtm) REVERT: C 720 CYS cc_start: 0.7287 (t) cc_final: 0.7026 (t) REVERT: C 768 LYS cc_start: 0.8708 (mmtt) cc_final: 0.7985 (mttp) REVERT: C 877 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: E 36 TRP cc_start: 0.7839 (m100) cc_final: 0.7155 (m100) REVERT: E 57 ARG cc_start: 0.6964 (ttp-170) cc_final: 0.6506 (ptt90) REVERT: E 90 ASP cc_start: 0.6859 (m-30) cc_final: 0.6270 (t70) REVERT: G 4 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5440 (tt) REVERT: G 26 TYR cc_start: 0.7980 (m-80) cc_final: 0.6620 (m-80) REVERT: G 32 TYR cc_start: 0.8758 (m-80) cc_final: 0.8475 (m-80) REVERT: G 50 ILE cc_start: 0.8818 (mt) cc_final: 0.8392 (tp) REVERT: G 80 LEU cc_start: 0.7700 (mt) cc_final: 0.7081 (tp) REVERT: G 85 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6191 (pt0) outliers start: 59 outliers final: 51 residues processed: 384 average time/residue: 0.3646 time to fit residues: 216.0281 Evaluate side-chains 387 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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 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 717 SER Chi-restraints excluded: chain A residue 877 GLN 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 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 533 THR Chi-restraints excluded: chain B residue 539 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 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 214 ASN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 533 THR 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 976 ASP Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.0000 chunk 36 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 290 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN B 951 ASN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122595 restraints weight = 31292.531| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.95 r_work: 0.3220 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 24399 Z= 0.191 Angle : 0.736 59.200 33240 Z= 0.408 Chirality : 0.045 0.226 3900 Planarity : 0.004 0.077 4197 Dihedral : 5.148 53.052 4104 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.38 % Allowed : 15.44 % Favored : 82.18 % Cbeta Deviations : 0.04 % 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: -0.06 (0.15), residues: 2961 helix: 1.77 (0.21), residues: 606 sheet: -0.22 (0.18), residues: 804 loop : -0.63 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 36 HIS 0.003 0.000 HIS E 32 PHE 0.014 0.001 PHE F 64 TYR 0.120 0.002 TYR B 195 ARG 0.031 0.001 ARG C 996 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 27) link_NAG-ASN : angle 1.72133 ( 81) link_BETA1-4 : bond 0.00443 ( 15) link_BETA1-4 : angle 1.20134 ( 45) hydrogen bonds : bond 0.03734 ( 1012) hydrogen bonds : angle 5.31846 ( 2856) SS BOND : bond 0.00367 ( 33) SS BOND : angle 1.84280 ( 66) covalent geometry : bond 0.00443 (24324) covalent geometry : angle 0.72724 (33048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11518.04 seconds wall clock time: 200 minutes 33.01 seconds (12033.01 seconds total)