Starting phenix.real_space_refine on Fri Sep 19 06:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpf_43407/09_2025/8vpf_43407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpf_43407/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vpf_43407/09_2025/8vpf_43407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpf_43407/09_2025/8vpf_43407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vpf_43407/09_2025/8vpf_43407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpf_43407/09_2025/8vpf_43407.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.09, per 1000 atoms: 0.21 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: 1.71 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.09 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: 4.84 Time building geometry restraints manager: 2.31 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.890 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG C 183 TYR 0.048 0.008 TYR C 778 PHE 0.036 0.006 PHE B 83 TRP 0.046 0.011 TRP G 37 HIS 0.007 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.02143 (24324) covalent geometry : angle 1.81880 (33048) SS BOND : bond 0.03293 ( 33) SS BOND : angle 2.78362 ( 66) hydrogen bonds : bond 0.15233 ( 1012) hydrogen bonds : angle 8.05400 ( 2856) link_BETA1-4 : bond 0.07303 ( 15) link_BETA1-4 : angle 4.51117 ( 45) link_NAG-ASN : bond 0.08185 ( 27) link_NAG-ASN : angle 2.39491 ( 81) *********************** 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 : 0.717 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: 0.1522 time to fit residues: 147.4085 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 : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 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 ** 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 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1088 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.160769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127841 restraints weight = 31009.105| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.89 r_work: 0.3283 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2595 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 : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.18 % Allowed : 8.19 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG A 306 TYR 0.026 0.002 TYR E 94 PHE 0.026 0.002 PHE A 83 TRP 0.023 0.002 TRP M 36 HIS 0.006 0.001 HIS M 32 Details of bonding type rmsd covalent geometry : bond 0.00423 (24324) covalent geometry : angle 0.70836 (33048) SS BOND : bond 0.00381 ( 33) SS BOND : angle 1.60590 ( 66) hydrogen bonds : bond 0.05305 ( 1012) hydrogen bonds : angle 6.25891 ( 2856) link_BETA1-4 : bond 0.00676 ( 15) link_BETA1-4 : angle 3.09508 ( 45) link_NAG-ASN : bond 0.00785 ( 27) link_NAG-ASN : angle 2.53217 ( 81) *********************** 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: 56 poor density : 418 time to evaluate : 0.855 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: 0.7891 (t0) cc_final: 0.7553 (m-30) REVERT: A 768 LYS cc_start: 0.8499 (mmtt) cc_final: 0.7881 (mtmm) REVERT: A 1104 VAL cc_start: 0.8393 (t) cc_final: 0.8148 (p) REVERT: N 26 TYR cc_start: 0.7971 (m-80) cc_final: 0.7048 (m-80) REVERT: N 47 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7733 (mtpp) REVERT: N 80 LEU cc_start: 0.7310 (mt) cc_final: 0.7028 (tt) REVERT: B 50 ASP cc_start: 0.7934 (t0) cc_final: 0.7561 (t0) REVERT: B 183 ARG cc_start: 0.7381 (mtt90) cc_final: 0.7076 (mpt180) REVERT: B 274 ASP cc_start: 0.7996 (t0) cc_final: 0.7488 (m-30) REVERT: B 289 SER cc_start: 0.8816 (t) cc_final: 0.8594 (p) REVERT: B 558 PHE cc_start: 0.5838 (m-80) cc_final: 0.5623 (m-80) REVERT: B 632 GLN cc_start: 0.8186 (mp10) cc_final: 0.7934 (mp10) REVERT: B 720 CYS cc_start: 0.7247 (t) cc_final: 0.6972 (t) REVERT: B 730 GLU cc_start: 0.7843 (mp0) cc_final: 0.7119 (mp0) REVERT: B 768 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7904 (mtmt) REVERT: B 951 ASN cc_start: 0.8505 (m-40) cc_final: 0.8261 (m-40) REVERT: D 22 CYS cc_start: 0.6184 (m) cc_final: 0.5879 (m) REVERT: D 60 TYR cc_start: 0.7496 (m-80) cc_final: 0.7163 (m-80) REVERT: F 62 ASP cc_start: 0.7726 (t0) cc_final: 0.7308 (t0) REVERT: F 85 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6750 (mm-30) REVERT: F 101 VAL cc_start: 0.9042 (p) cc_final: 0.8828 (m) REVERT: C 50 ASP cc_start: 0.8067 (t0) cc_final: 0.7691 (t0) REVERT: C 183 ARG cc_start: 0.7185 (mtt90) cc_final: 0.6855 (mpt180) REVERT: C 289 SER cc_start: 0.8861 (t) cc_final: 0.8637 (p) REVERT: C 733 ASN cc_start: 0.8265 (m-40) cc_final: 0.7988 (m110) REVERT: C 768 LYS cc_start: 0.8513 (mmtt) cc_final: 0.7946 (pttm) REVERT: E 60 TYR cc_start: 0.7423 (m-80) cc_final: 0.7210 (m-10) REVERT: G 17 SER cc_start: 0.7402 (OUTLIER) cc_final: 0.7164 (p) REVERT: G 80 LEU cc_start: 0.7377 (mt) cc_final: 0.7110 (tt) outliers start: 56 outliers final: 27 residues processed: 450 average time/residue: 0.1522 time to fit residues: 106.0654 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 : 0.831 ------------------------------------------------------------------------------- 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 167 optimal weight: 0.5980 chunk 294 optimal weight: 10.0000 chunk 232 optimal weight: 0.7980 chunk 200 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 270 optimal weight: 0.0770 chunk 125 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- 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 523 GLN B 992 GLN F 39 GLN C 214 ASN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 987 GLN C 992 GLN C 993 GLN G 39 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123471 restraints weight = 31150.003| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.01 r_work: 0.3222 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24399 Z= 0.200 Angle : 0.658 18.620 33240 Z= 0.342 Chirality : 0.048 0.192 3900 Planarity : 0.004 0.049 4197 Dihedral : 6.274 53.153 4104 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.85 % Allowed : 10.02 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.15), residues: 2961 helix: 1.73 (0.21), residues: 606 sheet: 0.13 (0.18), residues: 747 loop : -0.34 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 996 TYR 0.027 0.002 TYR B1049 PHE 0.018 0.002 PHE C 83 TRP 0.024 0.002 TRP M 36 HIS 0.006 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00476 (24324) covalent geometry : angle 0.64467 (33048) SS BOND : bond 0.00498 ( 33) SS BOND : angle 1.46210 ( 66) hydrogen bonds : bond 0.04599 ( 1012) hydrogen bonds : angle 5.77521 ( 2856) link_BETA1-4 : bond 0.00650 ( 15) link_BETA1-4 : angle 2.11606 ( 45) link_NAG-ASN : bond 0.00483 ( 27) link_NAG-ASN : angle 1.98235 ( 81) *********************** 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 441 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 368 time to evaluate : 0.746 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 183 ARG cc_start: 0.7501 (mtt90) cc_final: 0.7116 (mpt180) REVERT: A 274 ASP cc_start: 0.7906 (t0) cc_final: 0.7557 (m-30) REVERT: A 558 PHE cc_start: 0.6140 (OUTLIER) cc_final: 0.5880 (t80) REVERT: A 768 LYS cc_start: 0.8664 (mmtt) cc_final: 0.7950 (mttp) REVERT: A 877 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: A 996 ARG cc_start: 0.8699 (ttm-80) cc_final: 0.8491 (ttm-80) REVERT: A 1104 VAL cc_start: 0.8411 (t) cc_final: 0.8177 (p) REVERT: M 59 ASN cc_start: 0.7612 (t0) cc_final: 0.7272 (m-40) REVERT: M 90 ASP cc_start: 0.6972 (m-30) cc_final: 0.6139 (t0) REVERT: N 26 TYR cc_start: 0.7952 (m-80) cc_final: 0.6797 (m-80) REVERT: N 47 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7667 (mtpp) REVERT: N 80 LEU cc_start: 0.7384 (mt) cc_final: 0.7103 (tt) REVERT: N 85 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6257 (pt0) REVERT: B 183 ARG cc_start: 0.7565 (mtt90) cc_final: 0.7254 (mpt180) REVERT: B 221 LYS cc_start: 0.8007 (tttt) cc_final: 0.7591 (mmtm) REVERT: B 274 ASP cc_start: 0.7979 (t0) cc_final: 0.7411 (m-30) REVERT: B 301 GLN cc_start: 0.9169 (tt0) cc_final: 0.8864 (tt0) REVERT: B 632 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: B 720 CYS cc_start: 0.7319 (t) cc_final: 0.7028 (t) REVERT: B 768 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7884 (mtmm) REVERT: B 877 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: B 886 TYR cc_start: 0.8226 (t80) cc_final: 0.7849 (t80) REVERT: D 90 ASP cc_start: 0.7003 (m-30) cc_final: 0.6250 (t0) REVERT: D 98 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.6882 (ttp-110) REVERT: F 26 TYR cc_start: 0.8128 (m-80) cc_final: 0.7736 (m-80) REVERT: F 92 SER cc_start: 0.8624 (p) cc_final: 0.7949 (t) REVERT: C 45 GLU cc_start: 0.8150 (pm20) cc_final: 0.7870 (pm20) REVERT: C 50 ASP cc_start: 0.8104 (t0) cc_final: 0.7888 (t0) REVERT: C 183 ARG cc_start: 0.7329 (mtt90) cc_final: 0.7021 (mpt180) REVERT: C 263 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8650 (ttp) REVERT: C 720 CYS cc_start: 0.7190 (t) cc_final: 0.6921 (t) REVERT: C 768 LYS cc_start: 0.8628 (mmtt) cc_final: 0.7944 (mtmm) REVERT: C 877 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: E 36 TRP cc_start: 0.7740 (m100) cc_final: 0.7356 (m100) REVERT: G 26 TYR cc_start: 0.8159 (m-80) cc_final: 0.7020 (m-80) REVERT: G 55 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7148 (mttt) REVERT: G 80 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7194 (tp) REVERT: G 85 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6434 (pt0) outliers start: 73 outliers final: 54 residues processed: 415 average time/residue: 0.1426 time to fit residues: 91.8408 Evaluate side-chains 396 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 335 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 539 THR 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 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 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 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 792 LEU Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain F residue 19 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 214 ASN Chi-restraints excluded: chain C residue 215 THR 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 649 ASP Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 44 LYS 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 34 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 214 ASN B 626 ASN B 744 GLN B 992 GLN C 214 ASN C 737 GLN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122807 restraints weight = 31266.987| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.96 r_work: 0.3203 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24399 Z= 0.187 Angle : 0.615 14.200 33240 Z= 0.320 Chirality : 0.047 0.192 3900 Planarity : 0.004 0.039 4197 Dihedral : 5.720 52.716 4104 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.39 % Allowed : 11.50 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.15), residues: 2961 helix: 1.79 (0.21), residues: 603 sheet: -0.07 (0.18), residues: 768 loop : -0.46 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 996 TYR 0.023 0.002 TYR B1049 PHE 0.021 0.002 PHE C 213 TRP 0.026 0.002 TRP M 36 HIS 0.004 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00450 (24324) covalent geometry : angle 0.60259 (33048) SS BOND : bond 0.00450 ( 33) SS BOND : angle 1.38619 ( 66) hydrogen bonds : bond 0.04293 ( 1012) hydrogen bonds : angle 5.61400 ( 2856) link_BETA1-4 : bond 0.00505 ( 15) link_BETA1-4 : angle 1.82497 ( 45) link_NAG-ASN : bond 0.00482 ( 27) link_NAG-ASN : angle 1.91926 ( 81) *********************** 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 454 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 367 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7122 (mpt180) REVERT: A 274 ASP cc_start: 0.7934 (t0) cc_final: 0.7577 (m-30) REVERT: A 720 CYS cc_start: 0.7419 (t) cc_final: 0.7147 (t) REVERT: A 768 LYS cc_start: 0.8677 (mmtt) cc_final: 0.7958 (mttp) REVERT: A 996 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8479 (ttm-80) REVERT: A 1104 VAL cc_start: 0.8439 (t) cc_final: 0.8199 (p) REVERT: M 59 ASN cc_start: 0.7478 (t0) cc_final: 0.7182 (m-40) REVERT: M 90 ASP cc_start: 0.6910 (m-30) cc_final: 0.6177 (t0) REVERT: N 26 TYR cc_start: 0.7973 (m-80) cc_final: 0.6790 (m-80) REVERT: N 80 LEU cc_start: 0.7443 (mt) cc_final: 0.7060 (tt) REVERT: N 85 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6263 (pt0) REVERT: B 183 ARG cc_start: 0.7636 (mtt90) cc_final: 0.7336 (mpt180) REVERT: B 274 ASP cc_start: 0.7988 (t0) cc_final: 0.7448 (m-30) REVERT: B 301 GLN cc_start: 0.9189 (tt0) cc_final: 0.8900 (tt0) REVERT: B 632 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: B 720 CYS cc_start: 0.7363 (t) cc_final: 0.7050 (t) REVERT: B 768 LYS cc_start: 0.8536 (mmtt) cc_final: 0.7919 (mtmt) REVERT: B 877 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: B 886 TYR cc_start: 0.8233 (t80) cc_final: 0.7710 (t80) REVERT: D 59 ASN cc_start: 0.7474 (m110) cc_final: 0.7145 (t0) REVERT: D 90 ASP cc_start: 0.7000 (m-30) cc_final: 0.6326 (t0) REVERT: D 98 ARG cc_start: 0.7491 (ttp-170) cc_final: 0.7263 (ttp-110) REVERT: F 26 TYR cc_start: 0.8164 (m-80) cc_final: 0.7775 (m-80) REVERT: F 71 ASN cc_start: 0.8237 (m-40) cc_final: 0.7954 (m110) REVERT: F 85 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6551 (pt0) REVERT: C 45 GLU cc_start: 0.8205 (pm20) cc_final: 0.7953 (pm20) REVERT: C 183 ARG cc_start: 0.7379 (mtt90) cc_final: 0.7105 (mpt180) REVERT: C 263 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8659 (ttp) REVERT: C 720 CYS cc_start: 0.7235 (t) cc_final: 0.6954 (t) REVERT: C 768 LYS cc_start: 0.8614 (mmtt) cc_final: 0.7929 (mttp) REVERT: C 877 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: E 36 TRP cc_start: 0.7781 (m100) cc_final: 0.7250 (m100) REVERT: E 90 ASP cc_start: 0.7045 (m-30) cc_final: 0.6191 (t70) REVERT: G 26 TYR cc_start: 0.8205 (m-80) cc_final: 0.7036 (m-80) REVERT: G 71 ASN cc_start: 0.8322 (m110) cc_final: 0.8083 (m-40) REVERT: G 80 LEU cc_start: 0.7675 (mt) cc_final: 0.7192 (tp) REVERT: G 85 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6413 (pt0) outliers start: 87 outliers final: 60 residues processed: 427 average time/residue: 0.1512 time to fit residues: 100.5331 Evaluate side-chains 405 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 341 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 841 THR 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 48 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 51 PHE Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 92 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 539 THR 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 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 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 45 VAL 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 539 THR Chi-restraints excluded: chain C residue 556 SER 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 983 LEU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain G residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 115 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 202 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN A 744 GLN A 838 ASN A 992 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 737 GLN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 523 GLN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120935 restraints weight = 31343.150| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.01 r_work: 0.3184 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24399 Z= 0.225 Angle : 0.631 12.441 33240 Z= 0.329 Chirality : 0.048 0.198 3900 Planarity : 0.004 0.049 4197 Dihedral : 5.588 52.673 4104 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.55 % Allowed : 12.59 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 2961 helix: 1.62 (0.21), residues: 603 sheet: -0.21 (0.18), residues: 768 loop : -0.62 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 996 TYR 0.024 0.002 TYR B1049 PHE 0.026 0.002 PHE B 213 TRP 0.029 0.002 TRP D 36 HIS 0.005 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00547 (24324) covalent geometry : angle 0.61759 (33048) SS BOND : bond 0.00578 ( 33) SS BOND : angle 1.76339 ( 66) hydrogen bonds : bond 0.04399 ( 1012) hydrogen bonds : angle 5.64476 ( 2856) link_BETA1-4 : bond 0.00499 ( 15) link_BETA1-4 : angle 1.58488 ( 45) link_NAG-ASN : bond 0.00449 ( 27) link_NAG-ASN : angle 1.91236 ( 81) *********************** 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 448 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 357 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7490 (mtt90) cc_final: 0.7202 (mpt180) REVERT: A 185 PHE cc_start: 0.7734 (m-80) cc_final: 0.7525 (m-80) REVERT: A 221 LYS cc_start: 0.8088 (tttt) cc_final: 0.7687 (mmtm) REVERT: A 274 ASP cc_start: 0.7836 (t0) cc_final: 0.7514 (m-30) REVERT: A 604 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 720 CYS cc_start: 0.7282 (t) cc_final: 0.6889 (t) REVERT: A 768 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8027 (mttp) REVERT: A 1104 VAL cc_start: 0.8462 (t) cc_final: 0.8248 (p) REVERT: M 59 ASN cc_start: 0.7434 (t0) cc_final: 0.7044 (m-40) REVERT: M 90 ASP cc_start: 0.6925 (m-30) cc_final: 0.6225 (t0) REVERT: N 26 TYR cc_start: 0.7954 (m-80) cc_final: 0.6611 (m-80) REVERT: N 49 MET cc_start: 0.8890 (mmp) cc_final: 0.8652 (mmm) REVERT: N 50 ILE cc_start: 0.8982 (mt) cc_final: 0.8666 (tp) REVERT: N 80 LEU cc_start: 0.7475 (mt) cc_final: 0.7054 (tt) REVERT: N 85 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6212 (pt0) REVERT: B 183 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7358 (mpt180) REVERT: B 221 LYS cc_start: 0.8097 (tttt) cc_final: 0.7689 (mmtm) REVERT: B 274 ASP cc_start: 0.7962 (t0) cc_final: 0.7445 (m-30) REVERT: B 301 GLN cc_start: 0.9180 (tt0) cc_final: 0.8891 (tt0) REVERT: B 632 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: B 720 CYS cc_start: 0.7404 (t) cc_final: 0.7101 (t) REVERT: B 768 LYS cc_start: 0.8594 (mmtt) cc_final: 0.7911 (mttp) REVERT: B 877 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: B 886 TYR cc_start: 0.8232 (t80) cc_final: 0.7666 (t80) REVERT: D 59 ASN cc_start: 0.7513 (m110) cc_final: 0.7242 (t0) REVERT: D 90 ASP cc_start: 0.7040 (m-30) cc_final: 0.6376 (t0) REVERT: F 5 THR cc_start: 0.8665 (m) cc_final: 0.8344 (p) REVERT: F 50 ILE cc_start: 0.8999 (mt) cc_final: 0.8609 (tp) REVERT: F 71 ASN cc_start: 0.8348 (m-40) cc_final: 0.8032 (m110) REVERT: F 80 LEU cc_start: 0.7385 (tp) cc_final: 0.6850 (tt) REVERT: F 85 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6396 (pt0) REVERT: C 183 ARG cc_start: 0.7462 (mtt90) cc_final: 0.7103 (mpt180) REVERT: C 221 LYS cc_start: 0.8144 (tttt) cc_final: 0.7703 (mmtm) REVERT: C 604 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8360 (p) REVERT: C 720 CYS cc_start: 0.7239 (t) cc_final: 0.6958 (t) REVERT: C 768 LYS cc_start: 0.8677 (mmtt) cc_final: 0.7984 (mttp) REVERT: C 877 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: C 886 TYR cc_start: 0.8235 (t80) cc_final: 0.7732 (t80) REVERT: E 36 TRP cc_start: 0.7888 (m100) cc_final: 0.7464 (m100) REVERT: E 90 ASP cc_start: 0.6979 (m-30) cc_final: 0.6182 (t70) REVERT: G 26 TYR cc_start: 0.8206 (m-80) cc_final: 0.6929 (m-80) REVERT: G 80 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7170 (tp) REVERT: G 85 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6387 (pt0) outliers start: 91 outliers final: 76 residues processed: 415 average time/residue: 0.1354 time to fit residues: 89.0697 Evaluate side-chains 417 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 335 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 841 THR 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 48 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 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 632 GLN Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 984 GLN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain 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 215 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 556 SER 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 649 ASP Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 983 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 276 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 288 optimal weight: 9.9990 chunk 263 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 167 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 251 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN A 838 ASN A 992 GLN B 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123101 restraints weight = 31244.707| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.02 r_work: 0.3224 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24399 Z= 0.135 Angle : 0.573 11.963 33240 Z= 0.296 Chirality : 0.045 0.200 3900 Planarity : 0.004 0.040 4197 Dihedral : 5.361 53.179 4104 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.88 % Allowed : 14.27 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 2961 helix: 1.81 (0.21), residues: 603 sheet: -0.19 (0.18), residues: 762 loop : -0.63 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.027 0.002 TYR D 95 PHE 0.018 0.001 PHE C 185 TRP 0.035 0.001 TRP D 36 HIS 0.002 0.000 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00317 (24324) covalent geometry : angle 0.55796 (33048) SS BOND : bond 0.00407 ( 33) SS BOND : angle 2.00397 ( 66) hydrogen bonds : bond 0.03880 ( 1012) hydrogen bonds : angle 5.41255 ( 2856) link_BETA1-4 : bond 0.00528 ( 15) link_BETA1-4 : angle 1.39954 ( 45) link_NAG-ASN : bond 0.00463 ( 27) link_NAG-ASN : angle 1.83480 ( 81) *********************** 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 435 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 361 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7437 (mtt90) cc_final: 0.7115 (mpt180) REVERT: A 185 PHE cc_start: 0.7607 (m-80) cc_final: 0.7381 (m-80) REVERT: A 221 LYS cc_start: 0.8094 (tttt) cc_final: 0.7639 (mmtm) REVERT: A 274 ASP cc_start: 0.7830 (t0) cc_final: 0.7419 (m-30) REVERT: A 560 ASP cc_start: 0.8001 (t0) cc_final: 0.7568 (m-30) REVERT: A 604 THR cc_start: 0.8471 (m) cc_final: 0.8225 (p) REVERT: A 720 CYS cc_start: 0.7331 (t) cc_final: 0.6965 (t) REVERT: A 768 LYS cc_start: 0.8745 (mmtt) cc_final: 0.7993 (mttp) REVERT: A 1104 VAL cc_start: 0.8380 (t) cc_final: 0.8155 (p) REVERT: M 90 ASP cc_start: 0.6940 (m-30) cc_final: 0.6296 (t0) REVERT: M 94 TYR cc_start: 0.7833 (m-80) cc_final: 0.6865 (m-80) REVERT: N 5 THR cc_start: 0.8581 (m) cc_final: 0.8171 (p) REVERT: N 26 TYR cc_start: 0.7696 (m-80) cc_final: 0.6418 (m-80) REVERT: N 49 MET cc_start: 0.8822 (mmp) cc_final: 0.8550 (mmm) REVERT: N 50 ILE cc_start: 0.8924 (mt) cc_final: 0.8536 (tp) REVERT: N 80 LEU cc_start: 0.7484 (mt) cc_final: 0.6916 (tp) REVERT: N 85 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6170 (pt0) REVERT: B 50 ASP cc_start: 0.7995 (t0) cc_final: 0.7727 (t0) REVERT: B 183 ARG cc_start: 0.7596 (mtt90) cc_final: 0.7242 (mpt180) REVERT: B 221 LYS cc_start: 0.8143 (tttt) cc_final: 0.7712 (mmtm) REVERT: B 274 ASP cc_start: 0.7892 (t0) cc_final: 0.7273 (m-30) REVERT: B 301 GLN cc_start: 0.9179 (tt0) cc_final: 0.8870 (tt0) REVERT: B 604 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 720 CYS cc_start: 0.7351 (t) cc_final: 0.7046 (t) REVERT: B 768 LYS cc_start: 0.8603 (mmtt) cc_final: 0.7860 (mttp) REVERT: B 877 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7935 (pt0) REVERT: B 1104 VAL cc_start: 0.8414 (t) cc_final: 0.8155 (p) REVERT: D 59 ASN cc_start: 0.7550 (m110) cc_final: 0.7226 (t0) REVERT: D 90 ASP cc_start: 0.7010 (m-30) cc_final: 0.6374 (t70) REVERT: F 5 THR cc_start: 0.8593 (m) cc_final: 0.8268 (p) REVERT: F 26 TYR cc_start: 0.8058 (m-80) cc_final: 0.7714 (m-80) REVERT: F 50 ILE cc_start: 0.8851 (mt) cc_final: 0.8422 (tp) REVERT: F 71 ASN cc_start: 0.8319 (m-40) cc_final: 0.8070 (m110) REVERT: F 85 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6227 (pt0) REVERT: C 50 ASP cc_start: 0.7955 (t0) cc_final: 0.7670 (t0) REVERT: C 183 ARG cc_start: 0.7401 (mtt90) cc_final: 0.6975 (mpt180) REVERT: C 221 LYS cc_start: 0.8177 (tttt) cc_final: 0.7640 (mmtm) REVERT: C 720 CYS cc_start: 0.7160 (t) cc_final: 0.6885 (t) REVERT: C 768 LYS cc_start: 0.8668 (mmtt) cc_final: 0.7939 (mttp) REVERT: C 877 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: E 36 TRP cc_start: 0.7800 (m100) cc_final: 0.7298 (m100) REVERT: E 57 ARG cc_start: 0.6740 (ttp-170) cc_final: 0.6323 (ptt90) REVERT: E 90 ASP cc_start: 0.6873 (m-30) cc_final: 0.6190 (t70) REVERT: G 26 TYR cc_start: 0.7998 (m-80) cc_final: 0.6761 (m-80) REVERT: G 80 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7098 (tp) REVERT: G 85 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6363 (pt0) outliers start: 74 outliers final: 58 residues processed: 410 average time/residue: 0.1453 time to fit residues: 93.3808 Evaluate side-chains 403 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 341 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 301 GLN Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 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 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 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 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1118 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 556 SER 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 877 GLN Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1118 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 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 177 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 266 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 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 626 ASN A 992 GLN N 40 GLN B 214 ASN B 744 GLN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122634 restraints weight = 31277.566| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.99 r_work: 0.3220 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24399 Z= 0.153 Angle : 0.571 11.624 33240 Z= 0.295 Chirality : 0.045 0.195 3900 Planarity : 0.004 0.043 4197 Dihedral : 5.310 53.221 4104 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.27 % Allowed : 14.39 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.15), residues: 2961 helix: 1.86 (0.21), residues: 603 sheet: -0.19 (0.18), residues: 783 loop : -0.60 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 996 TYR 0.024 0.002 TYR A1049 PHE 0.014 0.001 PHE B 185 TRP 0.046 0.002 TRP D 36 HIS 0.004 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00367 (24324) covalent geometry : angle 0.55882 (33048) SS BOND : bond 0.00404 ( 33) SS BOND : angle 1.73388 ( 66) hydrogen bonds : bond 0.03855 ( 1012) hydrogen bonds : angle 5.35140 ( 2856) link_BETA1-4 : bond 0.00473 ( 15) link_BETA1-4 : angle 1.33737 ( 45) link_NAG-ASN : bond 0.00407 ( 27) link_NAG-ASN : angle 1.77662 ( 81) *********************** 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 429 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 345 time to evaluate : 0.767 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: 0.7491 (mtt90) cc_final: 0.7199 (mpt180) REVERT: A 185 PHE cc_start: 0.7786 (m-80) cc_final: 0.7577 (m-80) REVERT: A 221 LYS cc_start: 0.8135 (tttt) cc_final: 0.7748 (mmtm) REVERT: A 274 ASP cc_start: 0.7844 (t0) cc_final: 0.7487 (m-30) REVERT: A 604 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 720 CYS cc_start: 0.7274 (t) cc_final: 0.6874 (t) REVERT: A 768 LYS cc_start: 0.8699 (mmtt) cc_final: 0.7997 (mttp) REVERT: A 1104 VAL cc_start: 0.8351 (t) cc_final: 0.8143 (p) REVERT: M 90 ASP cc_start: 0.6965 (m-30) cc_final: 0.6447 (t0) REVERT: M 94 TYR cc_start: 0.7933 (m-80) cc_final: 0.6980 (m-80) REVERT: N 5 THR cc_start: 0.8566 (m) cc_final: 0.8147 (p) REVERT: N 26 TYR cc_start: 0.7769 (m-80) cc_final: 0.6457 (m-80) REVERT: N 50 ILE cc_start: 0.8912 (mt) cc_final: 0.8603 (tp) REVERT: N 80 LEU cc_start: 0.7502 (mt) cc_final: 0.6883 (tp) REVERT: N 85 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6042 (pt0) REVERT: B 50 ASP cc_start: 0.8033 (t0) cc_final: 0.7796 (t0) REVERT: B 183 ARG cc_start: 0.7660 (mtt90) cc_final: 0.7327 (mpt180) REVERT: B 221 LYS cc_start: 0.8115 (tttt) cc_final: 0.7759 (mmtm) REVERT: B 274 ASP cc_start: 0.7857 (t0) cc_final: 0.7272 (m-30) REVERT: B 301 GLN cc_start: 0.9158 (tt0) cc_final: 0.8859 (tt0) REVERT: B 604 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 720 CYS cc_start: 0.7371 (t) cc_final: 0.7070 (t) REVERT: B 768 LYS cc_start: 0.8615 (mmtt) cc_final: 0.7893 (mttp) REVERT: B 877 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: B 1104 VAL cc_start: 0.8400 (t) cc_final: 0.8167 (p) REVERT: D 59 ASN cc_start: 0.7549 (m110) cc_final: 0.7263 (t0) REVERT: D 90 ASP cc_start: 0.6978 (m-30) cc_final: 0.6418 (t70) REVERT: F 5 THR cc_start: 0.8609 (m) cc_final: 0.8302 (p) REVERT: F 26 TYR cc_start: 0.8057 (m-80) cc_final: 0.7667 (m-80) REVERT: F 50 ILE cc_start: 0.8803 (mt) cc_final: 0.8359 (tp) REVERT: F 85 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6204 (pt0) REVERT: C 50 ASP cc_start: 0.7965 (t0) cc_final: 0.7672 (t0) REVERT: C 183 ARG cc_start: 0.7476 (mtt90) cc_final: 0.7072 (mpt180) REVERT: C 221 LYS cc_start: 0.8093 (tttt) cc_final: 0.7606 (mmtm) REVERT: C 604 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.8272 (p) REVERT: C 720 CYS cc_start: 0.7235 (t) cc_final: 0.6978 (t) REVERT: C 768 LYS cc_start: 0.8665 (mmtt) cc_final: 0.7963 (mttp) REVERT: C 877 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: E 36 TRP cc_start: 0.7851 (m100) cc_final: 0.7288 (m100) REVERT: E 57 ARG cc_start: 0.6848 (ttp-170) cc_final: 0.6154 (ptt90) REVERT: E 59 ASN cc_start: 0.7374 (t0) cc_final: 0.6666 (m-40) REVERT: E 90 ASP cc_start: 0.6896 (m-30) cc_final: 0.6301 (t70) REVERT: G 4 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5361 (tt) REVERT: G 26 TYR cc_start: 0.8019 (m-80) cc_final: 0.6741 (m-80) REVERT: G 80 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7103 (tp) REVERT: G 85 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6344 (pt0) outliers start: 84 outliers final: 67 residues processed: 405 average time/residue: 0.1429 time to fit residues: 91.2920 Evaluate side-chains 403 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 329 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 301 GLN Chi-restraints excluded: chain A residue 533 THR 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 649 ASP 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 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 215 THR 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 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 75 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 ASN 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 792 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 983 LEU 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 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 1 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 259 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 273 optimal weight: 0.5980 chunk 264 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN A 992 GLN N 40 GLN B 214 ASN B 992 GLN D 39 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN F 71 ASN C 214 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.155341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122500 restraints weight = 31391.983| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.06 r_work: 0.3199 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24399 Z= 0.165 Angle : 0.575 11.651 33240 Z= 0.297 Chirality : 0.045 0.195 3900 Planarity : 0.004 0.045 4197 Dihedral : 5.313 58.001 4104 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.70 % Allowed : 14.27 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 2961 helix: 1.83 (0.21), residues: 603 sheet: -0.22 (0.18), residues: 795 loop : -0.63 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 996 TYR 0.025 0.002 TYR E 95 PHE 0.018 0.001 PHE C 213 TRP 0.032 0.001 TRP D 36 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00397 (24324) covalent geometry : angle 0.56412 (33048) SS BOND : bond 0.00519 ( 33) SS BOND : angle 1.55113 ( 66) hydrogen bonds : bond 0.03863 ( 1012) hydrogen bonds : angle 5.33883 ( 2856) link_BETA1-4 : bond 0.00483 ( 15) link_BETA1-4 : angle 1.30697 ( 45) link_NAG-ASN : bond 0.00389 ( 27) link_NAG-ASN : angle 1.76250 ( 81) *********************** 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 432 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 337 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7546 (mtt90) cc_final: 0.7221 (mpt180) REVERT: A 185 PHE cc_start: 0.7864 (m-80) cc_final: 0.7664 (m-80) REVERT: A 221 LYS cc_start: 0.8135 (tttt) cc_final: 0.7751 (mmtm) REVERT: A 274 ASP cc_start: 0.7864 (t0) cc_final: 0.7510 (m-30) REVERT: A 560 ASP cc_start: 0.8072 (t0) cc_final: 0.7621 (m-30) REVERT: A 604 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8307 (p) REVERT: A 720 CYS cc_start: 0.7318 (t) cc_final: 0.6915 (t) REVERT: A 768 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8044 (mttp) REVERT: A 1104 VAL cc_start: 0.8377 (t) cc_final: 0.8169 (p) REVERT: M 90 ASP cc_start: 0.6979 (m-30) cc_final: 0.6497 (t0) REVERT: M 94 TYR cc_start: 0.7982 (m-80) cc_final: 0.7056 (m-80) REVERT: N 5 THR cc_start: 0.8559 (m) cc_final: 0.8137 (p) REVERT: N 26 TYR cc_start: 0.7762 (m-80) cc_final: 0.6440 (m-80) REVERT: N 49 MET cc_start: 0.9026 (mmm) cc_final: 0.8435 (mmm) REVERT: N 50 ILE cc_start: 0.8925 (mt) cc_final: 0.8625 (tp) REVERT: N 80 LEU cc_start: 0.7503 (mt) cc_final: 0.6879 (tp) REVERT: N 85 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6050 (pt0) REVERT: B 50 ASP cc_start: 0.8063 (t0) cc_final: 0.7849 (t0) REVERT: B 183 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7344 (mpt180) REVERT: B 221 LYS cc_start: 0.8115 (tttt) cc_final: 0.7755 (mmtm) REVERT: B 274 ASP cc_start: 0.7871 (t0) cc_final: 0.7281 (m-30) REVERT: B 301 GLN cc_start: 0.9184 (tt0) cc_final: 0.8908 (tt0) REVERT: B 558 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5823 (t80) REVERT: B 604 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8347 (p) REVERT: B 720 CYS cc_start: 0.7432 (t) cc_final: 0.7150 (t) REVERT: B 768 LYS cc_start: 0.8599 (mmtt) cc_final: 0.7888 (mttp) REVERT: B 877 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: B 1104 VAL cc_start: 0.8422 (t) cc_final: 0.8194 (p) REVERT: D 59 ASN cc_start: 0.7523 (m110) cc_final: 0.7223 (t0) REVERT: D 90 ASP cc_start: 0.6962 (m-30) cc_final: 0.6430 (t70) REVERT: F 5 THR cc_start: 0.8612 (m) cc_final: 0.8259 (p) REVERT: F 26 TYR cc_start: 0.8171 (m-80) cc_final: 0.7727 (m-80) REVERT: F 50 ILE cc_start: 0.8816 (mt) cc_final: 0.8379 (tp) REVERT: F 85 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6146 (pt0) REVERT: C 50 ASP cc_start: 0.8028 (t0) cc_final: 0.7761 (t0) REVERT: C 183 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7129 (mpt180) REVERT: C 221 LYS cc_start: 0.8163 (tttt) cc_final: 0.7689 (mmtm) REVERT: C 599 GLN cc_start: 0.8702 (mt0) cc_final: 0.8454 (mt0) REVERT: C 604 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8300 (p) REVERT: C 720 CYS cc_start: 0.7274 (t) cc_final: 0.7018 (t) REVERT: C 768 LYS cc_start: 0.8697 (mmtt) cc_final: 0.7984 (mttp) REVERT: C 877 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: E 36 TRP cc_start: 0.7838 (m100) cc_final: 0.7159 (m100) REVERT: E 57 ARG cc_start: 0.6900 (ttp-170) cc_final: 0.6011 (ptt90) REVERT: E 59 ASN cc_start: 0.7341 (t0) cc_final: 0.6623 (m-40) REVERT: E 90 ASP cc_start: 0.6927 (m-30) cc_final: 0.6258 (t70) REVERT: G 4 LEU cc_start: 0.5758 (OUTLIER) cc_final: 0.5487 (tt) REVERT: G 26 TYR cc_start: 0.7981 (m-80) cc_final: 0.6718 (m-80) REVERT: G 80 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7143 (tp) REVERT: G 85 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6286 (pt0) outliers start: 95 outliers final: 73 residues processed: 405 average time/residue: 0.1459 time to fit residues: 93.0142 Evaluate side-chains 412 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 301 GLN Chi-restraints excluded: chain A residue 533 THR 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 649 ASP Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 877 GLN Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1059 THR 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 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 214 ASN Chi-restraints excluded: chain B residue 215 THR 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 558 PHE Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 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 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 215 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 589 ASN 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 769 GLN 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 48 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 194 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN A 992 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN B 214 ASN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN E 39 GLN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121773 restraints weight = 31590.848| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.06 r_work: 0.3182 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24399 Z= 0.184 Angle : 0.586 11.876 33240 Z= 0.302 Chirality : 0.046 0.195 3900 Planarity : 0.004 0.045 4197 Dihedral : 5.291 53.066 4104 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.43 % Allowed : 14.85 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 2961 helix: 1.76 (0.21), residues: 603 sheet: -0.26 (0.18), residues: 801 loop : -0.65 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 996 TYR 0.022 0.002 TYR A1049 PHE 0.016 0.002 PHE C1024 TRP 0.030 0.001 TRP D 36 HIS 0.004 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00445 (24324) covalent geometry : angle 0.57507 (33048) SS BOND : bond 0.00431 ( 33) SS BOND : angle 1.51000 ( 66) hydrogen bonds : bond 0.03942 ( 1012) hydrogen bonds : angle 5.37468 ( 2856) link_BETA1-4 : bond 0.00481 ( 15) link_BETA1-4 : angle 1.26931 ( 45) link_NAG-ASN : bond 0.00370 ( 27) link_NAG-ASN : angle 1.75731 ( 81) *********************** 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 425 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 337 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 183 ARG cc_start: 0.7514 (mtt90) cc_final: 0.7113 (mpt180) REVERT: A 185 PHE cc_start: 0.7817 (m-80) cc_final: 0.7614 (m-80) REVERT: A 221 LYS cc_start: 0.8180 (tttt) cc_final: 0.7753 (mmtm) REVERT: A 274 ASP cc_start: 0.7870 (t0) cc_final: 0.7473 (m-30) REVERT: A 560 ASP cc_start: 0.7986 (t0) cc_final: 0.7562 (m-30) REVERT: A 604 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 720 CYS cc_start: 0.7363 (t) cc_final: 0.6965 (t) REVERT: A 768 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8008 (mttp) REVERT: A 1104 VAL cc_start: 0.8463 (t) cc_final: 0.8227 (p) REVERT: M 90 ASP cc_start: 0.6917 (m-30) cc_final: 0.6473 (t0) REVERT: M 94 TYR cc_start: 0.7989 (m-80) cc_final: 0.7090 (m-80) REVERT: N 5 THR cc_start: 0.8570 (m) cc_final: 0.8124 (p) REVERT: N 26 TYR cc_start: 0.7741 (m-80) cc_final: 0.6356 (m-80) REVERT: N 49 MET cc_start: 0.9019 (mmm) cc_final: 0.8473 (mmm) REVERT: N 50 ILE cc_start: 0.8932 (mt) cc_final: 0.8519 (tp) REVERT: N 80 LEU cc_start: 0.7465 (mt) cc_final: 0.6812 (tp) REVERT: N 85 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6046 (pt0) REVERT: B 50 ASP cc_start: 0.8066 (t0) cc_final: 0.7859 (t0) REVERT: B 183 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7254 (mpt180) REVERT: B 274 ASP cc_start: 0.7869 (t0) cc_final: 0.7212 (m-30) REVERT: B 301 GLN cc_start: 0.9223 (tt0) cc_final: 0.8935 (tt0) REVERT: B 558 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5814 (t80) REVERT: B 604 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 720 CYS cc_start: 0.7461 (t) cc_final: 0.7165 (t) REVERT: B 768 LYS cc_start: 0.8674 (mmtt) cc_final: 0.7899 (mttp) REVERT: B 877 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: B 1104 VAL cc_start: 0.8462 (t) cc_final: 0.8212 (p) REVERT: D 59 ASN cc_start: 0.7523 (m110) cc_final: 0.7147 (t0) REVERT: D 90 ASP cc_start: 0.6967 (m-30) cc_final: 0.6468 (t70) REVERT: F 5 THR cc_start: 0.8597 (m) cc_final: 0.8219 (p) REVERT: F 26 TYR cc_start: 0.8131 (m-80) cc_final: 0.7673 (m-80) REVERT: F 50 ILE cc_start: 0.8819 (mt) cc_final: 0.8349 (tp) REVERT: F 85 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6137 (pt0) REVERT: C 183 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7036 (mpt180) REVERT: C 221 LYS cc_start: 0.8189 (tttt) cc_final: 0.7696 (mmtm) REVERT: C 604 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8281 (p) REVERT: C 720 CYS cc_start: 0.7302 (t) cc_final: 0.7043 (t) REVERT: C 768 LYS cc_start: 0.8734 (mmtt) cc_final: 0.7980 (mttp) REVERT: C 877 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: E 36 TRP cc_start: 0.7793 (m100) cc_final: 0.7085 (m100) REVERT: E 57 ARG cc_start: 0.6933 (ttp-170) cc_final: 0.5967 (ptt90) REVERT: E 59 ASN cc_start: 0.7339 (t0) cc_final: 0.6593 (m-40) REVERT: E 90 ASP cc_start: 0.6933 (m-30) cc_final: 0.6289 (t70) REVERT: G 4 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5441 (tt) REVERT: G 26 TYR cc_start: 0.7966 (m-80) cc_final: 0.6649 (m-80) REVERT: G 80 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7121 (tp) REVERT: G 85 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6357 (pt0) outliers start: 88 outliers final: 72 residues processed: 400 average time/residue: 0.1508 time to fit residues: 94.3698 Evaluate side-chains 410 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 301 GLN Chi-restraints excluded: chain A residue 533 THR 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 649 ASP Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 792 LEU 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 962 ILE Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1059 THR 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 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 214 ASN Chi-restraints excluded: chain B residue 215 THR 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 558 PHE Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 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 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 215 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 533 THR 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 649 ASP Chi-restraints excluded: chain C residue 717 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 983 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 155 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 255 optimal weight: 0.3980 chunk 184 optimal weight: 9.9990 chunk 290 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN A 992 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN B 214 ASN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 737 GLN ** 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 = 0.3911 r_free = 0.3911 target = 0.155401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122658 restraints weight = 31396.904| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.04 r_work: 0.3196 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24399 Z= 0.150 Angle : 0.571 12.107 33240 Z= 0.294 Chirality : 0.045 0.193 3900 Planarity : 0.004 0.046 4197 Dihedral : 5.205 53.173 4104 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.35 % Allowed : 14.93 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 2961 helix: 1.79 (0.21), residues: 606 sheet: -0.23 (0.18), residues: 801 loop : -0.63 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 996 TYR 0.024 0.002 TYR E 95 PHE 0.019 0.001 PHE C 213 TRP 0.027 0.001 TRP D 36 HIS 0.005 0.001 HIS M 32 Details of bonding type rmsd covalent geometry : bond 0.00359 (24324) covalent geometry : angle 0.56024 (33048) SS BOND : bond 0.00389 ( 33) SS BOND : angle 1.47861 ( 66) hydrogen bonds : bond 0.03786 ( 1012) hydrogen bonds : angle 5.31767 ( 2856) link_BETA1-4 : bond 0.00465 ( 15) link_BETA1-4 : angle 1.22493 ( 45) link_NAG-ASN : bond 0.00374 ( 27) link_NAG-ASN : angle 1.71946 ( 81) ********************** 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 424 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 338 time to evaluate : 0.799 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: 0.7559 (mtt90) cc_final: 0.7213 (mpt180) REVERT: A 185 PHE cc_start: 0.7882 (m-80) cc_final: 0.7667 (m-80) REVERT: A 221 LYS cc_start: 0.8126 (tttt) cc_final: 0.7748 (mmtm) REVERT: A 274 ASP cc_start: 0.7875 (t0) cc_final: 0.7527 (m-30) REVERT: A 560 ASP cc_start: 0.8010 (t0) cc_final: 0.7594 (m-30) REVERT: A 604 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 720 CYS cc_start: 0.7345 (t) cc_final: 0.6950 (t) REVERT: A 768 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8029 (mttp) REVERT: A 1104 VAL cc_start: 0.8396 (t) cc_final: 0.8187 (p) REVERT: M 90 ASP cc_start: 0.6966 (m-30) cc_final: 0.6454 (t0) REVERT: M 94 TYR cc_start: 0.8027 (m-80) cc_final: 0.7192 (m-80) REVERT: N 5 THR cc_start: 0.8612 (m) cc_final: 0.8188 (p) REVERT: N 26 TYR cc_start: 0.7732 (m-80) cc_final: 0.6394 (m-80) REVERT: N 49 MET cc_start: 0.9028 (mmm) cc_final: 0.8467 (mmm) REVERT: N 50 ILE cc_start: 0.8918 (mt) cc_final: 0.8594 (tp) REVERT: N 80 LEU cc_start: 0.7313 (mt) cc_final: 0.6794 (tp) REVERT: N 85 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6086 (pt0) REVERT: B 183 ARG cc_start: 0.7679 (mtt90) cc_final: 0.7342 (mpt180) REVERT: B 274 ASP cc_start: 0.7867 (t0) cc_final: 0.7260 (m-30) REVERT: B 285 GLU cc_start: 0.8434 (tp30) cc_final: 0.8176 (tp30) REVERT: B 301 GLN cc_start: 0.9191 (tt0) cc_final: 0.8911 (tt0) REVERT: B 558 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5917 (t80) REVERT: B 604 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 720 CYS cc_start: 0.7396 (t) cc_final: 0.7113 (t) REVERT: B 768 LYS cc_start: 0.8628 (mmtt) cc_final: 0.7908 (mttp) REVERT: B 877 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7935 (pt0) REVERT: B 1104 VAL cc_start: 0.8414 (t) cc_final: 0.8177 (p) REVERT: D 59 ASN cc_start: 0.7564 (m110) cc_final: 0.7234 (t0) REVERT: D 90 ASP cc_start: 0.6985 (m-30) cc_final: 0.6491 (t70) REVERT: F 5 THR cc_start: 0.8577 (m) cc_final: 0.8230 (p) REVERT: F 26 TYR cc_start: 0.8097 (m-80) cc_final: 0.7549 (m-80) REVERT: F 50 ILE cc_start: 0.8712 (mt) cc_final: 0.8254 (tp) REVERT: F 55 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6948 (mttt) REVERT: F 85 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6147 (pt0) REVERT: C 183 ARG cc_start: 0.7559 (mtt90) cc_final: 0.7160 (mpt180) REVERT: C 221 LYS cc_start: 0.8079 (tttt) cc_final: 0.7641 (mmtm) REVERT: C 599 GLN cc_start: 0.8711 (mt0) cc_final: 0.8471 (mt0) REVERT: C 720 CYS cc_start: 0.7280 (t) cc_final: 0.7026 (t) REVERT: C 768 LYS cc_start: 0.8711 (mmtt) cc_final: 0.7987 (mttp) REVERT: C 877 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: E 36 TRP cc_start: 0.7802 (m100) cc_final: 0.7110 (m100) REVERT: E 57 ARG cc_start: 0.6952 (ttp-170) cc_final: 0.6042 (ptt90) REVERT: E 59 ASN cc_start: 0.7275 (t0) cc_final: 0.6599 (m-40) REVERT: E 90 ASP cc_start: 0.6886 (m-30) cc_final: 0.6286 (t70) REVERT: G 4 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5520 (tt) REVERT: G 26 TYR cc_start: 0.7963 (m-80) cc_final: 0.6659 (m-80) REVERT: G 50 ILE cc_start: 0.8850 (mt) cc_final: 0.8422 (tp) REVERT: G 80 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7128 (tp) REVERT: G 85 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6391 (pt0) outliers start: 86 outliers final: 69 residues processed: 401 average time/residue: 0.1447 time to fit residues: 90.4457 Evaluate side-chains 409 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 333 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 533 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 649 ASP Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 837 PHE 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 1059 THR 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 40 GLN Chi-restraints excluded: chain N residue 58 SER 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 215 THR 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 558 PHE Chi-restraints excluded: chain B residue 589 ASN Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 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 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 215 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 539 THR 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 883 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 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 291 optimal weight: 0.1980 chunk 266 optimal weight: 0.8980 chunk 279 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 284 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN A 838 ASN A 992 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN B 992 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3920 r_free = 0.3920 target = 0.156277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123500 restraints weight = 31231.655| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.99 r_work: 0.3212 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4375 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= 0.130 Angle : 0.559 12.535 33240 Z= 0.287 Chirality : 0.045 0.190 3900 Planarity : 0.004 0.056 4197 Dihedral : 5.099 53.322 4104 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.85 % Allowed : 15.32 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 2961 helix: 1.86 (0.21), residues: 606 sheet: -0.16 (0.18), residues: 804 loop : -0.60 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 98 TYR 0.021 0.001 TYR A1049 PHE 0.022 0.001 PHE C 213 TRP 0.041 0.002 TRP M 36 HIS 0.014 0.001 HIS N 41 Details of bonding type rmsd covalent geometry : bond 0.00305 (24324) covalent geometry : angle 0.54913 (33048) SS BOND : bond 0.00360 ( 33) SS BOND : angle 1.41870 ( 66) hydrogen bonds : bond 0.03655 ( 1012) hydrogen bonds : angle 5.24594 ( 2856) link_BETA1-4 : bond 0.00498 ( 15) link_BETA1-4 : angle 1.19520 ( 45) link_NAG-ASN : bond 0.00373 ( 27) link_NAG-ASN : angle 1.66550 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5062.08 seconds wall clock time: 87 minutes 32.36 seconds (5252.36 seconds total)