Starting phenix.real_space_refine on Mon Feb 19 16:29:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9s_33690/02_2024/7y9s_33690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9s_33690/02_2024/7y9s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9s_33690/02_2024/7y9s_33690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9s_33690/02_2024/7y9s_33690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9s_33690/02_2024/7y9s_33690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9s_33690/02_2024/7y9s_33690.pdb" } 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 Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13.47, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 9.99 Conformation dependent library (CDL) restraints added in 4.8 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: 3.10 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: 13.66 Time building geometry restraints manager: 10.68 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: 99.43 - 106.35: 657 106.35 - 113.26: 14103 113.26 - 120.17: 8721 120.17 - 127.09: 11446 127.09 - 134.00: 209 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 2.440 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.239 2.440 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.258 2.520 nonbonded pdb=" OD2 ASP A 40 " pdb=" NH1 ARG A 44 " model vdw 2.264 2.520 ... (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 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: 4.720 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: 14.000 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 71.840 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.470 ------------------------------------------------------------------------------- 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 25840 Z= 0.247 Angle : 0.643 12.836 35136 Z= 0.342 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 527 time to evaluate : 2.859 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: 1.2828 time to fit residues: 789.7524 Evaluate side-chains 484 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 480 time to evaluate : 2.743 ------------------------------------------------------------------------------- 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: 0.7980 chunk 131 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 182 optimal weight: 0.1980 chunk 283 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 370 ASN B 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 81 ASN C 99 ASN C 690 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C 965 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25840 Z= 0.203 Angle : 0.579 9.791 35136 Z= 0.299 Chirality : 0.045 0.398 4138 Planarity : 0.005 0.076 4464 Dihedral : 7.402 81.428 4469 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % Rotamer: Outliers : 1.10 % Allowed : 10.27 % 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: -0.10 (0.15), residues: 3072 helix: 2.10 (0.21), residues: 690 sheet: 1.09 (0.19), residues: 686 loop : -1.60 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.004 0.001 HIS A 207 PHE 0.025 0.001 PHE A 347 TYR 0.023 0.001 TYR C 453 ARG 0.005 0.000 ARG C 237 *********************** 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 518 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 488 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 436 TRP cc_start: 0.7728 (p90) cc_final: 0.7375 (p90) REVERT: A 558 LYS cc_start: 0.8004 (mmpt) cc_final: 0.7257 (mmpt) REVERT: A 571 ASP cc_start: 0.7812 (t70) cc_final: 0.7350 (t0) REVERT: A 578 ASP cc_start: 0.7604 (t70) cc_final: 0.7398 (t0) REVERT: A 583 GLU cc_start: 0.7502 (pm20) cc_final: 0.7282 (pm20) REVERT: A 586 ASP cc_start: 0.7649 (m-30) cc_final: 0.7437 (m-30) REVERT: A 900 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7909 (mtp) REVERT: A 988 GLU cc_start: 0.7357 (tp30) cc_final: 0.6895 (tm-30) REVERT: A 1084 ASP cc_start: 0.7294 (t0) cc_final: 0.6833 (t0) REVERT: B 132 GLU cc_start: 0.6239 (pm20) cc_final: 0.5830 (pm20) REVERT: B 440 LYS cc_start: 0.8364 (ptmm) cc_final: 0.8095 (tmmm) REVERT: B 493 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7516 (mmm-85) REVERT: B 534 VAL cc_start: 0.8340 (m) cc_final: 0.8129 (t) REVERT: B 654 GLU cc_start: 0.7855 (tt0) cc_final: 0.7608 (tt0) REVERT: B 752 LEU cc_start: 0.8185 (mt) cc_final: 0.7906 (mt) REVERT: B 776 LYS cc_start: 0.8437 (ttpp) cc_final: 0.8223 (ttmm) REVERT: B 780 GLU cc_start: 0.7732 (tt0) cc_final: 0.7496 (tp30) REVERT: B 814 LYS cc_start: 0.8351 (mmtm) cc_final: 0.8045 (mmtt) REVERT: B 825 LYS cc_start: 0.8129 (tppp) cc_final: 0.7767 (tppp) REVERT: B 921 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7862 (mtpp) REVERT: B 1144 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7528 (tp30) REVERT: C 117 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7371 (mt) REVERT: C 194 PHE cc_start: 0.8604 (m-10) cc_final: 0.8284 (m-80) REVERT: C 370 ASN cc_start: 0.7597 (p0) cc_final: 0.7380 (p0) REVERT: C 371 LEU cc_start: 0.8772 (mp) cc_final: 0.8564 (mt) REVERT: C 586 ASP cc_start: 0.7838 (m-30) cc_final: 0.7635 (m-30) REVERT: C 751 ASN cc_start: 0.8325 (m110) cc_final: 0.7915 (m110) REVERT: C 754 LEU cc_start: 0.8440 (mt) cc_final: 0.8172 (mm) REVERT: C 790 LYS cc_start: 0.8251 (mttp) cc_final: 0.8009 (mttp) REVERT: C 900 MET cc_start: 0.8354 (mtt) cc_final: 0.8129 (mtm) REVERT: C 918 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 935 GLN cc_start: 0.7891 (pt0) cc_final: 0.7681 (pt0) REVERT: C 950 ASP cc_start: 0.7210 (m-30) cc_final: 0.6923 (m-30) REVERT: C 1010 GLN cc_start: 0.8270 (mp10) cc_final: 0.7853 (mp10) REVERT: C 1038 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8128 (mmmm) REVERT: C 1141 LEU cc_start: 0.8501 (tp) cc_final: 0.8212 (tt) outliers start: 30 outliers final: 9 residues processed: 497 average time/residue: 1.3186 time to fit residues: 758.0904 Evaluate side-chains 489 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 477 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 227 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 0.0670 chunk 306 optimal weight: 0.0980 chunk 252 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 0.0070 chunk 227 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 196 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 81 ASN C 99 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 603 ASN C 779 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25840 Z= 0.182 Angle : 0.555 9.297 35136 Z= 0.287 Chirality : 0.045 0.409 4138 Planarity : 0.005 0.065 4464 Dihedral : 6.874 56.831 4463 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 1.75 % Allowed : 12.71 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3072 helix: 1.99 (0.21), residues: 709 sheet: 1.11 (0.19), residues: 660 loop : -1.55 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.004 0.000 HIS A 207 PHE 0.023 0.001 PHE B 400 TYR 0.023 0.001 TYR C 453 ARG 0.005 0.000 ARG B1107 *********************** 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 548 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 500 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8292 (t) REVERT: A 436 TRP cc_start: 0.7774 (p90) cc_final: 0.7392 (p90) REVERT: A 529 LYS cc_start: 0.8330 (tmtt) cc_final: 0.8086 (tmtt) REVERT: A 558 LYS cc_start: 0.8010 (mmpt) cc_final: 0.7242 (mmpt) REVERT: A 571 ASP cc_start: 0.7829 (t70) cc_final: 0.7340 (t0) REVERT: A 578 ASP cc_start: 0.7587 (t70) cc_final: 0.7378 (t0) REVERT: A 752 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8453 (mt) REVERT: A 900 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7883 (mtp) REVERT: A 988 GLU cc_start: 0.7346 (tp30) cc_final: 0.6980 (tp30) REVERT: A 1073 LYS cc_start: 0.8067 (tttt) cc_final: 0.7813 (mtpp) REVERT: A 1084 ASP cc_start: 0.7297 (t0) cc_final: 0.6789 (t0) REVERT: B 132 GLU cc_start: 0.5934 (pm20) cc_final: 0.5312 (pm20) REVERT: B 324 GLU cc_start: 0.7677 (pm20) cc_final: 0.7394 (pm20) REVERT: B 440 LYS cc_start: 0.8380 (ptmm) cc_final: 0.8108 (tmmm) REVERT: B 493 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7498 (mmm-85) REVERT: B 534 VAL cc_start: 0.8338 (m) cc_final: 0.8129 (t) REVERT: B 583 GLU cc_start: 0.8235 (pt0) cc_final: 0.7975 (pt0) REVERT: B 752 LEU cc_start: 0.8137 (mt) cc_final: 0.7843 (mt) REVERT: B 790 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7619 (ptpp) REVERT: B 814 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7963 (mmtt) REVERT: B 921 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7862 (mtpp) REVERT: B 960 ASN cc_start: 0.8555 (t0) cc_final: 0.8132 (t0) REVERT: B 1144 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7612 (mm-30) REVERT: C 117 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7512 (mt) REVERT: C 194 PHE cc_start: 0.8599 (m-10) cc_final: 0.8296 (m-80) REVERT: C 370 ASN cc_start: 0.7617 (p0) cc_final: 0.7414 (p0) REVERT: C 371 LEU cc_start: 0.8775 (mp) cc_final: 0.8535 (mt) REVERT: C 465 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7187 (pp20) REVERT: C 474 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: C 586 ASP cc_start: 0.7825 (m-30) cc_final: 0.7617 (m-30) REVERT: C 751 ASN cc_start: 0.8313 (m110) cc_final: 0.7880 (m110) REVERT: C 754 LEU cc_start: 0.8445 (mt) cc_final: 0.8181 (mm) REVERT: C 918 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7670 (mt-10) REVERT: C 935 GLN cc_start: 0.7898 (pt0) cc_final: 0.7697 (pt0) REVERT: C 965 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: C 1010 GLN cc_start: 0.8301 (mp10) cc_final: 0.7909 (mp10) REVERT: C 1038 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8123 (mmmm) REVERT: C 1111 GLU cc_start: 0.7944 (tt0) cc_final: 0.7617 (mt-10) REVERT: C 1141 LEU cc_start: 0.8485 (tp) cc_final: 0.8145 (tt) outliers start: 48 outliers final: 22 residues processed: 516 average time/residue: 1.3048 time to fit residues: 776.5606 Evaluate side-chains 517 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 488 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 335 LEU 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 A residue 1002 GLN Chi-restraints excluded: chain A residue 1125 ASN 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 402 ILE Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL 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 339 ASP Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 965 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 239 GLN A 360 ASN A 777 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 66 HIS C 81 ASN C 99 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25840 Z= 0.252 Angle : 0.580 9.542 35136 Z= 0.300 Chirality : 0.046 0.411 4138 Planarity : 0.005 0.070 4464 Dihedral : 6.678 59.811 4462 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.76 % Rotamer: Outliers : 1.97 % Allowed : 14.32 % Favored : 83.70 % 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: 1.98 (0.21), residues: 703 sheet: 1.14 (0.19), residues: 676 loop : -1.63 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS C 66 PHE 0.023 0.002 PHE B 400 TYR 0.024 0.001 TYR C 453 ARG 0.005 0.000 ARG B1107 *********************** 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 fitting. rotamer outliers: 54 poor density : 509 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (t) REVERT: A 436 TRP cc_start: 0.7774 (p90) cc_final: 0.7477 (p90) REVERT: A 529 LYS cc_start: 0.8326 (tmtt) cc_final: 0.8106 (tmtt) REVERT: A 571 ASP cc_start: 0.7846 (t70) cc_final: 0.7356 (t0) REVERT: A 988 GLU cc_start: 0.7364 (tp30) cc_final: 0.7048 (tp30) REVERT: A 1073 LYS cc_start: 0.8124 (tttt) cc_final: 0.7877 (mtpp) REVERT: A 1084 ASP cc_start: 0.7371 (t0) cc_final: 0.6814 (t0) REVERT: B 81 ASN cc_start: 0.7647 (m-40) cc_final: 0.7329 (m-40) REVERT: B 132 GLU cc_start: 0.5917 (pm20) cc_final: 0.4879 (pm20) REVERT: B 242 LEU cc_start: 0.8002 (mm) cc_final: 0.7752 (mp) REVERT: B 324 GLU cc_start: 0.7571 (pm20) cc_final: 0.7328 (pm20) REVERT: B 440 LYS cc_start: 0.8414 (ptmm) cc_final: 0.8132 (tmmm) REVERT: B 493 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7503 (mmm-85) REVERT: B 534 VAL cc_start: 0.8339 (m) cc_final: 0.8139 (t) REVERT: B 556 ASN cc_start: 0.8047 (m110) cc_final: 0.7843 (m110) REVERT: B 583 GLU cc_start: 0.8266 (pt0) cc_final: 0.8015 (pt0) REVERT: B 752 LEU cc_start: 0.8103 (mt) cc_final: 0.7790 (mt) REVERT: B 814 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7969 (mmtt) REVERT: B 918 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7488 (mt-10) REVERT: B 921 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7959 (mtpp) REVERT: B 1111 GLU cc_start: 0.8232 (tt0) cc_final: 0.7997 (tt0) REVERT: C 83 VAL cc_start: 0.8253 (t) cc_final: 0.8044 (p) REVERT: C 118 LEU cc_start: 0.8137 (mp) cc_final: 0.7784 (mp) REVERT: C 194 PHE cc_start: 0.8623 (m-10) cc_final: 0.8275 (m-80) REVERT: C 370 ASN cc_start: 0.7648 (p0) cc_final: 0.7444 (p0) REVERT: C 371 LEU cc_start: 0.8783 (mp) cc_final: 0.8514 (mt) REVERT: C 751 ASN cc_start: 0.8336 (m110) cc_final: 0.8076 (m-40) REVERT: C 754 LEU cc_start: 0.8464 (mt) cc_final: 0.8205 (mm) REVERT: C 776 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8183 (ttpp) REVERT: C 935 GLN cc_start: 0.7943 (pt0) cc_final: 0.7733 (pt0) REVERT: C 945 LEU cc_start: 0.8188 (mt) cc_final: 0.7977 (mm) REVERT: C 950 ASP cc_start: 0.7354 (m-30) cc_final: 0.7083 (m-30) REVERT: C 1010 GLN cc_start: 0.8326 (mp10) cc_final: 0.7921 (mp10) REVERT: C 1038 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8156 (mmmm) REVERT: C 1141 LEU cc_start: 0.8463 (tp) cc_final: 0.8149 (tt) outliers start: 54 outliers final: 31 residues processed: 534 average time/residue: 1.3290 time to fit residues: 822.1075 Evaluate side-chains 520 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 488 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 323 THR 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 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 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 402 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 618 THR 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 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 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 549 THR 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 251 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 224 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 0.5980 chunk 208 optimal weight: 100.0000 chunk 0 optimal weight: 120.0000 chunk 153 optimal weight: 0.5980 chunk 270 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 A 777 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25840 Z= 0.276 Angle : 0.597 9.500 35136 Z= 0.309 Chirality : 0.046 0.405 4138 Planarity : 0.005 0.070 4464 Dihedral : 6.574 58.915 4462 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 2.74 % Allowed : 14.87 % Favored : 82.39 % 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: 1.91 (0.21), residues: 703 sheet: 1.01 (0.19), residues: 701 loop : -1.63 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.003 0.001 HIS C 66 PHE 0.023 0.002 PHE C 456 TYR 0.027 0.002 TYR C 453 ARG 0.006 0.000 ARG B1107 *********************** 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 588 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 513 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 364 ASP cc_start: 0.8403 (t0) cc_final: 0.8113 (t70) REVERT: A 436 TRP cc_start: 0.7819 (p90) cc_final: 0.7597 (p90) REVERT: A 571 ASP cc_start: 0.7879 (t70) cc_final: 0.7380 (t0) REVERT: A 988 GLU cc_start: 0.7386 (tp30) cc_final: 0.7060 (tp30) REVERT: A 1017 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 1084 ASP cc_start: 0.7426 (t0) cc_final: 0.6885 (t0) REVERT: B 81 ASN cc_start: 0.7812 (m-40) cc_final: 0.7436 (m-40) REVERT: B 132 GLU cc_start: 0.5954 (pm20) cc_final: 0.4914 (pm20) REVERT: B 242 LEU cc_start: 0.8092 (mm) cc_final: 0.7790 (mp) REVERT: B 324 GLU cc_start: 0.7578 (pm20) cc_final: 0.7315 (pm20) REVERT: B 440 LYS cc_start: 0.8446 (ptmm) cc_final: 0.8147 (tmmm) REVERT: B 493 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7513 (mmm-85) REVERT: B 556 ASN cc_start: 0.8073 (m110) cc_final: 0.7857 (m110) REVERT: B 583 GLU cc_start: 0.8283 (pt0) cc_final: 0.8041 (pt0) REVERT: B 752 LEU cc_start: 0.8110 (mt) cc_final: 0.7783 (mt) REVERT: B 814 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7972 (mmtt) REVERT: B 902 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8179 (mmt) REVERT: B 921 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7995 (mtpp) REVERT: B 1050 MET cc_start: 0.8376 (ptm) cc_final: 0.8163 (ptm) REVERT: B 1111 GLU cc_start: 0.8235 (tt0) cc_final: 0.7985 (tt0) REVERT: B 1144 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7595 (mm-30) REVERT: C 99 ASN cc_start: 0.8508 (t0) cc_final: 0.7108 (t0) REVERT: C 102 ARG cc_start: 0.6907 (mmt90) cc_final: 0.6365 (mmt-90) REVERT: C 118 LEU cc_start: 0.8168 (mp) cc_final: 0.7861 (mp) REVERT: C 194 PHE cc_start: 0.8622 (m-10) cc_final: 0.8275 (m-80) REVERT: C 371 LEU cc_start: 0.8792 (mp) cc_final: 0.8526 (mt) REVERT: C 465 GLU cc_start: 0.7560 (pp20) cc_final: 0.7310 (pp20) REVERT: C 751 ASN cc_start: 0.8367 (m110) cc_final: 0.8109 (m-40) REVERT: C 754 LEU cc_start: 0.8474 (mt) cc_final: 0.8225 (mm) REVERT: C 776 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8212 (ttpp) REVERT: C 935 GLN cc_start: 0.7977 (pt0) cc_final: 0.7769 (pt0) REVERT: C 945 LEU cc_start: 0.8177 (mt) cc_final: 0.7968 (mm) REVERT: C 950 ASP cc_start: 0.7420 (m-30) cc_final: 0.7108 (m-30) REVERT: C 1010 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: C 1014 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7851 (mtm180) REVERT: C 1038 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8159 (mmmm) REVERT: C 1073 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7996 (mtpp) REVERT: C 1141 LEU cc_start: 0.8446 (tp) cc_final: 0.8221 (tt) outliers start: 75 outliers final: 43 residues processed: 548 average time/residue: 1.2837 time to fit residues: 815.2818 Evaluate side-chains 544 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 498 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL 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 602 THR Chi-restraints excluded: chain A residue 666 ILE 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 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 380 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 523 THR 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 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1125 ASN 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 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 360 ASN Chi-restraints excluded: chain C residue 362 VAL 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 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 1002 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 0.0370 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 603 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 907 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25840 Z= 0.252 Angle : 0.591 10.084 35136 Z= 0.307 Chirality : 0.046 0.479 4138 Planarity : 0.005 0.074 4464 Dihedral : 6.458 59.800 4462 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 2.52 % Allowed : 16.22 % Favored : 81.26 % 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: 1.91 (0.21), residues: 703 sheet: 0.99 (0.19), residues: 698 loop : -1.63 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS C 505 PHE 0.029 0.002 PHE A 168 TYR 0.022 0.001 TYR C 453 ARG 0.004 0.000 ARG B1107 *********************** 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 576 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 507 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8394 (t0) cc_final: 0.8084 (t0) REVERT: A 436 TRP cc_start: 0.7807 (p90) cc_final: 0.7605 (p90) REVERT: A 571 ASP cc_start: 0.7884 (t70) cc_final: 0.7384 (t0) REVERT: A 581 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7423 (p) REVERT: A 960 ASN cc_start: 0.8419 (t0) cc_final: 0.8114 (t0) REVERT: A 988 GLU cc_start: 0.7378 (tp30) cc_final: 0.7054 (tp30) REVERT: A 1017 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 1045 LYS cc_start: 0.7957 (tppp) cc_final: 0.7473 (tppp) REVERT: A 1084 ASP cc_start: 0.7457 (t0) cc_final: 0.6922 (t0) REVERT: B 81 ASN cc_start: 0.7814 (m-40) cc_final: 0.7445 (m-40) REVERT: B 132 GLU cc_start: 0.5999 (pm20) cc_final: 0.4969 (pm20) REVERT: B 242 LEU cc_start: 0.8086 (mm) cc_final: 0.7780 (mp) REVERT: B 324 GLU cc_start: 0.7587 (pm20) cc_final: 0.7349 (pm20) REVERT: B 378 LYS cc_start: 0.7553 (mmmm) cc_final: 0.7289 (mmmm) REVERT: B 403 ARG cc_start: 0.7802 (ptt180) cc_final: 0.7280 (ptp90) REVERT: B 440 LYS cc_start: 0.8445 (ptmm) cc_final: 0.8190 (tmmm) REVERT: B 467 ASP cc_start: 0.8115 (p0) cc_final: 0.7739 (p0) REVERT: B 493 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7482 (mmm-85) REVERT: B 583 GLU cc_start: 0.8301 (pt0) cc_final: 0.8057 (pt0) REVERT: B 588 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8333 (p) REVERT: B 752 LEU cc_start: 0.8115 (mt) cc_final: 0.7804 (mt) REVERT: B 814 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7963 (mmtt) REVERT: B 848 ASP cc_start: 0.6913 (t0) cc_final: 0.6677 (t0) REVERT: B 902 MET cc_start: 0.8406 (mmm) cc_final: 0.8185 (mmt) REVERT: B 921 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7982 (mtpp) REVERT: B 1050 MET cc_start: 0.8355 (ptm) cc_final: 0.8029 (ptm) REVERT: B 1111 GLU cc_start: 0.8234 (tt0) cc_final: 0.7962 (tt0) REVERT: C 118 LEU cc_start: 0.8163 (mp) cc_final: 0.7863 (mp) REVERT: C 194 PHE cc_start: 0.8618 (m-10) cc_final: 0.8287 (m-80) REVERT: C 226 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7673 (tm) REVERT: C 371 LEU cc_start: 0.8794 (mp) cc_final: 0.8560 (mt) REVERT: C 465 GLU cc_start: 0.7483 (pp20) cc_final: 0.7252 (pp20) REVERT: C 751 ASN cc_start: 0.8354 (m110) cc_final: 0.8104 (m-40) REVERT: C 754 LEU cc_start: 0.8470 (mt) cc_final: 0.8224 (mm) REVERT: C 776 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8200 (ttpp) REVERT: C 950 ASP cc_start: 0.7429 (m-30) cc_final: 0.7108 (m-30) REVERT: C 1010 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: C 1014 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7805 (mtm180) REVERT: C 1038 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8154 (mmmm) REVERT: C 1141 LEU cc_start: 0.8512 (tp) cc_final: 0.8239 (tt) outliers start: 69 outliers final: 47 residues processed: 537 average time/residue: 1.3704 time to fit residues: 852.1217 Evaluate side-chains 545 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 493 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 581 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 754 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 523 THR 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 588 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1125 ASN 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 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 461 LEU 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 1002 GLN 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 291 optimal weight: 0.0070 chunk 34 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 254 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 300 optimal weight: 0.0770 chunk 188 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 603 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 703 ASN C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 907 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25840 Z= 0.189 Angle : 0.573 10.350 35136 Z= 0.295 Chirality : 0.046 0.637 4138 Planarity : 0.005 0.070 4464 Dihedral : 6.265 59.225 4462 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 2.56 % Allowed : 17.28 % Favored : 80.16 % 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: 2.04 (0.21), residues: 701 sheet: 0.98 (0.19), residues: 698 loop : -1.56 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.000 HIS A 207 PHE 0.024 0.001 PHE A 377 TYR 0.027 0.001 TYR C 351 ARG 0.004 0.000 ARG B1107 *********************** 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 573 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 503 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8391 (t0) cc_final: 0.8097 (t70) REVERT: A 571 ASP cc_start: 0.7876 (t70) cc_final: 0.7392 (t0) REVERT: A 578 ASP cc_start: 0.7416 (t0) cc_final: 0.7201 (t70) REVERT: A 581 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7316 (p) REVERT: A 900 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: A 960 ASN cc_start: 0.8453 (t0) cc_final: 0.8144 (t0) REVERT: A 988 GLU cc_start: 0.7362 (tp30) cc_final: 0.7010 (tp30) REVERT: A 1017 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 1045 LYS cc_start: 0.7951 (tppp) cc_final: 0.7469 (tppp) REVERT: A 1084 ASP cc_start: 0.7452 (t0) cc_final: 0.6909 (t0) REVERT: B 65 PHE cc_start: 0.8424 (m-80) cc_final: 0.8190 (m-10) REVERT: B 81 ASN cc_start: 0.7814 (m-40) cc_final: 0.7572 (m-40) REVERT: B 242 LEU cc_start: 0.8104 (mm) cc_final: 0.7851 (mt) REVERT: B 324 GLU cc_start: 0.7573 (pm20) cc_final: 0.7274 (pm20) REVERT: B 403 ARG cc_start: 0.7711 (ptt180) cc_final: 0.7311 (ptp-170) REVERT: B 440 LYS cc_start: 0.8426 (ptmm) cc_final: 0.8173 (tmmm) REVERT: B 467 ASP cc_start: 0.8082 (p0) cc_final: 0.7733 (p0) REVERT: B 493 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7489 (mmm-85) REVERT: B 583 GLU cc_start: 0.8304 (pt0) cc_final: 0.8058 (pt0) REVERT: B 588 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8323 (p) REVERT: B 752 LEU cc_start: 0.8108 (mt) cc_final: 0.7789 (mt) REVERT: B 814 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7953 (mmtt) REVERT: B 848 ASP cc_start: 0.6915 (t0) cc_final: 0.6685 (t0) REVERT: B 902 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8176 (mmt) REVERT: B 921 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7920 (mtpp) REVERT: B 1050 MET cc_start: 0.8305 (ptm) cc_final: 0.8049 (ptm) REVERT: C 118 LEU cc_start: 0.8180 (mp) cc_final: 0.7774 (mp) REVERT: C 133 PHE cc_start: 0.7088 (m-80) cc_final: 0.6609 (m-10) REVERT: C 194 PHE cc_start: 0.8605 (m-10) cc_final: 0.8280 (m-80) REVERT: C 226 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7648 (tm) REVERT: C 333 THR cc_start: 0.8948 (t) cc_final: 0.8632 (p) REVERT: C 371 LEU cc_start: 0.8799 (mp) cc_final: 0.8569 (mt) REVERT: C 465 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7179 (pp20) REVERT: C 751 ASN cc_start: 0.8339 (m110) cc_final: 0.8117 (m-40) REVERT: C 754 LEU cc_start: 0.8461 (mt) cc_final: 0.8219 (mm) REVERT: C 776 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8169 (ttpp) REVERT: C 950 ASP cc_start: 0.7363 (m-30) cc_final: 0.7039 (m-30) REVERT: C 1010 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: C 1014 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7846 (mtm180) REVERT: C 1038 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8147 (mmmm) REVERT: C 1141 LEU cc_start: 0.8483 (tp) cc_final: 0.8230 (tt) outliers start: 70 outliers final: 38 residues processed: 535 average time/residue: 1.3400 time to fit residues: 835.2510 Evaluate side-chains 542 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 496 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 581 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 740 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN 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 523 THR 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 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 361 CYS 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 525 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 0.0570 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 603 ASN A 777 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25840 Z= 0.214 Angle : 0.591 11.134 35136 Z= 0.303 Chirality : 0.046 0.516 4138 Planarity : 0.005 0.072 4464 Dihedral : 6.234 56.991 4462 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 2.34 % Allowed : 17.94 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3072 helix: 2.00 (0.21), residues: 703 sheet: 0.94 (0.19), residues: 711 loop : -1.56 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 436 HIS 0.003 0.001 HIS A 207 PHE 0.027 0.001 PHE C 456 TYR 0.023 0.001 TYR C 453 ARG 0.007 0.000 ARG C 577 *********************** 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 569 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 505 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8576 (mttt) cc_final: 0.8351 (mttt) REVERT: A 364 ASP cc_start: 0.8386 (t0) cc_final: 0.8098 (t70) REVERT: A 571 ASP cc_start: 0.7884 (t70) cc_final: 0.7386 (t0) REVERT: A 578 ASP cc_start: 0.7461 (t0) cc_final: 0.7252 (t70) REVERT: A 581 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7426 (p) REVERT: A 900 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: A 960 ASN cc_start: 0.8456 (t0) cc_final: 0.8149 (t0) REVERT: A 988 GLU cc_start: 0.7358 (tp30) cc_final: 0.7013 (tp30) REVERT: A 1017 GLU cc_start: 0.7376 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 1045 LYS cc_start: 0.7961 (tppp) cc_final: 0.7472 (tppp) REVERT: A 1084 ASP cc_start: 0.7470 (t0) cc_final: 0.6928 (t0) REVERT: B 81 ASN cc_start: 0.7866 (m-40) cc_final: 0.7640 (m-40) REVERT: B 132 GLU cc_start: 0.6196 (pm20) cc_final: 0.5708 (pm20) REVERT: B 242 LEU cc_start: 0.8066 (mm) cc_final: 0.7779 (mt) REVERT: B 324 GLU cc_start: 0.7662 (pm20) cc_final: 0.7363 (pm20) REVERT: B 403 ARG cc_start: 0.7764 (ptt180) cc_final: 0.7381 (ptp-170) REVERT: B 440 LYS cc_start: 0.8434 (ptmm) cc_final: 0.8176 (tmmm) REVERT: B 467 ASP cc_start: 0.8077 (p0) cc_final: 0.7731 (p0) REVERT: B 493 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7532 (mmm-85) REVERT: B 583 GLU cc_start: 0.8323 (pt0) cc_final: 0.8080 (pt0) REVERT: B 588 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8330 (p) REVERT: B 702 GLU cc_start: 0.7688 (tp30) cc_final: 0.7357 (tt0) REVERT: B 752 LEU cc_start: 0.8069 (mt) cc_final: 0.7735 (mt) REVERT: B 814 LYS cc_start: 0.8260 (mmtm) cc_final: 0.7960 (mmtt) REVERT: B 848 ASP cc_start: 0.6932 (t0) cc_final: 0.6694 (t0) REVERT: B 902 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8181 (mmt) REVERT: B 921 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7941 (mtpp) REVERT: B 960 ASN cc_start: 0.8584 (t0) cc_final: 0.8243 (t0) REVERT: B 1050 MET cc_start: 0.8298 (ptm) cc_final: 0.8030 (ptm) REVERT: C 118 LEU cc_start: 0.8186 (mp) cc_final: 0.7954 (mp) REVERT: C 133 PHE cc_start: 0.7183 (m-80) cc_final: 0.6969 (m-80) REVERT: C 194 PHE cc_start: 0.8611 (m-10) cc_final: 0.8288 (m-80) REVERT: C 226 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7651 (tm) REVERT: C 357 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7750 (ttt90) REVERT: C 371 LEU cc_start: 0.8790 (mp) cc_final: 0.8573 (mt) REVERT: C 465 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7223 (pp20) REVERT: C 754 LEU cc_start: 0.8454 (mt) cc_final: 0.8212 (mm) REVERT: C 776 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8174 (ttpp) REVERT: C 790 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7806 (mmtp) REVERT: C 950 ASP cc_start: 0.7381 (m-30) cc_final: 0.7042 (m-30) REVERT: C 1010 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: C 1014 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7844 (mtm180) REVERT: C 1038 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8152 (mmmm) REVERT: C 1141 LEU cc_start: 0.8486 (tp) cc_final: 0.8208 (tt) outliers start: 64 outliers final: 45 residues processed: 538 average time/residue: 1.2990 time to fit residues: 809.1591 Evaluate side-chains 549 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 495 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 335 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER 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 402 ILE Chi-restraints excluded: chain B residue 523 THR 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 618 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1125 ASN 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 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 361 CYS 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 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 976 VAL Chi-restraints excluded: chain C residue 1002 GLN 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 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.9990 chunk 288 optimal weight: 0.5980 chunk 262 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 265 optimal weight: 0.6980 chunk 279 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 603 ASN A 777 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 607 GLN C 751 ASN C 824 ASN C 907 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25840 Z= 0.246 Angle : 0.608 11.030 35136 Z= 0.311 Chirality : 0.046 0.492 4138 Planarity : 0.005 0.071 4464 Dihedral : 6.272 58.365 4462 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 2.19 % Allowed : 18.27 % Favored : 79.54 % 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: 1.93 (0.21), residues: 703 sheet: 0.93 (0.19), residues: 707 loop : -1.59 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 436 HIS 0.003 0.001 HIS A 207 PHE 0.023 0.001 PHE A 32 TYR 0.031 0.001 TYR C 351 ARG 0.007 0.000 ARG C 577 *********************** 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 564 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 504 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8372 (t0) cc_final: 0.8066 (t70) REVERT: A 571 ASP cc_start: 0.7898 (t70) cc_final: 0.7413 (t0) REVERT: A 574 ASP cc_start: 0.7826 (p0) cc_final: 0.7520 (OUTLIER) REVERT: A 960 ASN cc_start: 0.8462 (t0) cc_final: 0.8158 (t0) REVERT: A 988 GLU cc_start: 0.7370 (tp30) cc_final: 0.7018 (tp30) REVERT: A 1017 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7170 (tm-30) REVERT: A 1045 LYS cc_start: 0.7953 (tppp) cc_final: 0.7466 (tppp) REVERT: A 1084 ASP cc_start: 0.7490 (t0) cc_final: 0.7073 (t0) REVERT: B 65 PHE cc_start: 0.8459 (m-80) cc_final: 0.8227 (m-10) REVERT: B 81 ASN cc_start: 0.7838 (m-40) cc_final: 0.7573 (m-40) REVERT: B 95 ILE cc_start: 0.8152 (mm) cc_final: 0.7762 (tp) REVERT: B 132 GLU cc_start: 0.6092 (pm20) cc_final: 0.5586 (pm20) REVERT: B 242 LEU cc_start: 0.8125 (mm) cc_final: 0.7839 (mt) REVERT: B 324 GLU cc_start: 0.7672 (pm20) cc_final: 0.7406 (pm20) REVERT: B 440 LYS cc_start: 0.8445 (ptmm) cc_final: 0.8187 (tmmm) REVERT: B 467 ASP cc_start: 0.8071 (p0) cc_final: 0.7705 (p0) REVERT: B 493 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7547 (mmm-85) REVERT: B 583 GLU cc_start: 0.8331 (pt0) cc_final: 0.8083 (pt0) REVERT: B 588 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8345 (p) REVERT: B 702 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: B 752 LEU cc_start: 0.8106 (mt) cc_final: 0.7782 (mt) REVERT: B 902 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8191 (mmt) REVERT: B 918 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7400 (mt-10) REVERT: B 921 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7971 (mtpp) REVERT: B 960 ASN cc_start: 0.8587 (t0) cc_final: 0.8251 (t0) REVERT: B 1050 MET cc_start: 0.8303 (ptm) cc_final: 0.8027 (ptm) REVERT: B 1111 GLU cc_start: 0.8236 (tt0) cc_final: 0.7983 (tt0) REVERT: C 118 LEU cc_start: 0.8178 (mp) cc_final: 0.7852 (mp) REVERT: C 133 PHE cc_start: 0.7463 (m-80) cc_final: 0.7221 (m-80) REVERT: C 194 PHE cc_start: 0.8614 (m-10) cc_final: 0.8264 (m-80) REVERT: C 226 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7652 (tm) REVERT: C 357 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7743 (ttt90) REVERT: C 371 LEU cc_start: 0.8810 (mp) cc_final: 0.8573 (mt) REVERT: C 465 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7224 (pp20) REVERT: C 754 LEU cc_start: 0.8455 (mt) cc_final: 0.8215 (mm) REVERT: C 776 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8199 (ttpp) REVERT: C 790 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7763 (mmtp) REVERT: C 950 ASP cc_start: 0.7423 (m-30) cc_final: 0.7086 (m-30) REVERT: C 1010 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: C 1014 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7796 (mtm180) REVERT: C 1038 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8150 (mmmm) REVERT: C 1141 LEU cc_start: 0.8465 (tp) cc_final: 0.8246 (tt) outliers start: 60 outliers final: 46 residues processed: 538 average time/residue: 1.3431 time to fit residues: 836.9384 Evaluate side-chains 555 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 502 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL 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 398 ASP 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 602 THR 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 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 523 THR 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 618 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 361 CYS 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 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 909 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN 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 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.8980 chunk 296 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 310 optimal weight: 0.2980 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.0050 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 A 603 ASN A 777 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 779 GLN C 804 GLN C 824 ASN C 907 ASN C 935 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25840 Z= 0.192 Angle : 0.602 11.675 35136 Z= 0.308 Chirality : 0.045 0.478 4138 Planarity : 0.005 0.071 4464 Dihedral : 6.173 57.251 4462 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 2.12 % Allowed : 18.49 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3072 helix: 2.00 (0.21), residues: 701 sheet: 0.99 (0.19), residues: 689 loop : -1.55 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 436 HIS 0.002 0.000 HIS B 505 PHE 0.031 0.001 PHE C 456 TYR 0.028 0.001 TYR C 351 ARG 0.007 0.000 ARG C 577 ********************** 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 559 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 501 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 ASP cc_start: 0.8367 (t0) cc_final: 0.8075 (t70) REVERT: A 571 ASP cc_start: 0.7887 (t70) cc_final: 0.7390 (t0) REVERT: A 574 ASP cc_start: 0.7815 (p0) cc_final: 0.7509 (OUTLIER) REVERT: A 900 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7914 (mtp) REVERT: A 960 ASN cc_start: 0.8435 (t0) cc_final: 0.8138 (t0) REVERT: A 988 GLU cc_start: 0.7355 (tp30) cc_final: 0.7009 (tp30) REVERT: A 1017 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 1084 ASP cc_start: 0.7495 (t0) cc_final: 0.7078 (t0) REVERT: B 65 PHE cc_start: 0.8418 (m-80) cc_final: 0.8179 (m-10) REVERT: B 81 ASN cc_start: 0.7817 (m-40) cc_final: 0.7552 (m-40) REVERT: B 95 ILE cc_start: 0.8134 (mm) cc_final: 0.7745 (tp) REVERT: B 132 GLU cc_start: 0.6078 (pm20) cc_final: 0.5707 (pm20) REVERT: B 242 LEU cc_start: 0.8122 (mm) cc_final: 0.7853 (mt) REVERT: B 324 GLU cc_start: 0.7660 (pm20) cc_final: 0.7393 (pm20) REVERT: B 440 LYS cc_start: 0.8419 (ptmm) cc_final: 0.8185 (tmmm) REVERT: B 467 ASP cc_start: 0.8016 (p0) cc_final: 0.7671 (p0) REVERT: B 493 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7524 (mmm-85) REVERT: B 583 GLU cc_start: 0.8327 (pt0) cc_final: 0.8081 (pt0) REVERT: B 588 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 702 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: B 752 LEU cc_start: 0.8096 (mt) cc_final: 0.7778 (mt) REVERT: B 902 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8172 (mmt) REVERT: B 921 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7918 (mtpp) REVERT: B 960 ASN cc_start: 0.8545 (t0) cc_final: 0.8218 (t0) REVERT: B 1050 MET cc_start: 0.8264 (ptm) cc_final: 0.8050 (ptm) REVERT: B 1111 GLU cc_start: 0.8220 (tt0) cc_final: 0.7989 (tt0) REVERT: C 112 SER cc_start: 0.6884 (p) cc_final: 0.6513 (m) REVERT: C 118 LEU cc_start: 0.8171 (mp) cc_final: 0.7850 (mp) REVERT: C 133 PHE cc_start: 0.7478 (m-80) cc_final: 0.7265 (m-80) REVERT: C 194 PHE cc_start: 0.8600 (m-10) cc_final: 0.8275 (m-80) REVERT: C 226 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7641 (tm) REVERT: C 357 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7722 (ttt90) REVERT: C 371 LEU cc_start: 0.8790 (mp) cc_final: 0.8579 (mt) REVERT: C 754 LEU cc_start: 0.8446 (mt) cc_final: 0.8207 (mm) REVERT: C 776 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8160 (ttpp) REVERT: C 790 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7710 (mmtp) REVERT: C 804 GLN cc_start: 0.8236 (mt0) cc_final: 0.8032 (mt0) REVERT: C 950 ASP cc_start: 0.7369 (m-30) cc_final: 0.7025 (m-30) REVERT: C 1010 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: C 1014 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: C 1038 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8146 (mmmm) REVERT: C 1141 LEU cc_start: 0.8488 (tp) cc_final: 0.8251 (tt) outliers start: 58 outliers final: 44 residues processed: 531 average time/residue: 1.3194 time to fit residues: 809.7312 Evaluate side-chains 545 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 494 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 398 ASP 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 602 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN 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 523 THR 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 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 361 CYS 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 461 LEU 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 976 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1014 ARG Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 228 optimal weight: 0.0870 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 0.3980 chunk 247 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 254 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 777 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 703 ASN C 52 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN C 907 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112576 restraints weight = 38322.121| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.55 r_work: 0.3351 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25840 Z= 0.205 Angle : 0.605 11.621 35136 Z= 0.309 Chirality : 0.045 0.469 4138 Planarity : 0.005 0.071 4464 Dihedral : 6.155 57.380 4462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 1.86 % Allowed : 18.96 % 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: -0.11 (0.15), residues: 3072 helix: 1.98 (0.21), residues: 703 sheet: 1.06 (0.19), residues: 682 loop : -1.56 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 436 HIS 0.002 0.000 HIS B 505 PHE 0.025 0.001 PHE A 32 TYR 0.025 0.001 TYR C 453 ARG 0.008 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11814.20 seconds wall clock time: 209 minutes 20.64 seconds (12560.64 seconds total)