Starting phenix.real_space_refine on Thu Jun 26 05:52:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h00_34407/06_2025/8h00_34407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h00_34407/06_2025/8h00_34407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h00_34407/06_2025/8h00_34407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h00_34407/06_2025/8h00_34407.map" model { file = "/net/cci-nas-00/data/ceres_data/8h00_34407/06_2025/8h00_34407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h00_34407/06_2025/8h00_34407.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.044 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 141 5.16 5 C 19242 2.51 5 N 4940 2.21 5 O 5858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 2.54s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30181 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8121 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 57, 'TRANS': 976} Chain breaks: 8 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} 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: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 19.60, per 1000 atoms: 0.65 Number of scatterers: 30181 At special positions: 0 Unit cell: (146.432, 153.92, 196.352, 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 141 16.00 O 5858 8.00 N 4940 7.00 C 19242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 50 " distance=2.04 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1074 " " NAG W 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 3.8 seconds 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7078 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 62 sheets defined 20.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.527A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.718A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.142A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.595A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.228A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.426A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.237A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.266A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.904A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.549A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.534A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.233A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.683A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.645A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.036A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.431A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.931A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.867A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.572A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.732A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.671A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.561A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.110A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.580A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.235A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.613A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.608A pdb=" N LYS E 66 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.914A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.630A pdb=" N LYS G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.024A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.602A pdb=" N LYS I 66 " --> pdb=" O SER I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.878A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.533A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.169A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.578A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.078A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.199A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.972A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.593A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.087A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.798A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.520A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.499A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.323A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.514A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.703A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.282A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.807A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.976A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.626A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.626A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.958A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.776A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.616A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.808A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.062A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.395A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.617A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.183A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.910A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.621A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.621A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.350A pdb=" N VAL D 11 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 105 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.627A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.340A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.570A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.471A pdb=" N VAL F 11 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS F 110 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU F 13 " --> pdb=" O LYS F 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.438A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.781A pdb=" N MET G 83 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.886A pdb=" N LEU G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 60 through 61 removed outlier: 4.249A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP G 36 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 51 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.511A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.378A pdb=" N VAL H 11 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 105 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.525A pdb=" N THR I 20 " --> pdb=" O SER I 6 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.372A pdb=" N MET I 34 " --> pdb=" O CYS I 50 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3237 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: 14.99 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9551 1.34 - 1.46: 7701 1.46 - 1.59: 13448 1.59 - 1.71: 0 1.71 - 1.83: 177 Bond restraints: 30877 Sorted by residual: bond pdb=" N VAL A1033 " pdb=" CA VAL A1033 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.21e+00 bond pdb=" N GLN F 70 " pdb=" CA GLN F 70 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.10e+00 bond pdb=" N GLY A1035 " pdb=" CA GLY A1035 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.19e-02 7.06e+03 7.62e+00 bond pdb=" N GLN F 38 " pdb=" CA GLN F 38 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.78e+00 bond pdb=" N LEU A1034 " pdb=" CA LEU A1034 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.66e+00 ... (remaining 30872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 40642 1.50 - 3.01: 1178 3.01 - 4.51: 166 4.51 - 6.01: 21 6.01 - 7.51: 7 Bond angle restraints: 42014 Sorted by residual: angle pdb=" N GLU B 516 " pdb=" CA GLU B 516 " pdb=" C GLU B 516 " ideal model delta sigma weight residual 114.75 110.04 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CA GLY A1035 " pdb=" C GLY A1035 " pdb=" O GLY A1035 " ideal model delta sigma weight residual 121.38 118.23 3.15 9.40e-01 1.13e+00 1.12e+01 angle pdb=" N ARG C 102 " pdb=" CA ARG C 102 " pdb=" C ARG C 102 " ideal model delta sigma weight residual 113.88 110.10 3.78 1.23e+00 6.61e-01 9.43e+00 angle pdb=" N SER I 6 " pdb=" CA SER I 6 " pdb=" C SER I 6 " ideal model delta sigma weight residual 108.34 112.26 -3.92 1.31e+00 5.83e-01 8.94e+00 angle pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " ideal model delta sigma weight residual 112.00 118.51 -6.51 2.20e+00 2.07e-01 8.77e+00 ... (remaining 42009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17282 17.92 - 35.84: 1331 35.84 - 53.76: 238 53.76 - 71.68: 59 71.68 - 89.60: 35 Dihedral angle restraints: 18945 sinusoidal: 7926 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -11.80 -74.20 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 33.41 59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 33.61 59.39 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 18942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4016 0.057 - 0.113: 782 0.113 - 0.170: 80 0.170 - 0.227: 1 0.227 - 0.283: 4 Chirality restraints: 4883 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4880 not shown) Planarity restraints: 5384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 112 " -0.017 2.00e-02 2.50e+03 1.80e-02 8.10e+00 pdb=" CG TRP G 112 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP G 112 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 112 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 112 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP G 112 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO C 987 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO C 986 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.029 5.00e-02 4.00e+02 ... (remaining 5381 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1738 2.73 - 3.27: 29664 3.27 - 3.81: 47931 3.81 - 4.36: 56474 4.36 - 4.90: 100762 Nonbonded interactions: 236569 Sorted by model distance: nonbonded pdb=" OD1 ASP B 53 " pdb=" N LEU B 54 " model vdw 2.184 3.120 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLN C 992 " pdb=" NH2 ARG C 995 " model vdw 2.222 3.120 ... (remaining 236564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) selection = (chain 'C' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 9.690 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: 0.070 Extract box with map and model: 1.240 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 73.900 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30973 Z= 0.209 Angle : 0.628 11.874 42251 Z= 0.331 Chirality : 0.046 0.283 4883 Planarity : 0.004 0.058 5354 Dihedral : 13.254 89.605 11714 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3737 helix: 1.87 (0.21), residues: 651 sheet: 0.08 (0.17), residues: 915 loop : -0.88 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 112 HIS 0.004 0.001 HIS B1058 PHE 0.032 0.002 PHE C 823 TYR 0.033 0.001 TYR C 904 ARG 0.013 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 30) link_NAG-ASN : angle 3.36100 ( 90) link_BETA1-4 : bond 0.00340 ( 15) link_BETA1-4 : angle 1.04814 ( 45) hydrogen bonds : bond 0.19103 ( 1157) hydrogen bonds : angle 8.06085 ( 3237) SS BOND : bond 0.00297 ( 51) SS BOND : angle 1.29396 ( 102) covalent geometry : bond 0.00455 (30877) covalent geometry : angle 0.60583 (42014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8304 (ptm) cc_final: 0.8026 (ptm) REVERT: B 368 LEU cc_start: 0.8858 (mt) cc_final: 0.8099 (tp) REVERT: E 11 VAL cc_start: 0.7489 (t) cc_final: 0.7121 (m) REVERT: E 34 MET cc_start: 0.7986 (tpp) cc_final: 0.7599 (tpp) REVERT: E 71 ILE cc_start: 0.8027 (tt) cc_final: 0.7800 (tt) REVERT: F 76 ASN cc_start: 0.8387 (m-40) cc_final: 0.7892 (p0) REVERT: F 106 GLU cc_start: 0.8611 (pm20) cc_final: 0.8305 (pm20) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.5722 time to fit residues: 253.9720 Evaluate side-chains 183 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 8.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 343 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 779 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN D 31 ASN D 90 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 37 GLN F 70 GLN H 31 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.063048 restraints weight = 76030.136| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.45 r_work: 0.2860 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30973 Z= 0.162 Angle : 0.581 10.635 42251 Z= 0.299 Chirality : 0.045 0.310 4883 Planarity : 0.004 0.067 5354 Dihedral : 6.341 59.125 5012 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.26 % Favored : 96.66 % Rotamer: Outliers : 0.55 % Allowed : 5.39 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 3737 helix: 1.84 (0.21), residues: 666 sheet: 0.27 (0.17), residues: 936 loop : -0.91 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 112 HIS 0.004 0.001 HIS B 519 PHE 0.027 0.001 PHE A 374 TYR 0.021 0.001 TYR B 756 ARG 0.006 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 30) link_NAG-ASN : angle 3.10327 ( 90) link_BETA1-4 : bond 0.00454 ( 15) link_BETA1-4 : angle 1.07402 ( 45) hydrogen bonds : bond 0.04905 ( 1157) hydrogen bonds : angle 6.04679 ( 3237) SS BOND : bond 0.00321 ( 51) SS BOND : angle 1.12665 ( 102) covalent geometry : bond 0.00377 (30877) covalent geometry : angle 0.56076 (42014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8631 (m-10) cc_final: 0.8386 (m-10) REVERT: B 200 TYR cc_start: 0.8440 (m-80) cc_final: 0.8046 (m-80) REVERT: B 318 PHE cc_start: 0.8016 (t80) cc_final: 0.7745 (t80) REVERT: B 368 LEU cc_start: 0.8887 (mt) cc_final: 0.8211 (tp) REVERT: B 1092 GLU cc_start: 0.8412 (pm20) cc_final: 0.8096 (pt0) REVERT: E 71 ILE cc_start: 0.7927 (tt) cc_final: 0.7648 (tt) REVERT: F 106 GLU cc_start: 0.8746 (pm20) cc_final: 0.8288 (pm20) REVERT: G 34 MET cc_start: 0.7701 (tpp) cc_final: 0.7440 (tpp) outliers start: 18 outliers final: 11 residues processed: 217 average time/residue: 0.3662 time to fit residues: 134.7487 Evaluate side-chains 187 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 105 optimal weight: 6.9990 chunk 333 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 505 HIS C1142 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060408 restraints weight = 75660.092| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.36 r_work: 0.2823 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30973 Z= 0.258 Angle : 0.623 9.201 42251 Z= 0.319 Chirality : 0.047 0.303 4883 Planarity : 0.004 0.061 5354 Dihedral : 5.988 59.684 5012 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 1.00 % Allowed : 8.19 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 3737 helix: 1.70 (0.21), residues: 668 sheet: 0.04 (0.16), residues: 988 loop : -0.99 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 112 HIS 0.006 0.001 HIS A1058 PHE 0.038 0.002 PHE B 374 TYR 0.019 0.002 TYR C1067 ARG 0.009 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 30) link_NAG-ASN : angle 3.20673 ( 90) link_BETA1-4 : bond 0.00258 ( 15) link_BETA1-4 : angle 1.19046 ( 45) hydrogen bonds : bond 0.05120 ( 1157) hydrogen bonds : angle 5.67378 ( 3237) SS BOND : bond 0.00396 ( 51) SS BOND : angle 1.29067 ( 102) covalent geometry : bond 0.00612 (30877) covalent geometry : angle 0.60228 (42014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 3.624 Fit side-chains revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8572 (m-10) cc_final: 0.8165 (m-10) REVERT: B 200 TYR cc_start: 0.8495 (m-80) cc_final: 0.8052 (m-80) REVERT: B 368 LEU cc_start: 0.8922 (mt) cc_final: 0.8208 (tp) REVERT: B 1092 GLU cc_start: 0.8495 (pm20) cc_final: 0.8212 (pt0) REVERT: B 1106 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8814 (pt0) REVERT: C 314 GLN cc_start: 0.8843 (tt0) cc_final: 0.8481 (tm-30) REVERT: C 1002 GLN cc_start: 0.8692 (mm110) cc_final: 0.8361 (tm-30) REVERT: E 46 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: E 71 ILE cc_start: 0.7936 (tt) cc_final: 0.7679 (tt) REVERT: F 106 GLU cc_start: 0.8672 (pm20) cc_final: 0.8208 (pm20) outliers start: 33 outliers final: 22 residues processed: 209 average time/residue: 0.4068 time to fit residues: 146.7774 Evaluate side-chains 199 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 323 optimal weight: 4.9990 chunk 327 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 285 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 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 901 GLN B 218 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063207 restraints weight = 75741.271| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.38 r_work: 0.2871 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30973 Z= 0.112 Angle : 0.533 10.857 42251 Z= 0.272 Chirality : 0.044 0.292 4883 Planarity : 0.004 0.057 5354 Dihedral : 5.485 59.905 5012 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.76 % Favored : 97.16 % Rotamer: Outliers : 1.07 % Allowed : 9.56 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3737 helix: 1.92 (0.21), residues: 671 sheet: 0.20 (0.17), residues: 948 loop : -0.92 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.000 HIS B 519 PHE 0.021 0.001 PHE A 374 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 30) link_NAG-ASN : angle 2.75801 ( 90) link_BETA1-4 : bond 0.00400 ( 15) link_BETA1-4 : angle 1.01690 ( 45) hydrogen bonds : bond 0.04069 ( 1157) hydrogen bonds : angle 5.35808 ( 3237) SS BOND : bond 0.00305 ( 51) SS BOND : angle 1.21039 ( 102) covalent geometry : bond 0.00251 (30877) covalent geometry : angle 0.51417 (42014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8541 (m-10) cc_final: 0.8318 (m-10) REVERT: B 200 TYR cc_start: 0.8472 (m-80) cc_final: 0.8044 (m-80) REVERT: B 368 LEU cc_start: 0.8942 (mt) cc_final: 0.8280 (tp) REVERT: B 1092 GLU cc_start: 0.8535 (pm20) cc_final: 0.8159 (pt0) REVERT: C 314 GLN cc_start: 0.8820 (tt0) cc_final: 0.8498 (tm-30) REVERT: C 393 THR cc_start: 0.8183 (p) cc_final: 0.7826 (t) REVERT: C 1002 GLN cc_start: 0.8694 (mm110) cc_final: 0.8343 (tm-30) REVERT: E 71 ILE cc_start: 0.7936 (tt) cc_final: 0.7720 (tt) REVERT: F 106 GLU cc_start: 0.8671 (pm20) cc_final: 0.8423 (pm20) outliers start: 35 outliers final: 20 residues processed: 220 average time/residue: 0.3679 time to fit residues: 138.1916 Evaluate side-chains 196 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 101 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 338 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 376 optimal weight: 0.0020 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.063169 restraints weight = 75566.313| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.35 r_work: 0.2867 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30973 Z= 0.120 Angle : 0.527 10.327 42251 Z= 0.267 Chirality : 0.044 0.281 4883 Planarity : 0.004 0.056 5354 Dihedral : 5.177 58.475 5012 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 1.55 % Allowed : 9.89 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3737 helix: 1.98 (0.21), residues: 671 sheet: 0.29 (0.17), residues: 933 loop : -0.91 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS B 519 PHE 0.035 0.001 PHE B 374 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 30) link_NAG-ASN : angle 2.66328 ( 90) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.01674 ( 45) hydrogen bonds : bond 0.03920 ( 1157) hydrogen bonds : angle 5.19363 ( 3237) SS BOND : bond 0.00363 ( 51) SS BOND : angle 0.97821 ( 102) covalent geometry : bond 0.00278 (30877) covalent geometry : angle 0.51085 (42014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8532 (m-10) cc_final: 0.8322 (m-10) REVERT: B 200 TYR cc_start: 0.8433 (m-80) cc_final: 0.8044 (m-80) REVERT: B 368 LEU cc_start: 0.8948 (mt) cc_final: 0.8299 (tp) REVERT: B 1092 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8167 (pt0) REVERT: C 314 GLN cc_start: 0.8783 (tt0) cc_final: 0.8537 (tm-30) REVERT: C 393 THR cc_start: 0.8140 (p) cc_final: 0.7759 (t) REVERT: C 1002 GLN cc_start: 0.8685 (mm110) cc_final: 0.8339 (tm-30) REVERT: D 76 ASN cc_start: 0.8007 (p0) cc_final: 0.7238 (m-40) REVERT: F 106 GLU cc_start: 0.8599 (pm20) cc_final: 0.8323 (pm20) REVERT: G 34 MET cc_start: 0.7777 (tpp) cc_final: 0.7508 (tpp) outliers start: 51 outliers final: 30 residues processed: 229 average time/residue: 0.3949 time to fit residues: 155.6124 Evaluate side-chains 203 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 22 optimal weight: 3.9990 chunk 365 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 101 optimal weight: 0.0870 chunk 315 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 314 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 367 optimal weight: 8.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.089946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063281 restraints weight = 75707.678| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.36 r_work: 0.2870 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30973 Z= 0.118 Angle : 0.522 10.701 42251 Z= 0.263 Chirality : 0.043 0.273 4883 Planarity : 0.004 0.053 5354 Dihedral : 4.971 56.074 5012 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 1.55 % Allowed : 11.02 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3737 helix: 2.03 (0.21), residues: 671 sheet: 0.39 (0.17), residues: 934 loop : -0.87 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS B 519 PHE 0.016 0.001 PHE C 559 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 30) link_NAG-ASN : angle 2.56272 ( 90) link_BETA1-4 : bond 0.00345 ( 15) link_BETA1-4 : angle 0.99737 ( 45) hydrogen bonds : bond 0.03798 ( 1157) hydrogen bonds : angle 5.10141 ( 3237) SS BOND : bond 0.00299 ( 51) SS BOND : angle 0.95526 ( 102) covalent geometry : bond 0.00272 (30877) covalent geometry : angle 0.50649 (42014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8517 (m-10) cc_final: 0.8309 (m-10) REVERT: B 200 TYR cc_start: 0.8401 (m-80) cc_final: 0.8026 (m-80) REVERT: B 368 LEU cc_start: 0.8951 (mt) cc_final: 0.8306 (tp) REVERT: B 1092 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: C 164 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7196 (p0) REVERT: C 314 GLN cc_start: 0.8772 (tt0) cc_final: 0.8521 (tm-30) REVERT: C 393 THR cc_start: 0.8089 (p) cc_final: 0.7760 (t) REVERT: C 1002 GLN cc_start: 0.8672 (mm110) cc_final: 0.8317 (tm-30) REVERT: D 76 ASN cc_start: 0.7967 (p0) cc_final: 0.7217 (m-40) REVERT: F 106 GLU cc_start: 0.8564 (pm20) cc_final: 0.8270 (pm20) outliers start: 51 outliers final: 36 residues processed: 224 average time/residue: 0.3688 time to fit residues: 143.9660 Evaluate side-chains 214 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 231 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.088231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.061176 restraints weight = 76157.224| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.41 r_work: 0.2839 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30973 Z= 0.208 Angle : 0.582 10.133 42251 Z= 0.296 Chirality : 0.045 0.280 4883 Planarity : 0.004 0.070 5354 Dihedral : 5.084 55.202 5012 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 1.77 % Allowed : 11.51 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3737 helix: 1.95 (0.21), residues: 668 sheet: 0.23 (0.17), residues: 960 loop : -0.96 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 36 HIS 0.010 0.001 HIS B 519 PHE 0.042 0.001 PHE B 374 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 30) link_NAG-ASN : angle 2.76036 ( 90) link_BETA1-4 : bond 0.00237 ( 15) link_BETA1-4 : angle 1.06975 ( 45) hydrogen bonds : bond 0.04362 ( 1157) hydrogen bonds : angle 5.18975 ( 3237) SS BOND : bond 0.00331 ( 51) SS BOND : angle 1.39698 ( 102) covalent geometry : bond 0.00495 (30877) covalent geometry : angle 0.56465 (42014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 3.394 Fit side-chains revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8596 (m-10) cc_final: 0.8228 (m-10) REVERT: A 1029 MET cc_start: 0.9445 (tpp) cc_final: 0.9227 (ttm) REVERT: B 137 ASN cc_start: 0.8603 (t0) cc_final: 0.8295 (t0) REVERT: B 200 TYR cc_start: 0.8431 (m-80) cc_final: 0.8062 (m-80) REVERT: B 368 LEU cc_start: 0.8951 (mt) cc_final: 0.8302 (tp) REVERT: C 164 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7354 (p0) REVERT: C 314 GLN cc_start: 0.8793 (tt0) cc_final: 0.8495 (tm-30) REVERT: C 393 THR cc_start: 0.8169 (p) cc_final: 0.7846 (t) REVERT: C 950 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: C 1002 GLN cc_start: 0.8724 (mm110) cc_final: 0.8372 (tm-30) REVERT: D 76 ASN cc_start: 0.8030 (p0) cc_final: 0.7283 (m-40) REVERT: F 36 TYR cc_start: 0.8431 (m-80) cc_final: 0.8157 (m-80) REVERT: F 39 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7990 (mmmt) REVERT: G 5 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6496 (mp0) REVERT: G 34 MET cc_start: 0.7853 (tpp) cc_final: 0.7613 (tpp) REVERT: I 32 TYR cc_start: 0.5122 (m-80) cc_final: 0.4892 (m-80) REVERT: I 98 ARG cc_start: 0.7304 (ttp-170) cc_final: 0.6382 (ttp-110) outliers start: 58 outliers final: 45 residues processed: 231 average time/residue: 0.3762 time to fit residues: 149.3589 Evaluate side-chains 220 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 163 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 chunk 360 optimal weight: 0.0470 chunk 110 optimal weight: 5.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062718 restraints weight = 75757.192| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.37 r_work: 0.2868 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30973 Z= 0.125 Angle : 0.546 11.548 42251 Z= 0.275 Chirality : 0.044 0.270 4883 Planarity : 0.004 0.067 5354 Dihedral : 4.917 55.702 5012 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 1.43 % Allowed : 12.05 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3737 helix: 2.12 (0.21), residues: 662 sheet: 0.20 (0.17), residues: 976 loop : -0.88 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.008 0.001 HIS B 519 PHE 0.039 0.001 PHE B 374 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 30) link_NAG-ASN : angle 2.55840 ( 90) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 0.99078 ( 45) hydrogen bonds : bond 0.03921 ( 1157) hydrogen bonds : angle 5.09237 ( 3237) SS BOND : bond 0.00311 ( 51) SS BOND : angle 1.14614 ( 102) covalent geometry : bond 0.00293 (30877) covalent geometry : angle 0.53010 (42014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8759 (tt0) cc_final: 0.8498 (tm-30) REVERT: A 904 TYR cc_start: 0.8575 (m-10) cc_final: 0.8232 (m-10) REVERT: B 137 ASN cc_start: 0.8614 (t0) cc_final: 0.8313 (t0) REVERT: B 200 TYR cc_start: 0.8408 (m-80) cc_final: 0.8066 (m-80) REVERT: B 368 LEU cc_start: 0.8961 (mt) cc_final: 0.8336 (tp) REVERT: B 1092 GLU cc_start: 0.8509 (pm20) cc_final: 0.8171 (pt0) REVERT: C 164 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7326 (p0) REVERT: C 314 GLN cc_start: 0.8746 (tt0) cc_final: 0.8458 (tm-30) REVERT: C 393 THR cc_start: 0.8076 (p) cc_final: 0.7750 (t) REVERT: C 950 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: C 1002 GLN cc_start: 0.8693 (mm110) cc_final: 0.8347 (tm-30) REVERT: D 76 ASN cc_start: 0.8001 (p0) cc_final: 0.7227 (m-40) REVERT: F 36 TYR cc_start: 0.8393 (m-80) cc_final: 0.8064 (m-80) REVERT: I 98 ARG cc_start: 0.7150 (ttp-170) cc_final: 0.6801 (ttt90) outliers start: 47 outliers final: 38 residues processed: 224 average time/residue: 0.3719 time to fit residues: 143.9748 Evaluate side-chains 221 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 218 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 349 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 108 optimal weight: 8.9990 chunk 244 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 361 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061889 restraints weight = 75897.973| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.36 r_work: 0.2851 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30973 Z= 0.164 Angle : 0.570 11.883 42251 Z= 0.287 Chirality : 0.044 0.273 4883 Planarity : 0.004 0.067 5354 Dihedral : 4.914 55.256 5012 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Rotamer: Outliers : 1.58 % Allowed : 12.12 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3737 helix: 2.07 (0.21), residues: 662 sheet: 0.18 (0.17), residues: 959 loop : -0.94 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 36 HIS 0.008 0.001 HIS B 519 PHE 0.037 0.001 PHE B 374 TYR 0.019 0.001 TYR C1067 ARG 0.007 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 30) link_NAG-ASN : angle 2.62550 ( 90) link_BETA1-4 : bond 0.00270 ( 15) link_BETA1-4 : angle 1.02861 ( 45) hydrogen bonds : bond 0.04125 ( 1157) hydrogen bonds : angle 5.09911 ( 3237) SS BOND : bond 0.00292 ( 51) SS BOND : angle 1.39877 ( 102) covalent geometry : bond 0.00391 (30877) covalent geometry : angle 0.55314 (42014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 3.211 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8751 (tt0) cc_final: 0.8501 (tm-30) REVERT: A 904 TYR cc_start: 0.8623 (m-10) cc_final: 0.8290 (m-10) REVERT: A 1029 MET cc_start: 0.9455 (tpp) cc_final: 0.9201 (ttm) REVERT: B 137 ASN cc_start: 0.8606 (t0) cc_final: 0.8289 (t0) REVERT: B 200 TYR cc_start: 0.8417 (m-80) cc_final: 0.8069 (m-80) REVERT: B 368 LEU cc_start: 0.8972 (mt) cc_final: 0.8347 (tp) REVERT: B 1092 GLU cc_start: 0.8515 (pm20) cc_final: 0.8242 (pt0) REVERT: C 164 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7329 (p0) REVERT: C 314 GLN cc_start: 0.8755 (tt0) cc_final: 0.8460 (tm-30) REVERT: C 393 THR cc_start: 0.8117 (p) cc_final: 0.7795 (t) REVERT: C 950 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: C 1002 GLN cc_start: 0.8714 (mm110) cc_final: 0.8370 (tm-30) REVERT: D 76 ASN cc_start: 0.8039 (p0) cc_final: 0.7244 (m-40) REVERT: E 34 MET cc_start: 0.7670 (tpp) cc_final: 0.7352 (tpp) REVERT: F 36 TYR cc_start: 0.8413 (m-80) cc_final: 0.8083 (m-80) REVERT: F 106 GLU cc_start: 0.8699 (pm20) cc_final: 0.8417 (pm20) REVERT: I 98 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.6968 (ttt90) outliers start: 52 outliers final: 47 residues processed: 223 average time/residue: 0.3629 time to fit residues: 140.2248 Evaluate side-chains 226 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 125 optimal weight: 0.5980 chunk 305 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 268 optimal weight: 0.6980 chunk 135 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 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.062515 restraints weight = 75632.527| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.36 r_work: 0.2857 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30973 Z= 0.127 Angle : 0.551 12.349 42251 Z= 0.276 Chirality : 0.044 0.269 4883 Planarity : 0.004 0.067 5354 Dihedral : 4.786 55.595 5012 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 1.49 % Allowed : 12.36 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3737 helix: 2.16 (0.21), residues: 662 sheet: 0.26 (0.17), residues: 956 loop : -0.90 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.009 0.001 HIS B 519 PHE 0.037 0.001 PHE B 374 TYR 0.019 0.001 TYR C1067 ARG 0.008 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 30) link_NAG-ASN : angle 2.49628 ( 90) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 0.97447 ( 45) hydrogen bonds : bond 0.03862 ( 1157) hydrogen bonds : angle 5.03453 ( 3237) SS BOND : bond 0.00373 ( 51) SS BOND : angle 1.28020 ( 102) covalent geometry : bond 0.00298 (30877) covalent geometry : angle 0.53596 (42014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 3.651 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8759 (tt0) cc_final: 0.8525 (tm-30) REVERT: A 904 TYR cc_start: 0.8606 (m-10) cc_final: 0.8303 (m-10) REVERT: B 137 ASN cc_start: 0.8611 (t0) cc_final: 0.8305 (t0) REVERT: B 200 TYR cc_start: 0.8426 (m-80) cc_final: 0.8086 (m-80) REVERT: B 368 LEU cc_start: 0.8992 (mt) cc_final: 0.8382 (tp) REVERT: C 164 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7329 (p0) REVERT: C 314 GLN cc_start: 0.8732 (tt0) cc_final: 0.8460 (tm-30) REVERT: C 393 THR cc_start: 0.8090 (p) cc_final: 0.7768 (t) REVERT: C 950 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7978 (m-30) REVERT: C 1002 GLN cc_start: 0.8693 (mm110) cc_final: 0.8353 (tm-30) REVERT: D 76 ASN cc_start: 0.8018 (p0) cc_final: 0.7208 (m-40) REVERT: E 34 MET cc_start: 0.7805 (tpp) cc_final: 0.7462 (tpp) REVERT: F 36 TYR cc_start: 0.8417 (m-80) cc_final: 0.8092 (m-80) REVERT: F 106 GLU cc_start: 0.8668 (pm20) cc_final: 0.8369 (pm20) REVERT: G 34 MET cc_start: 0.8009 (tpp) cc_final: 0.7370 (tpp) REVERT: I 98 ARG cc_start: 0.7220 (ttp-170) cc_final: 0.6465 (ttp-110) outliers start: 49 outliers final: 44 residues processed: 225 average time/residue: 0.3872 time to fit residues: 151.0998 Evaluate side-chains 227 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain I residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 188 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 363 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 258 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 186 optimal weight: 0.0170 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.089662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.063044 restraints weight = 75300.771| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.36 r_work: 0.2869 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30973 Z= 0.110 Angle : 0.538 11.892 42251 Z= 0.271 Chirality : 0.043 0.267 4883 Planarity : 0.004 0.066 5354 Dihedral : 4.659 55.466 5012 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 1.55 % Allowed : 12.42 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3737 helix: 2.22 (0.21), residues: 662 sheet: 0.42 (0.17), residues: 960 loop : -0.88 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 36 HIS 0.008 0.001 HIS B 519 PHE 0.037 0.001 PHE B 374 TYR 0.022 0.001 TYR B 904 ARG 0.007 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 30) link_NAG-ASN : angle 2.41545 ( 90) link_BETA1-4 : bond 0.00350 ( 15) link_BETA1-4 : angle 0.96326 ( 45) hydrogen bonds : bond 0.03685 ( 1157) hydrogen bonds : angle 4.96503 ( 3237) SS BOND : bond 0.00317 ( 51) SS BOND : angle 1.17638 ( 102) covalent geometry : bond 0.00255 (30877) covalent geometry : angle 0.52345 (42014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13850.75 seconds wall clock time: 245 minutes 6.94 seconds (14706.94 seconds total)