Starting phenix.real_space_refine on Sun Jun 22 00:07:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y9s_33690/06_2025/7y9s_33690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y9s_33690/06_2025/7y9s_33690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y9s_33690/06_2025/7y9s_33690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y9s_33690/06_2025/7y9s_33690.map" model { file = "/net/cci-nas-00/data/ceres_data/7y9s_33690/06_2025/7y9s_33690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y9s_33690/06_2025/7y9s_33690.cif" } resolution = 3.0 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= 0.020 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 114 5.16 5 C 16135 2.51 5 N 4139 2.21 5 O 4885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25273 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Chain: "B" Number of atoms: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8191 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 8 Chain: "C" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 16.28, per 1000 atoms: 0.64 Number of scatterers: 25273 At special positions: 0 Unit cell: (138.75, 152.07, 203.13, 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 114 16.00 O 4885 8.00 N 4139 7.00 C 16135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 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=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 122 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 234 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 61 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 282 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 3.6 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.890A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.051A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.945A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.656A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.537A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 806 removed outlier: 3.578A pdb=" N ILE A 805 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 802 through 806' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.034A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.200A 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: 3.656A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (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 982 removed outlier: 4.065A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.076A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.625A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.871A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.608A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.050A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.570A 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 848 through 855 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.558A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.539A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.384A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.583A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) 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 removed outlier: 3.675A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.226A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.575A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.847A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.540A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.565A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.722A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.528A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 937 removed outlier: 3.821A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.577A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.734A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.899A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.276A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.162A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.025A 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: 3.610A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.577A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.695A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.061A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.120A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.568A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.643A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.344A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.159A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.805A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 142 removed outlier: 7.615A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.098A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.720A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.548A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.470A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.692A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.240A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.600A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.612A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.544A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.224A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.639A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 1014 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.25 Time building geometry restraints manager: 8.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7793 1.34 - 1.46: 6606 1.46 - 1.59: 11300 1.59 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25840 Sorted by residual: bond pdb=" N THR B 376 " pdb=" CA THR B 376 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.27e-02 6.20e+03 8.83e+00 bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.53e-02 4.27e+03 8.28e+00 bond pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 1.452 1.480 -0.028 1.11e-02 8.12e+03 6.27e+00 bond pdb=" C PHE A 374 " pdb=" N PHE A 375 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.23e-02 6.61e+03 6.25e+00 bond pdb=" CA ALA B 372 " pdb=" CB ALA B 372 " ideal model delta sigma weight residual 1.536 1.505 0.031 1.25e-02 6.40e+03 6.13e+00 ... (remaining 25835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 34745 2.57 - 5.13: 366 5.13 - 7.70: 21 7.70 - 10.27: 2 10.27 - 12.84: 2 Bond angle restraints: 35136 Sorted by residual: angle pdb=" CA PHE B 375 " pdb=" CB PHE B 375 " pdb=" CG PHE B 375 " ideal model delta sigma weight residual 113.80 120.88 -7.08 1.00e+00 1.00e+00 5.02e+01 angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 112.47 99.63 12.84 2.06e+00 2.36e-01 3.88e+01 angle pdb=" CA THR B 376 " pdb=" C THR B 376 " pdb=" O THR B 376 " ideal model delta sigma weight residual 121.88 115.72 6.16 1.13e+00 7.83e-01 2.97e+01 angle pdb=" N PRO B 373 " pdb=" CA PRO B 373 " pdb=" C PRO B 373 " ideal model delta sigma weight residual 112.47 101.80 10.67 2.06e+00 2.36e-01 2.68e+01 angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 113.41 107.86 5.55 1.22e+00 6.72e-01 2.07e+01 ... (remaining 35131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 14399 17.61 - 35.23: 1317 35.23 - 52.84: 307 52.84 - 70.46: 66 70.46 - 88.07: 23 Dihedral angle restraints: 16112 sinusoidal: 6995 harmonic: 9117 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 12.14 80.86 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 27.02 65.98 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 155.69 -62.69 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 16109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3278 0.054 - 0.108: 705 0.108 - 0.162: 138 0.162 - 0.216: 12 0.216 - 0.269: 5 Chirality restraints: 4138 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" C PRO A 373 " pdb=" CB PRO A 373 " both_signs ideal model delta sigma weight residual False 2.72 2.98 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4135 not shown) Planarity restraints: 4501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 498 " 0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO C 499 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 498 " 0.064 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO B 499 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.063 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO A 322 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.051 5.00e-02 4.00e+02 ... (remaining 4498 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1982 2.74 - 3.28: 23509 3.28 - 3.82: 37880 3.82 - 4.36: 42499 4.36 - 4.90: 78505 Nonbonded interactions: 184375 Sorted by model distance: nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP A 40 " pdb=" NH1 ARG A 44 " model vdw 2.264 3.120 ... (remaining 184370 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 15 through 827 or resid 848 through 1147 or resid 1301 thr \ ough 1306)) selection = (chain 'C' and (resid 15 through 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = 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' } 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: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 60.650 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.004 0.060 25935 Z= 0.191 Angle : 0.672 16.387 35379 Z= 0.348 Chirality : 0.047 0.269 4138 Planarity : 0.005 0.098 4464 Dihedral : 14.215 88.070 10106 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.92 % Favored : 94.79 % Rotamer: Outliers : 0.26 % Allowed : 0.33 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3072 helix: 2.02 (0.21), residues: 679 sheet: 1.05 (0.19), residues: 682 loop : -1.55 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.002 0.000 HIS B 505 PHE 0.020 0.001 PHE A 486 TYR 0.019 0.001 TYR C 351 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 37) link_NAG-ASN : angle 3.23757 ( 111) link_BETA1-4 : bond 0.00397 ( 16) link_BETA1-4 : angle 1.00582 ( 48) hydrogen bonds : bond 0.12452 ( 1014) hydrogen bonds : angle 5.76921 ( 2748) SS BOND : bond 0.00588 ( 42) SS BOND : angle 1.54281 ( 84) covalent geometry : bond 0.00381 (25840) covalent geometry : angle 0.64331 (35136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 527 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7624 (t80) cc_final: 0.7277 (t80) REVERT: A 331 ASN cc_start: 0.6430 (m110) cc_final: 0.5965 (t0) REVERT: A 368 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 558 LYS cc_start: 0.8001 (mmpt) cc_final: 0.7283 (mmpt) REVERT: A 571 ASP cc_start: 0.7813 (t70) cc_final: 0.7400 (t0) REVERT: A 586 ASP cc_start: 0.7679 (m-30) cc_final: 0.7442 (m-30) REVERT: A 955 ASN cc_start: 0.8343 (m-40) cc_final: 0.8135 (m110) REVERT: A 988 GLU cc_start: 0.7257 (tp30) cc_final: 0.6851 (tm-30) REVERT: A 1017 GLU cc_start: 0.7089 (tp30) cc_final: 0.6622 (tp30) REVERT: A 1084 ASP cc_start: 0.7290 (t0) cc_final: 0.6908 (OUTLIER) REVERT: B 81 ASN cc_start: 0.7917 (m110) cc_final: 0.7651 (m110) REVERT: B 349 SER cc_start: 0.8564 (p) cc_final: 0.8275 (p) REVERT: B 440 LYS cc_start: 0.8383 (ptmm) cc_final: 0.8116 (tmmm) REVERT: B 493 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7551 (mmm-85) REVERT: B 534 VAL cc_start: 0.8372 (m) cc_final: 0.8128 (t) REVERT: B 654 GLU cc_start: 0.7842 (tt0) cc_final: 0.7590 (tt0) REVERT: B 752 LEU cc_start: 0.8175 (mt) cc_final: 0.7923 (mt) REVERT: B 776 LYS cc_start: 0.8437 (ttpp) cc_final: 0.8217 (ttmm) REVERT: B 780 GLU cc_start: 0.7716 (tt0) cc_final: 0.7494 (tp30) REVERT: B 814 LYS cc_start: 0.8323 (mmtm) cc_final: 0.8036 (mmtt) REVERT: B 817 PHE cc_start: 0.7760 (t80) cc_final: 0.7517 (t80) REVERT: B 921 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7839 (mtpp) REVERT: B 1144 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7445 (tp30) REVERT: C 194 PHE cc_start: 0.8591 (m-10) cc_final: 0.8280 (m-80) REVERT: C 370 ASN cc_start: 0.7547 (p0) cc_final: 0.7255 (p0) REVERT: C 371 LEU cc_start: 0.8740 (mp) cc_final: 0.8536 (mt) REVERT: C 465 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6972 (tm-30) REVERT: C 478 LYS cc_start: 0.8814 (ptpp) cc_final: 0.8612 (ptpp) REVERT: C 493 ARG cc_start: 0.7836 (mmt-90) cc_final: 0.7632 (mmt-90) REVERT: C 556 ASN cc_start: 0.8383 (m-40) cc_final: 0.8147 (m-40) REVERT: C 577 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: C 603 ASN cc_start: 0.8344 (t0) cc_final: 0.8115 (t0) REVERT: C 751 ASN cc_start: 0.8328 (m110) cc_final: 0.7962 (m110) REVERT: C 754 LEU cc_start: 0.8445 (mt) cc_final: 0.8168 (mm) REVERT: C 790 LYS cc_start: 0.8166 (mttp) cc_final: 0.7935 (mttm) REVERT: C 935 GLN cc_start: 0.7848 (pt0) cc_final: 0.7597 (pt0) REVERT: C 1010 GLN cc_start: 0.8137 (mp10) cc_final: 0.7711 (mp10) REVERT: C 1038 LYS cc_start: 0.8362 (mmmt) cc_final: 0.8112 (mmmm) REVERT: C 1141 LEU cc_start: 0.8562 (tp) cc_final: 0.8286 (tm) outliers start: 7 outliers final: 4 residues processed: 531 average time/residue: 1.6651 time to fit residues: 1029.9737 Evaluate side-chains 484 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 480 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 676 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 131 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN A 603 ASN A 777 ASN B 81 ASN B 370 ASN B 409 GLN C 52 GLN C 81 ASN C 99 ASN C 690 GLN C 907 ASN C 960 ASN C 965 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111814 restraints weight = 38353.135| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.64 r_work: 0.3331 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25935 Z= 0.171 Angle : 0.644 15.870 35379 Z= 0.325 Chirality : 0.046 0.418 4138 Planarity : 0.005 0.078 4464 Dihedral : 7.347 83.704 4469 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 1.13 % Allowed : 10.23 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3072 helix: 1.93 (0.21), residues: 695 sheet: 1.11 (0.19), residues: 692 loop : -1.65 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 436 HIS 0.004 0.001 HIS A 207 PHE 0.024 0.002 PHE B 400 TYR 0.023 0.001 TYR C 453 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 37) link_NAG-ASN : angle 3.27221 ( 111) link_BETA1-4 : bond 0.00321 ( 16) link_BETA1-4 : angle 1.07934 ( 48) hydrogen bonds : bond 0.06138 ( 1014) hydrogen bonds : angle 5.10525 ( 2748) SS BOND : bond 0.00474 ( 42) SS BOND : angle 1.68895 ( 84) covalent geometry : bond 0.00401 (25840) covalent geometry : angle 0.61268 (35136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 507 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 TRP cc_start: 0.7785 (p90) cc_final: 0.7419 (p90) REVERT: A 558 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7460 (mmpt) REVERT: A 571 ASP cc_start: 0.7869 (t70) cc_final: 0.7418 (t0) REVERT: A 988 GLU cc_start: 0.7480 (tp30) cc_final: 0.7140 (tp30) REVERT: A 1084 ASP cc_start: 0.7685 (t0) cc_final: 0.7246 (t0) REVERT: B 129 LYS cc_start: 0.8082 (mttm) cc_final: 0.7784 (mttp) REVERT: B 132 GLU cc_start: 0.6418 (pm20) cc_final: 0.5876 (pm20) REVERT: B 169 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 324 GLU cc_start: 0.7884 (pm20) cc_final: 0.7565 (pm20) REVERT: B 402 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 440 LYS cc_start: 0.8573 (ptmm) cc_final: 0.8373 (tmmm) REVERT: B 493 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7972 (mmm-85) REVERT: B 534 VAL cc_start: 0.8347 (m) cc_final: 0.8140 (t) REVERT: B 583 GLU cc_start: 0.8355 (pt0) cc_final: 0.8118 (pt0) REVERT: B 752 LEU cc_start: 0.8182 (mt) cc_final: 0.7876 (mt) REVERT: B 768 THR cc_start: 0.8300 (m) cc_final: 0.8082 (p) REVERT: B 814 LYS cc_start: 0.8369 (mmtm) cc_final: 0.8073 (mmtt) REVERT: B 825 LYS cc_start: 0.8310 (tppp) cc_final: 0.8012 (tppp) REVERT: B 1144 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7724 (mm-30) REVERT: C 117 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7449 (mt) REVERT: C 194 PHE cc_start: 0.8684 (m-10) cc_final: 0.8393 (m-80) REVERT: C 370 ASN cc_start: 0.7828 (p0) cc_final: 0.7592 (p0) REVERT: C 371 LEU cc_start: 0.8805 (mp) cc_final: 0.8578 (mt) REVERT: C 405 ASP cc_start: 0.7942 (p0) cc_final: 0.7412 (p0) REVERT: C 474 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7501 (tm-30) REVERT: C 478 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8609 (ptpp) REVERT: C 751 ASN cc_start: 0.8428 (m110) cc_final: 0.8184 (m-40) REVERT: C 754 LEU cc_start: 0.8501 (mt) cc_final: 0.8240 (mm) REVERT: C 780 GLU cc_start: 0.8205 (tt0) cc_final: 0.7968 (tp30) REVERT: C 790 LYS cc_start: 0.8448 (mttp) cc_final: 0.8223 (mttp) REVERT: C 804 GLN cc_start: 0.8625 (mt0) cc_final: 0.8320 (mt0) REVERT: C 900 MET cc_start: 0.8394 (mtt) cc_final: 0.8188 (mtm) REVERT: C 918 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7991 (mt-10) REVERT: C 950 ASP cc_start: 0.7495 (m-30) cc_final: 0.7259 (m-30) REVERT: C 1010 GLN cc_start: 0.8403 (mp10) cc_final: 0.8007 (mp10) REVERT: C 1038 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8287 (mmmm) REVERT: C 1141 LEU cc_start: 0.8520 (tp) cc_final: 0.8169 (tt) outliers start: 31 outliers final: 11 residues processed: 516 average time/residue: 1.3490 time to fit residues: 802.1557 Evaluate side-chains 500 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 487 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 278 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 137 optimal weight: 0.0170 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN B 556 ASN B 703 ASN B 804 GLN C 52 GLN C 66 HIS C 81 ASN C 317 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 779 GLN C 804 GLN C 907 ASN C1002 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111769 restraints weight = 38258.856| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.63 r_work: 0.3335 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25935 Z= 0.150 Angle : 0.621 15.175 35379 Z= 0.312 Chirality : 0.046 0.431 4138 Planarity : 0.005 0.068 4464 Dihedral : 6.810 57.548 4463 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 1.83 % Allowed : 12.75 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3072 helix: 1.86 (0.21), residues: 709 sheet: 1.07 (0.19), residues: 679 loop : -1.58 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.005 0.001 HIS C 66 PHE 0.023 0.001 PHE B 400 TYR 0.023 0.001 TYR C 453 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 37) link_NAG-ASN : angle 3.18198 ( 111) link_BETA1-4 : bond 0.00421 ( 16) link_BETA1-4 : angle 1.08958 ( 48) hydrogen bonds : bond 0.05905 ( 1014) hydrogen bonds : angle 4.98082 ( 2748) SS BOND : bond 0.00450 ( 42) SS BOND : angle 1.58976 ( 84) covalent geometry : bond 0.00346 (25840) covalent geometry : angle 0.58998 (35136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 490 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 TRP cc_start: 0.7836 (p90) cc_final: 0.7440 (p90) REVERT: A 529 LYS cc_start: 0.8468 (tmtt) cc_final: 0.8192 (tmtt) REVERT: A 558 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7451 (mmpt) REVERT: A 571 ASP cc_start: 0.7918 (t70) cc_final: 0.7445 (t0) REVERT: A 752 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8519 (mt) REVERT: A 900 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8016 (mtp) REVERT: A 988 GLU cc_start: 0.7498 (tp30) cc_final: 0.7154 (tp30) REVERT: A 1084 ASP cc_start: 0.7718 (t0) cc_final: 0.7209 (t0) REVERT: B 129 LYS cc_start: 0.8095 (mttm) cc_final: 0.7848 (mtpp) REVERT: B 340 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 440 LYS cc_start: 0.8628 (ptmm) cc_final: 0.8394 (tmmm) REVERT: B 493 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7919 (mmm-85) REVERT: B 654 GLU cc_start: 0.8477 (tt0) cc_final: 0.8235 (tt0) REVERT: B 751 ASN cc_start: 0.8572 (m-40) cc_final: 0.7941 (m-40) REVERT: B 752 LEU cc_start: 0.8128 (mt) cc_final: 0.7796 (mt) REVERT: B 768 THR cc_start: 0.8191 (m) cc_final: 0.7933 (p) REVERT: B 780 GLU cc_start: 0.8318 (tt0) cc_final: 0.7921 (tp30) REVERT: B 790 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7810 (ptpp) REVERT: B 814 LYS cc_start: 0.8349 (mmtm) cc_final: 0.8047 (mmtt) REVERT: B 1031 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 1050 MET cc_start: 0.8431 (ptm) cc_final: 0.8219 (ptm) REVERT: B 1072 GLU cc_start: 0.8483 (pm20) cc_final: 0.8274 (pm20) REVERT: B 1144 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7675 (tp30) REVERT: C 117 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7562 (mt) REVERT: C 194 PHE cc_start: 0.8701 (m-10) cc_final: 0.8385 (m-80) REVERT: C 370 ASN cc_start: 0.7902 (p0) cc_final: 0.7666 (p0) REVERT: C 371 LEU cc_start: 0.8811 (mp) cc_final: 0.8547 (mt) REVERT: C 405 ASP cc_start: 0.7830 (p0) cc_final: 0.7525 (p0) REVERT: C 465 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: C 478 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8535 (ptpp) REVERT: C 751 ASN cc_start: 0.8405 (m110) cc_final: 0.7977 (m110) REVERT: C 754 LEU cc_start: 0.8499 (mt) cc_final: 0.8239 (mm) REVERT: C 780 GLU cc_start: 0.8160 (tt0) cc_final: 0.7909 (tp30) REVERT: C 900 MET cc_start: 0.8377 (mtt) cc_final: 0.8151 (mtm) REVERT: C 918 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7987 (mt-10) REVERT: C 950 ASP cc_start: 0.7551 (m-30) cc_final: 0.7286 (m-30) REVERT: C 1010 GLN cc_start: 0.8441 (mp10) cc_final: 0.8071 (mp10) REVERT: C 1038 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8309 (mmmm) REVERT: C 1141 LEU cc_start: 0.8422 (tp) cc_final: 0.8123 (tt) outliers start: 50 outliers final: 23 residues processed: 510 average time/residue: 2.0060 time to fit residues: 1204.7414 Evaluate side-chains 507 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 479 time to evaluate : 5.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 203 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 277 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN B 703 ASN C 66 HIS C 81 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 779 GLN C 907 ASN C 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111595 restraints weight = 38709.605| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.68 r_work: 0.3335 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25935 Z= 0.158 Angle : 0.616 14.629 35379 Z= 0.311 Chirality : 0.046 0.433 4138 Planarity : 0.005 0.067 4464 Dihedral : 6.495 59.414 4463 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 2.19 % Allowed : 14.14 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3072 helix: 1.88 (0.21), residues: 704 sheet: 1.03 (0.19), residues: 681 loop : -1.59 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.004 0.001 HIS C 66 PHE 0.022 0.001 PHE B 400 TYR 0.025 0.001 TYR C 453 ARG 0.006 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 37) link_NAG-ASN : angle 3.09623 ( 111) link_BETA1-4 : bond 0.00389 ( 16) link_BETA1-4 : angle 1.10258 ( 48) hydrogen bonds : bond 0.05997 ( 1014) hydrogen bonds : angle 4.93079 ( 2748) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.66419 ( 84) covalent geometry : bond 0.00368 (25840) covalent geometry : angle 0.58634 (35136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 503 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8641 (mttt) cc_final: 0.8319 (mtpt) REVERT: A 169 GLU cc_start: 0.7637 (mp0) cc_final: 0.7282 (mm-30) REVERT: A 436 TRP cc_start: 0.7833 (p90) cc_final: 0.7518 (p90) REVERT: A 529 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8237 (tmtt) REVERT: A 571 ASP cc_start: 0.7928 (t70) cc_final: 0.7447 (t0) REVERT: A 988 GLU cc_start: 0.7516 (tp30) cc_final: 0.7183 (tp30) REVERT: A 1084 ASP cc_start: 0.7735 (t0) cc_final: 0.7213 (t0) REVERT: B 81 ASN cc_start: 0.7796 (m-40) cc_final: 0.7460 (m-40) REVERT: B 132 GLU cc_start: 0.6423 (pm20) cc_final: 0.5478 (pm20) REVERT: B 242 LEU cc_start: 0.8253 (mm) cc_final: 0.7957 (mp) REVERT: B 440 LYS cc_start: 0.8597 (ptmm) cc_final: 0.8284 (tmmm) REVERT: B 493 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7933 (mmm-85) REVERT: B 654 GLU cc_start: 0.8436 (tt0) cc_final: 0.8196 (tt0) REVERT: B 751 ASN cc_start: 0.8532 (m-40) cc_final: 0.7878 (m-40) REVERT: B 752 LEU cc_start: 0.8130 (mt) cc_final: 0.7780 (mt) REVERT: B 780 GLU cc_start: 0.8306 (tt0) cc_final: 0.7902 (tp30) REVERT: B 790 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7896 (mtmm) REVERT: B 814 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8052 (mmtt) REVERT: B 1050 MET cc_start: 0.8427 (ptm) cc_final: 0.8179 (ptm) REVERT: B 1072 GLU cc_start: 0.8382 (pm20) cc_final: 0.8155 (pm20) REVERT: B 1144 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7672 (tp30) REVERT: C 83 VAL cc_start: 0.8301 (t) cc_final: 0.8085 (p) REVERT: C 118 LEU cc_start: 0.8384 (mp) cc_final: 0.8045 (mp) REVERT: C 133 PHE cc_start: 0.6782 (m-80) cc_final: 0.6017 (m-80) REVERT: C 194 PHE cc_start: 0.8698 (m-10) cc_final: 0.8382 (m-80) REVERT: C 370 ASN cc_start: 0.7892 (p0) cc_final: 0.7651 (p0) REVERT: C 371 LEU cc_start: 0.8817 (mp) cc_final: 0.8538 (mt) REVERT: C 405 ASP cc_start: 0.7884 (p0) cc_final: 0.7602 (p0) REVERT: C 465 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: C 478 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8548 (ptpp) REVERT: C 751 ASN cc_start: 0.8423 (m110) cc_final: 0.8163 (m-40) REVERT: C 754 LEU cc_start: 0.8516 (mt) cc_final: 0.8262 (mm) REVERT: C 780 GLU cc_start: 0.8142 (tt0) cc_final: 0.7911 (tp30) REVERT: C 918 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7974 (mt-10) REVERT: C 950 ASP cc_start: 0.7588 (m-30) cc_final: 0.7286 (m-30) REVERT: C 1010 GLN cc_start: 0.8476 (mp10) cc_final: 0.8090 (mp10) REVERT: C 1038 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8271 (mmmm) REVERT: C 1141 LEU cc_start: 0.8458 (tp) cc_final: 0.8204 (tt) outliers start: 60 outliers final: 36 residues processed: 531 average time/residue: 1.4650 time to fit residues: 911.8835 Evaluate side-chains 532 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 495 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 137 optimal weight: 0.0170 chunk 124 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 198 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 44 optimal weight: 0.0030 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN A 777 ASN B 556 ASN B 703 ASN C 66 HIS C 81 ASN C 317 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 824 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112594 restraints weight = 38550.176| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.58 r_work: 0.3347 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25935 Z= 0.127 Angle : 0.596 14.044 35379 Z= 0.299 Chirality : 0.045 0.421 4138 Planarity : 0.005 0.067 4464 Dihedral : 6.230 56.370 4463 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 2.08 % Allowed : 15.45 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3072 helix: 1.96 (0.21), residues: 703 sheet: 0.97 (0.19), residues: 705 loop : -1.53 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.000 HIS C 66 PHE 0.023 0.001 PHE C 456 TYR 0.026 0.001 TYR C 453 ARG 0.006 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 37) link_NAG-ASN : angle 2.99786 ( 111) link_BETA1-4 : bond 0.00398 ( 16) link_BETA1-4 : angle 1.09817 ( 48) hydrogen bonds : bond 0.05385 ( 1014) hydrogen bonds : angle 4.82534 ( 2748) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.46921 ( 84) covalent geometry : bond 0.00285 (25840) covalent geometry : angle 0.56789 (35136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 497 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7526 (mp0) cc_final: 0.7163 (mm-30) REVERT: A 347 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7106 (t80) REVERT: A 436 TRP cc_start: 0.7846 (p90) cc_final: 0.7529 (p90) REVERT: A 529 LYS cc_start: 0.8453 (tmtt) cc_final: 0.8237 (tmtt) REVERT: A 571 ASP cc_start: 0.7943 (t70) cc_final: 0.7451 (t0) REVERT: A 900 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7948 (mtp) REVERT: A 988 GLU cc_start: 0.7502 (tp30) cc_final: 0.7167 (tp30) REVERT: A 1084 ASP cc_start: 0.7747 (t0) cc_final: 0.7214 (t0) REVERT: B 81 ASN cc_start: 0.7796 (m-40) cc_final: 0.7428 (m-40) REVERT: B 132 GLU cc_start: 0.6069 (pm20) cc_final: 0.5033 (pm20) REVERT: B 242 LEU cc_start: 0.8237 (mm) cc_final: 0.7881 (mp) REVERT: B 440 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8287 (tmmm) REVERT: B 493 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7895 (mmm-85) REVERT: B 654 GLU cc_start: 0.8421 (tt0) cc_final: 0.8184 (tt0) REVERT: B 751 ASN cc_start: 0.8435 (m-40) cc_final: 0.7835 (m-40) REVERT: B 752 LEU cc_start: 0.8073 (mt) cc_final: 0.7723 (mt) REVERT: B 780 GLU cc_start: 0.8300 (tt0) cc_final: 0.7928 (tp30) REVERT: B 814 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8062 (mmtt) REVERT: B 960 ASN cc_start: 0.8742 (t0) cc_final: 0.8331 (t0) REVERT: B 1050 MET cc_start: 0.8388 (ptm) cc_final: 0.8133 (ptm) REVERT: B 1144 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7660 (tp30) REVERT: C 118 LEU cc_start: 0.8322 (mp) cc_final: 0.8017 (mp) REVERT: C 133 PHE cc_start: 0.6810 (m-80) cc_final: 0.6027 (m-80) REVERT: C 194 PHE cc_start: 0.8664 (m-10) cc_final: 0.8370 (m-80) REVERT: C 370 ASN cc_start: 0.7895 (p0) cc_final: 0.7655 (p0) REVERT: C 371 LEU cc_start: 0.8796 (mp) cc_final: 0.8516 (mt) REVERT: C 405 ASP cc_start: 0.7841 (p0) cc_final: 0.7557 (p0) REVERT: C 465 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: C 478 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8548 (ptpp) REVERT: C 751 ASN cc_start: 0.8417 (m110) cc_final: 0.8182 (m-40) REVERT: C 754 LEU cc_start: 0.8506 (mt) cc_final: 0.8251 (mm) REVERT: C 780 GLU cc_start: 0.8096 (tt0) cc_final: 0.7894 (tp30) REVERT: C 822 LEU cc_start: 0.8025 (mt) cc_final: 0.7816 (mp) REVERT: C 950 ASP cc_start: 0.7502 (m-30) cc_final: 0.7216 (m-30) REVERT: C 1010 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: C 1014 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8203 (mtm180) REVERT: C 1038 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8274 (mmmm) REVERT: C 1141 LEU cc_start: 0.8484 (tp) cc_final: 0.8207 (tt) outliers start: 57 outliers final: 27 residues processed: 524 average time/residue: 1.2968 time to fit residues: 788.9326 Evaluate side-chains 506 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 474 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 118 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 220 optimal weight: 0.0050 chunk 243 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN B 703 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 779 GLN C 804 GLN C 824 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.137033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109408 restraints weight = 38441.898| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.59 r_work: 0.3293 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25935 Z= 0.228 Angle : 0.674 14.503 35379 Z= 0.343 Chirality : 0.048 0.532 4138 Planarity : 0.005 0.072 4464 Dihedral : 6.405 59.974 4462 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.11 % Rotamer: Outliers : 2.41 % Allowed : 16.30 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3072 helix: 1.66 (0.20), residues: 710 sheet: 0.93 (0.19), residues: 719 loop : -1.65 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 436 HIS 0.005 0.001 HIS C1064 PHE 0.022 0.002 PHE C 456 TYR 0.027 0.002 TYR C 265 ARG 0.005 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 37) link_NAG-ASN : angle 3.16609 ( 111) link_BETA1-4 : bond 0.00370 ( 16) link_BETA1-4 : angle 1.16323 ( 48) hydrogen bonds : bond 0.07027 ( 1014) hydrogen bonds : angle 5.02106 ( 2748) SS BOND : bond 0.00541 ( 42) SS BOND : angle 2.01598 ( 84) covalent geometry : bond 0.00547 (25840) covalent geometry : angle 0.64376 (35136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 506 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8672 (mttt) cc_final: 0.8465 (mttt) REVERT: A 324 GLU cc_start: 0.7503 (mp0) cc_final: 0.7231 (pm20) REVERT: A 571 ASP cc_start: 0.8019 (t70) cc_final: 0.7489 (t0) REVERT: A 702 GLU cc_start: 0.7018 (tp30) cc_final: 0.6733 (tp30) REVERT: A 979 ASP cc_start: 0.7898 (p0) cc_final: 0.7495 (p0) REVERT: A 988 GLU cc_start: 0.7586 (tp30) cc_final: 0.7239 (tp30) REVERT: A 1045 LYS cc_start: 0.8240 (tppp) cc_final: 0.7757 (tppp) REVERT: A 1084 ASP cc_start: 0.7771 (t0) cc_final: 0.7254 (t0) REVERT: B 81 ASN cc_start: 0.7997 (m-40) cc_final: 0.7633 (m-40) REVERT: B 132 GLU cc_start: 0.6156 (pm20) cc_final: 0.5367 (pm20) REVERT: B 196 ASN cc_start: 0.8910 (t0) cc_final: 0.8654 (t0) REVERT: B 241 LEU cc_start: 0.8055 (mt) cc_final: 0.7850 (mt) REVERT: B 242 LEU cc_start: 0.8307 (mm) cc_final: 0.7917 (mp) REVERT: B 324 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: B 440 LYS cc_start: 0.8608 (ptmm) cc_final: 0.8301 (tmmm) REVERT: B 493 ARG cc_start: 0.8268 (mtp85) cc_final: 0.7940 (mmm-85) REVERT: B 588 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8392 (p) REVERT: B 654 GLU cc_start: 0.8429 (tt0) cc_final: 0.8205 (tt0) REVERT: B 748 GLU cc_start: 0.7787 (mp0) cc_final: 0.7563 (mp0) REVERT: B 751 ASN cc_start: 0.8497 (m-40) cc_final: 0.7908 (m-40) REVERT: B 752 LEU cc_start: 0.8155 (mt) cc_final: 0.7818 (mt) REVERT: B 780 GLU cc_start: 0.8333 (tt0) cc_final: 0.7809 (tp30) REVERT: B 790 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7866 (ptpp) REVERT: B 1050 MET cc_start: 0.8476 (ptm) cc_final: 0.8186 (ptm) REVERT: B 1144 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7666 (tp30) REVERT: C 95 ILE cc_start: 0.7789 (mm) cc_final: 0.7430 (tp) REVERT: C 110 LEU cc_start: 0.7696 (mp) cc_final: 0.7494 (mm) REVERT: C 118 LEU cc_start: 0.8344 (mp) cc_final: 0.8109 (mp) REVERT: C 194 PHE cc_start: 0.8700 (m-10) cc_final: 0.8383 (m-80) REVERT: C 357 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8251 (ttt180) REVERT: C 371 LEU cc_start: 0.8825 (mp) cc_final: 0.8576 (mt) REVERT: C 405 ASP cc_start: 0.7876 (p0) cc_final: 0.7630 (p0) REVERT: C 465 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7589 (pp20) REVERT: C 478 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8509 (ptpp) REVERT: C 751 ASN cc_start: 0.8471 (m110) cc_final: 0.8248 (m-40) REVERT: C 754 LEU cc_start: 0.8528 (mt) cc_final: 0.8288 (mm) REVERT: C 780 GLU cc_start: 0.8199 (tt0) cc_final: 0.7939 (tp30) REVERT: C 804 GLN cc_start: 0.8522 (mt0) cc_final: 0.8308 (mt0) REVERT: C 945 LEU cc_start: 0.8188 (mt) cc_final: 0.7970 (mm) REVERT: C 950 ASP cc_start: 0.7685 (m-30) cc_final: 0.7375 (m-30) REVERT: C 1010 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: C 1014 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8209 (mtm180) REVERT: C 1038 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8305 (mmmm) REVERT: C 1073 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8158 (mtpm) REVERT: C 1141 LEU cc_start: 0.8507 (tp) cc_final: 0.8235 (tt) outliers start: 66 outliers final: 39 residues processed: 539 average time/residue: 1.3350 time to fit residues: 838.9306 Evaluate side-chains 532 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 488 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 33 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 211 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 658 ASN B 556 ASN B 703 ASN B 804 GLN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN C 779 GLN C 824 ASN C 907 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110958 restraints weight = 38284.597| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.62 r_work: 0.3328 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25935 Z= 0.155 Angle : 0.640 14.135 35379 Z= 0.322 Chirality : 0.047 0.610 4138 Planarity : 0.005 0.071 4464 Dihedral : 6.237 57.770 4462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.01 % Allowed : 17.76 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3072 helix: 1.81 (0.21), residues: 704 sheet: 0.90 (0.19), residues: 701 loop : -1.58 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 436 HIS 0.002 0.001 HIS C 66 PHE 0.022 0.001 PHE A 377 TYR 0.027 0.001 TYR C 351 ARG 0.004 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 37) link_NAG-ASN : angle 3.06106 ( 111) link_BETA1-4 : bond 0.00381 ( 16) link_BETA1-4 : angle 1.17156 ( 48) hydrogen bonds : bond 0.06085 ( 1014) hydrogen bonds : angle 4.93152 ( 2748) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.75115 ( 84) covalent geometry : bond 0.00360 (25840) covalent geometry : angle 0.61093 (35136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 497 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8651 (mttt) cc_final: 0.8338 (mttt) REVERT: A 356 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8360 (mmmm) REVERT: A 571 ASP cc_start: 0.7998 (t70) cc_final: 0.7467 (t0) REVERT: A 702 GLU cc_start: 0.7045 (tp30) cc_final: 0.6756 (tp30) REVERT: A 979 ASP cc_start: 0.7877 (p0) cc_final: 0.7529 (p0) REVERT: A 988 GLU cc_start: 0.7552 (tp30) cc_final: 0.7205 (tp30) REVERT: A 1084 ASP cc_start: 0.7779 (t0) cc_final: 0.7252 (t0) REVERT: B 81 ASN cc_start: 0.7956 (m-40) cc_final: 0.7742 (m-40) REVERT: B 132 GLU cc_start: 0.6197 (pm20) cc_final: 0.5412 (pm20) REVERT: B 169 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7957 (tp30) REVERT: B 196 ASN cc_start: 0.8898 (t0) cc_final: 0.8646 (t0) REVERT: B 220 PHE cc_start: 0.8698 (t80) cc_final: 0.8270 (t80) REVERT: B 324 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: B 440 LYS cc_start: 0.8591 (ptmm) cc_final: 0.8301 (tmmm) REVERT: B 493 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7966 (mmm-85) REVERT: B 588 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8370 (p) REVERT: B 654 GLU cc_start: 0.8439 (tt0) cc_final: 0.8205 (tt0) REVERT: B 751 ASN cc_start: 0.8454 (m-40) cc_final: 0.7875 (m110) REVERT: B 752 LEU cc_start: 0.8125 (mt) cc_final: 0.7798 (mt) REVERT: B 780 GLU cc_start: 0.8325 (tt0) cc_final: 0.7919 (tp30) REVERT: B 790 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7789 (ptpp) REVERT: B 1050 MET cc_start: 0.8405 (ptm) cc_final: 0.8143 (ptm) REVERT: B 1144 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7670 (tp30) REVERT: C 95 ILE cc_start: 0.7737 (mm) cc_final: 0.7401 (tp) REVERT: C 110 LEU cc_start: 0.7716 (mp) cc_final: 0.7502 (mm) REVERT: C 118 LEU cc_start: 0.8401 (mp) cc_final: 0.8046 (mp) REVERT: C 133 PHE cc_start: 0.7299 (m-80) cc_final: 0.6931 (m-80) REVERT: C 194 PHE cc_start: 0.8683 (m-10) cc_final: 0.8355 (m-80) REVERT: C 333 THR cc_start: 0.9018 (t) cc_final: 0.8705 (p) REVERT: C 371 LEU cc_start: 0.8812 (mp) cc_final: 0.8564 (mt) REVERT: C 405 ASP cc_start: 0.7851 (p0) cc_final: 0.7612 (p0) REVERT: C 465 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7624 (pp20) REVERT: C 478 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8436 (ptpp) REVERT: C 751 ASN cc_start: 0.8453 (m110) cc_final: 0.8239 (m-40) REVERT: C 754 LEU cc_start: 0.8514 (mt) cc_final: 0.8275 (mm) REVERT: C 780 GLU cc_start: 0.8164 (tt0) cc_final: 0.7930 (tp30) REVERT: C 950 ASP cc_start: 0.7605 (m-30) cc_final: 0.7325 (m-30) REVERT: C 1010 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: C 1014 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8204 (mtm180) REVERT: C 1038 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8276 (mmmm) REVERT: C 1073 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8146 (mtpm) REVERT: C 1141 LEU cc_start: 0.8494 (tp) cc_final: 0.8245 (tt) outliers start: 55 outliers final: 34 residues processed: 524 average time/residue: 1.3052 time to fit residues: 794.2705 Evaluate side-chains 523 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 484 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 981 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 278 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 289 optimal weight: 0.5980 chunk 126 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 239 GLN A 360 ASN A 603 ASN B 703 ASN B 804 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 804 GLN C 824 ASN C 907 ASN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.138738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111134 restraints weight = 38349.144| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.65 r_work: 0.3321 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25935 Z= 0.159 Angle : 0.645 13.895 35379 Z= 0.326 Chirality : 0.047 0.522 4138 Planarity : 0.005 0.074 4464 Dihedral : 6.194 57.481 4462 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 2.12 % Allowed : 18.45 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3072 helix: 1.82 (0.21), residues: 704 sheet: 0.96 (0.19), residues: 705 loop : -1.58 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 436 HIS 0.003 0.001 HIS C 505 PHE 0.027 0.001 PHE C 456 TYR 0.024 0.001 TYR C 453 ARG 0.006 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 37) link_NAG-ASN : angle 3.01497 ( 111) link_BETA1-4 : bond 0.00382 ( 16) link_BETA1-4 : angle 1.15176 ( 48) hydrogen bonds : bond 0.06015 ( 1014) hydrogen bonds : angle 4.89981 ( 2748) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.73748 ( 84) covalent geometry : bond 0.00371 (25840) covalent geometry : angle 0.61770 (35136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 503 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8657 (mttt) cc_final: 0.8406 (mttt) REVERT: A 323 THR cc_start: 0.6348 (OUTLIER) cc_final: 0.6004 (t) REVERT: A 331 ASN cc_start: 0.6642 (m110) cc_final: 0.6127 (t0) REVERT: A 571 ASP cc_start: 0.8004 (t70) cc_final: 0.7476 (t0) REVERT: A 979 ASP cc_start: 0.7873 (p0) cc_final: 0.7530 (p0) REVERT: A 988 GLU cc_start: 0.7551 (tp30) cc_final: 0.7184 (tp30) REVERT: A 1084 ASP cc_start: 0.7802 (t0) cc_final: 0.7290 (t0) REVERT: B 65 PHE cc_start: 0.8515 (m-80) cc_final: 0.8281 (m-10) REVERT: B 81 ASN cc_start: 0.8020 (m-40) cc_final: 0.7809 (m-40) REVERT: B 132 GLU cc_start: 0.6236 (pm20) cc_final: 0.5652 (pm20) REVERT: B 196 ASN cc_start: 0.8896 (t0) cc_final: 0.8645 (t0) REVERT: B 324 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: B 440 LYS cc_start: 0.8579 (ptmm) cc_final: 0.8314 (tmmm) REVERT: B 493 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7989 (mmm-85) REVERT: B 583 GLU cc_start: 0.8440 (pt0) cc_final: 0.8226 (pt0) REVERT: B 588 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 748 GLU cc_start: 0.7804 (mp0) cc_final: 0.7536 (mp0) REVERT: B 751 ASN cc_start: 0.8466 (m-40) cc_final: 0.7899 (m110) REVERT: B 752 LEU cc_start: 0.8141 (mt) cc_final: 0.7816 (mt) REVERT: B 790 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7874 (ptpp) REVERT: B 918 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7554 (mt-10) REVERT: B 1050 MET cc_start: 0.8442 (ptm) cc_final: 0.8167 (ptm) REVERT: C 95 ILE cc_start: 0.7753 (mm) cc_final: 0.7415 (tp) REVERT: C 118 LEU cc_start: 0.8359 (mp) cc_final: 0.8074 (mp) REVERT: C 194 PHE cc_start: 0.8692 (m-10) cc_final: 0.8360 (m-80) REVERT: C 371 LEU cc_start: 0.8810 (mp) cc_final: 0.8570 (mt) REVERT: C 405 ASP cc_start: 0.7876 (p0) cc_final: 0.7634 (p0) REVERT: C 465 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7661 (pp20) REVERT: C 478 LYS cc_start: 0.8662 (ptpp) cc_final: 0.8434 (ptpp) REVERT: C 754 LEU cc_start: 0.8513 (mt) cc_final: 0.8279 (mm) REVERT: C 780 GLU cc_start: 0.8161 (tt0) cc_final: 0.7941 (tp30) REVERT: C 950 ASP cc_start: 0.7607 (m-30) cc_final: 0.7329 (m-30) REVERT: C 1010 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: C 1014 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8213 (mtm180) REVERT: C 1038 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8277 (mmmm) REVERT: C 1141 LEU cc_start: 0.8508 (tp) cc_final: 0.8236 (tt) outliers start: 58 outliers final: 38 residues processed: 531 average time/residue: 1.3206 time to fit residues: 814.2920 Evaluate side-chains 545 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 501 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 229 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 216 optimal weight: 2.9990 chunk 213 optimal weight: 0.1980 chunk 197 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 360 ASN B 556 ASN B 703 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 824 ASN C 907 ASN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112050 restraints weight = 38507.569| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.66 r_work: 0.3343 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25935 Z= 0.138 Angle : 0.639 13.560 35379 Z= 0.321 Chirality : 0.046 0.505 4138 Planarity : 0.005 0.072 4464 Dihedral : 6.151 59.992 4462 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 1.97 % Allowed : 18.85 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3072 helix: 1.92 (0.21), residues: 698 sheet: 0.98 (0.19), residues: 695 loop : -1.56 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 436 HIS 0.002 0.000 HIS C 505 PHE 0.023 0.001 PHE A 32 TYR 0.028 0.001 TYR C 351 ARG 0.005 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 37) link_NAG-ASN : angle 2.94644 ( 111) link_BETA1-4 : bond 0.00398 ( 16) link_BETA1-4 : angle 1.15574 ( 48) hydrogen bonds : bond 0.05622 ( 1014) hydrogen bonds : angle 4.86380 ( 2748) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.61042 ( 84) covalent geometry : bond 0.00313 (25840) covalent geometry : angle 0.61343 (35136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 500 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8637 (mttt) cc_final: 0.8396 (mttt) REVERT: A 323 THR cc_start: 0.6210 (OUTLIER) cc_final: 0.5792 (t) REVERT: A 331 ASN cc_start: 0.6626 (m110) cc_final: 0.6136 (t0) REVERT: A 364 ASP cc_start: 0.8541 (t0) cc_final: 0.8247 (t0) REVERT: A 571 ASP cc_start: 0.7991 (t70) cc_final: 0.7482 (t0) REVERT: A 702 GLU cc_start: 0.7041 (tp30) cc_final: 0.6685 (tp30) REVERT: A 988 GLU cc_start: 0.7514 (tp30) cc_final: 0.7126 (tp30) REVERT: A 1084 ASP cc_start: 0.7795 (t0) cc_final: 0.7274 (t0) REVERT: B 81 ASN cc_start: 0.8027 (m-40) cc_final: 0.7810 (m-40) REVERT: B 196 ASN cc_start: 0.8884 (t0) cc_final: 0.8642 (t0) REVERT: B 220 PHE cc_start: 0.8702 (t80) cc_final: 0.8272 (t80) REVERT: B 324 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: B 440 LYS cc_start: 0.8605 (ptmm) cc_final: 0.8323 (tmmm) REVERT: B 493 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7959 (mmm-85) REVERT: B 583 GLU cc_start: 0.8446 (pt0) cc_final: 0.8221 (pt0) REVERT: B 588 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8356 (p) REVERT: B 751 ASN cc_start: 0.8440 (m-40) cc_final: 0.7856 (m110) REVERT: B 752 LEU cc_start: 0.8106 (mt) cc_final: 0.7778 (mt) REVERT: B 790 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7760 (ptpp) REVERT: B 848 ASP cc_start: 0.7051 (t0) cc_final: 0.6709 (t0) REVERT: B 960 ASN cc_start: 0.8742 (t0) cc_final: 0.8408 (t0) REVERT: B 1050 MET cc_start: 0.8389 (ptm) cc_final: 0.8126 (ptm) REVERT: B 1144 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7742 (mm-30) REVERT: C 118 LEU cc_start: 0.8337 (mp) cc_final: 0.8116 (mp) REVERT: C 133 PHE cc_start: 0.7398 (m-80) cc_final: 0.7179 (m-80) REVERT: C 194 PHE cc_start: 0.8688 (m-10) cc_final: 0.8352 (m-80) REVERT: C 333 THR cc_start: 0.9032 (t) cc_final: 0.8701 (p) REVERT: C 371 LEU cc_start: 0.8801 (mp) cc_final: 0.8566 (mt) REVERT: C 405 ASP cc_start: 0.7829 (p0) cc_final: 0.7622 (p0) REVERT: C 465 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: C 478 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8396 (ptpp) REVERT: C 754 LEU cc_start: 0.8492 (mt) cc_final: 0.8259 (mm) REVERT: C 780 GLU cc_start: 0.8122 (tt0) cc_final: 0.7904 (tp30) REVERT: C 790 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: C 950 ASP cc_start: 0.7543 (m-30) cc_final: 0.7256 (m-30) REVERT: C 1010 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: C 1014 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8186 (mtm180) REVERT: C 1038 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8268 (mmmm) REVERT: C 1141 LEU cc_start: 0.8465 (tp) cc_final: 0.8262 (tt) outliers start: 54 outliers final: 38 residues processed: 525 average time/residue: 1.9097 time to fit residues: 1169.0773 Evaluate side-chains 531 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 486 time to evaluate : 5.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 205 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 210 optimal weight: 0.1980 chunk 296 optimal weight: 0.3980 chunk 214 optimal weight: 0.0070 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 360 ASN A 777 ASN B 703 ASN B 804 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 658 ASN C 751 ASN C 804 GLN C 824 ASN C 907 ASN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112509 restraints weight = 38295.454| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.63 r_work: 0.3355 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25935 Z= 0.129 Angle : 0.633 13.105 35379 Z= 0.319 Chirality : 0.046 0.495 4138 Planarity : 0.005 0.073 4464 Dihedral : 6.075 57.388 4462 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 1.86 % Allowed : 19.15 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3072 helix: 1.95 (0.21), residues: 698 sheet: 1.04 (0.19), residues: 697 loop : -1.53 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 436 HIS 0.002 0.000 HIS C 505 PHE 0.028 0.001 PHE C 456 TYR 0.029 0.001 TYR C 351 ARG 0.007 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 37) link_NAG-ASN : angle 2.94905 ( 111) link_BETA1-4 : bond 0.00402 ( 16) link_BETA1-4 : angle 1.13466 ( 48) hydrogen bonds : bond 0.05326 ( 1014) hydrogen bonds : angle 4.80472 ( 2748) SS BOND : bond 0.00423 ( 42) SS BOND : angle 1.51849 ( 84) covalent geometry : bond 0.00292 (25840) covalent geometry : angle 0.60753 (35136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 492 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 SER cc_start: 0.8626 (p) cc_final: 0.8407 (m) REVERT: A 331 ASN cc_start: 0.6613 (m110) cc_final: 0.6205 (t0) REVERT: A 571 ASP cc_start: 0.8007 (t70) cc_final: 0.7492 (t0) REVERT: A 702 GLU cc_start: 0.7035 (tp30) cc_final: 0.6679 (tp30) REVERT: A 988 GLU cc_start: 0.7486 (tp30) cc_final: 0.7116 (tp30) REVERT: A 1084 ASP cc_start: 0.7782 (t0) cc_final: 0.7358 (t0) REVERT: B 65 PHE cc_start: 0.8442 (m-80) cc_final: 0.8217 (m-10) REVERT: B 81 ASN cc_start: 0.8032 (m-40) cc_final: 0.7820 (m-40) REVERT: B 132 GLU cc_start: 0.6213 (pm20) cc_final: 0.5789 (pm20) REVERT: B 169 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7897 (tp30) REVERT: B 196 ASN cc_start: 0.8870 (t0) cc_final: 0.8618 (t0) REVERT: B 324 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: B 406 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7658 (mp0) REVERT: B 440 LYS cc_start: 0.8565 (ptmm) cc_final: 0.8307 (tmmm) REVERT: B 467 ASP cc_start: 0.8380 (p0) cc_final: 0.8152 (p0) REVERT: B 493 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7967 (mmm-85) REVERT: B 588 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8339 (p) REVERT: B 751 ASN cc_start: 0.8436 (m-40) cc_final: 0.7855 (m110) REVERT: B 752 LEU cc_start: 0.8107 (mt) cc_final: 0.7781 (mt) REVERT: B 780 GLU cc_start: 0.8312 (tt0) cc_final: 0.7947 (tp30) REVERT: B 790 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7762 (ptpp) REVERT: B 848 ASP cc_start: 0.7065 (t0) cc_final: 0.6734 (t0) REVERT: B 960 ASN cc_start: 0.8747 (t0) cc_final: 0.8401 (t0) REVERT: B 1050 MET cc_start: 0.8404 (ptm) cc_final: 0.8161 (ptm) REVERT: B 1144 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7658 (tp30) REVERT: C 110 LEU cc_start: 0.7775 (mp) cc_final: 0.7519 (mm) REVERT: C 112 SER cc_start: 0.6942 (p) cc_final: 0.6574 (m) REVERT: C 118 LEU cc_start: 0.8343 (mp) cc_final: 0.8134 (mp) REVERT: C 133 PHE cc_start: 0.7443 (m-80) cc_final: 0.7216 (m-80) REVERT: C 194 PHE cc_start: 0.8669 (m-10) cc_final: 0.8373 (m-80) REVERT: C 237 ARG cc_start: 0.8246 (mtp-110) cc_final: 0.7410 (mtp-110) REVERT: C 333 THR cc_start: 0.9037 (t) cc_final: 0.8706 (p) REVERT: C 371 LEU cc_start: 0.8791 (mp) cc_final: 0.8557 (mt) REVERT: C 405 ASP cc_start: 0.7777 (p0) cc_final: 0.7565 (p0) REVERT: C 465 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: C 478 LYS cc_start: 0.8633 (ptpp) cc_final: 0.8397 (ptpp) REVERT: C 754 LEU cc_start: 0.8493 (mt) cc_final: 0.8261 (mm) REVERT: C 790 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8063 (mttp) REVERT: C 822 LEU cc_start: 0.8051 (mt) cc_final: 0.7833 (mp) REVERT: C 950 ASP cc_start: 0.7508 (m-30) cc_final: 0.7223 (m-30) REVERT: C 1010 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: C 1038 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8253 (mmmm) REVERT: C 1141 LEU cc_start: 0.8525 (tp) cc_final: 0.8288 (tt) outliers start: 51 outliers final: 37 residues processed: 520 average time/residue: 1.3059 time to fit residues: 790.6749 Evaluate side-chains 526 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 485 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 300 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 303 optimal weight: 0.0980 chunk 297 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 360 ASN A 603 ASN A 777 ASN B 703 ASN C 30 ASN C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 824 ASN C 907 ASN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111729 restraints weight = 38144.499| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.67 r_work: 0.3339 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25935 Z= 0.154 Angle : 0.657 13.124 35379 Z= 0.328 Chirality : 0.046 0.490 4138 Planarity : 0.005 0.074 4464 Dihedral : 6.145 59.486 4462 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 1.75 % Allowed : 19.51 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3072 helix: 1.96 (0.21), residues: 692 sheet: 1.03 (0.19), residues: 693 loop : -1.58 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 436 HIS 0.002 0.000 HIS B 505 PHE 0.029 0.001 PHE A 32 TYR 0.029 0.001 TYR C 351 ARG 0.005 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 37) link_NAG-ASN : angle 2.93464 ( 111) link_BETA1-4 : bond 0.00385 ( 16) link_BETA1-4 : angle 1.13005 ( 48) hydrogen bonds : bond 0.05686 ( 1014) hydrogen bonds : angle 4.83495 ( 2748) SS BOND : bond 0.00424 ( 42) SS BOND : angle 1.67702 ( 84) covalent geometry : bond 0.00359 (25840) covalent geometry : angle 0.63186 (35136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24428.40 seconds wall clock time: 430 minutes 30.26 seconds (25830.26 seconds total)