Starting phenix.real_space_refine on Fri Sep 19 11:50:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elh_48149/09_2025/9elh_48149.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elh_48149/09_2025/9elh_48149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elh_48149/09_2025/9elh_48149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elh_48149/09_2025/9elh_48149.map" model { file = "/net/cci-nas-00/data/ceres_data/9elh_48149/09_2025/9elh_48149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elh_48149/09_2025/9elh_48149.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 110 5.16 5 C 16283 2.51 5 N 4148 2.21 5 O 4971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25512 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8286 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 56, 'TRANS': 999} Chain breaks: 6 Chain: "B" Number of atoms: 8173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8173 Classifications: {'peptide': 1045} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 54, 'TRANS': 990} Chain breaks: 8 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 8248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8248 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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 Time building chain proxies: 6.51, per 1000 atoms: 0.26 Number of scatterers: 25512 At special positions: 0 Unit cell: (129.958, 129.24, 201.04, 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 110 16.00 O 4971 8.00 N 4148 7.00 C 16283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=1.69 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.55 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 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=1.87 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 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=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM25314 O5 NAG A1310 .*. O " rejected from bonding due to valence issues. 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 354 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 30 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 165 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 354 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 30 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 709 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 40 sheets defined 27.1% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.572A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.769A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.354A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.607A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.296A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.313A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.949A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.426A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.269A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.198A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1149 removed outlier: 3.657A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B1147 " --> pdb=" O LEU B1143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.877A pdb=" N GLY C 75 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.661A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.680A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.715A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.135A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.908A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C 411 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.289A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.952A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.942A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.901A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1149 removed outlier: 3.908A pdb=" N SER C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.109A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.128A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.892A 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: 5.865A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.268A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.055A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.785A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.678A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.503A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.637A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.637A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 4.144A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.934A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 29 removed outlier: 5.751A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.636A 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: 3.662A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC3, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.491A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.193A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.533A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.694A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.545A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 28 removed outlier: 5.716A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.638A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.026A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.449A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.812A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.111A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.635A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 2970 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: 6.86 Time building geometry restraints manager: 3.51 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: 7804 1.34 - 1.47: 6732 1.47 - 1.59: 11428 1.59 - 1.72: 2 1.72 - 1.84: 136 Bond restraints: 26102 Sorted by residual: bond pdb=" CA ALA B 668 " pdb=" CB ALA B 668 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.54e-02 4.22e+03 1.66e+01 bond pdb=" CB ASN B 121 " pdb=" CG ASN B 121 " ideal model delta sigma weight residual 1.516 1.599 -0.083 2.50e-02 1.60e+03 1.11e+01 bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.93e+00 bond pdb=" N SER B 349 " pdb=" CA SER B 349 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.26e-02 6.30e+03 9.51e+00 bond pdb=" N GLU C 493 " pdb=" CA GLU C 493 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.13e+00 ... (remaining 26097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 34547 3.20 - 6.39: 863 6.39 - 9.59: 74 9.59 - 12.78: 13 12.78 - 15.98: 2 Bond angle restraints: 35499 Sorted by residual: angle pdb=" N ALA B 123 " pdb=" CA ALA B 123 " pdb=" C ALA B 123 " ideal model delta sigma weight residual 113.55 98.95 14.60 1.26e+00 6.30e-01 1.34e+02 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 100.53 11.47 1.40e+00 5.10e-01 6.71e+01 angle pdb=" N TYR B 200 " pdb=" CA TYR B 200 " pdb=" C TYR B 200 " ideal model delta sigma weight residual 108.14 97.69 10.45 1.52e+00 4.33e-01 4.73e+01 angle pdb=" N ALA B 163 " pdb=" CA ALA B 163 " pdb=" C ALA B 163 " ideal model delta sigma weight residual 113.56 104.12 9.44 1.39e+00 5.18e-01 4.61e+01 angle pdb=" C ILE B 358 " pdb=" N SER B 359 " pdb=" CA SER B 359 " ideal model delta sigma weight residual 122.89 112.31 10.58 1.72e+00 3.38e-01 3.78e+01 ... (remaining 35494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 15285 21.32 - 42.64: 714 42.64 - 63.96: 184 63.96 - 85.27: 77 85.27 - 106.59: 37 Dihedral angle restraints: 16297 sinusoidal: 7126 harmonic: 9171 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 163.31 -70.31 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -146.62 60.62 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 52.25 40.75 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 16294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3344 0.075 - 0.151: 727 0.151 - 0.226: 84 0.226 - 0.302: 16 0.302 - 0.377: 5 Chirality restraints: 4176 Sorted by residual: chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.10e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 30 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 4173 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 30 " -0.143 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" CG ASN C 30 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 30 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 30 " 0.271 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 30 " -0.089 2.00e-02 2.50e+03 9.54e-02 1.14e+02 pdb=" CG ASN B 30 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 30 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 30 " 0.147 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " 0.112 2.00e-02 2.50e+03 9.50e-02 1.13e+02 pdb=" C7 NAG A1310 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " -0.153 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " 0.089 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 89 2.51 - 3.11: 18461 3.11 - 3.70: 37541 3.70 - 4.30: 56201 4.30 - 4.90: 93345 Nonbonded interactions: 205637 Sorted by model distance: nonbonded pdb=" OD1 ASP B 985 " pdb=" OE1 GLU B 988 " model vdw 1.909 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OD1 ASN C 394 " model vdw 1.951 3.040 nonbonded pdb=" O LEU A1141 " pdb=" CD1 LEU A1145 " model vdw 2.041 3.460 nonbonded pdb=" O GLY A 744 " pdb=" OD1 ASP A 745 " model vdw 2.067 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" CG ASN C 394 " model vdw 2.073 3.270 ... (remaining 205632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 65 or resid 74 through 138 or resid 157 through \ 173 or resid 188 through 350 or (resid 351 through 352 and (name N or name CA o \ r name C or name O or name CB )) or resid 353 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 385 or res \ id 390 through 676 or resid 689 through 837 or resid 852 through 1306)) selection = (chain 'B' and (resid 26 through 676 or resid 689 through 837 or resid 852 throu \ gh 1306)) selection = (chain 'C' and (resid 26 through 65 or resid 74 through 138 or resid 157 through \ 173 or resid 188 through 350 or (resid 351 through 352 and (name N or name CA o \ r name C or name O or name CB )) or resid 353 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 385 or res \ id 390 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'Q' } 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: 13.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.540 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.008 0.480 26199 Z= 0.374 Angle : 1.229 36.259 35752 Z= 0.678 Chirality : 0.063 0.377 4176 Planarity : 0.008 0.170 4499 Dihedral : 14.913 106.592 10283 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.04 % Allowed : 11.38 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.14), residues: 3104 helix: 1.42 (0.18), residues: 670 sheet: 1.03 (0.20), residues: 622 loop : -0.19 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 319 TYR 0.032 0.003 TYR A 269 PHE 0.042 0.003 PHE C 562 TRP 0.025 0.003 TRP A 886 HIS 0.012 0.002 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00692 (26102) covalent geometry : angle 1.16042 (35499) SS BOND : bond 0.09929 ( 38) SS BOND : angle 6.22843 ( 76) hydrogen bonds : bond 0.12903 ( 1028) hydrogen bonds : angle 7.56300 ( 2970) link_BETA1-4 : bond 0.00447 ( 21) link_BETA1-4 : angle 1.73188 ( 63) link_NAG-ASN : bond 0.01036 ( 38) link_NAG-ASN : angle 5.18465 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8384 (p) cc_final: 0.7900 (m) REVERT: A 493 GLU cc_start: 0.5114 (pp20) cc_final: 0.4895 (pp20) REVERT: A 529 LYS cc_start: 0.8667 (mtmt) cc_final: 0.8452 (mtpt) REVERT: A 1010 GLN cc_start: 0.8145 (mp10) cc_final: 0.7156 (mp10) REVERT: A 1119 ASN cc_start: 0.7353 (m-40) cc_final: 0.7145 (m110) REVERT: B 41 LYS cc_start: 0.7680 (mmtp) cc_final: 0.7403 (mmpt) REVERT: B 128 ILE cc_start: 0.7717 (mt) cc_final: 0.7424 (mp) REVERT: B 239 GLN cc_start: 0.8444 (tt0) cc_final: 0.8106 (tt0) REVERT: B 396 TYR cc_start: 0.7388 (m-10) cc_final: 0.6854 (t80) REVERT: B 432 CYS cc_start: 0.6047 (m) cc_final: 0.5582 (m) REVERT: B 646 ARG cc_start: 0.7882 (tpp-160) cc_final: 0.7417 (tpp80) REVERT: B 900 MET cc_start: 0.8710 (mtp) cc_final: 0.7907 (mtm) REVERT: B 1038 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8543 (mptt) REVERT: B 1092 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 1142 GLN cc_start: 0.6955 (mm110) cc_final: 0.6485 (tp40) outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.5201 time to fit residues: 191.4817 Evaluate side-chains 260 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 641 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A1101 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 505 HIS C 26 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124091 restraints weight = 30728.519| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.41 r_work: 0.3248 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 26199 Z= 0.161 Angle : 0.703 13.853 35752 Z= 0.352 Chirality : 0.049 0.708 4176 Planarity : 0.004 0.067 4499 Dihedral : 8.544 66.206 4597 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.21 % Allowed : 10.08 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.14), residues: 3104 helix: 2.48 (0.19), residues: 673 sheet: 0.65 (0.19), residues: 650 loop : -0.37 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 577 TYR 0.024 0.001 TYR B 904 PHE 0.018 0.002 PHE A 186 TRP 0.026 0.002 TRP A 452 HIS 0.006 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00352 (26102) covalent geometry : angle 0.66810 (35499) SS BOND : bond 0.00387 ( 38) SS BOND : angle 1.52428 ( 76) hydrogen bonds : bond 0.04800 ( 1028) hydrogen bonds : angle 5.94619 ( 2970) link_BETA1-4 : bond 0.00613 ( 21) link_BETA1-4 : angle 2.21251 ( 63) link_NAG-ASN : bond 0.01050 ( 38) link_NAG-ASN : angle 3.41885 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8515 (p) cc_final: 0.8198 (m) REVERT: A 200 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6825 (m-80) REVERT: A 237 ARG cc_start: 0.7260 (mtp-110) cc_final: 0.6699 (mtt90) REVERT: A 241 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.5369 (mp) REVERT: A 298 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 493 GLU cc_start: 0.5080 (pp20) cc_final: 0.4596 (pp20) REVERT: A 516 GLU cc_start: 0.7166 (tt0) cc_final: 0.6936 (tt0) REVERT: A 529 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8473 (mtpt) REVERT: A 574 ASP cc_start: 0.8580 (t0) cc_final: 0.8348 (t0) REVERT: A 618 THR cc_start: 0.8266 (m) cc_final: 0.8028 (p) REVERT: A 794 ILE cc_start: 0.8652 (mp) cc_final: 0.8336 (mm) REVERT: A 974 SER cc_start: 0.8493 (t) cc_final: 0.8289 (p) REVERT: A 994 ASP cc_start: 0.7625 (m-30) cc_final: 0.7253 (t70) REVERT: A 995 ARG cc_start: 0.7749 (mtt180) cc_final: 0.6946 (mtp180) REVERT: A 1119 ASN cc_start: 0.7659 (m-40) cc_final: 0.7438 (m110) REVERT: B 41 LYS cc_start: 0.7432 (mmtp) cc_final: 0.6990 (mmpt) REVERT: B 128 ILE cc_start: 0.7673 (mt) cc_final: 0.7437 (mm) REVERT: B 202 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7109 (mptt) REVERT: B 233 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7061 (tp) REVERT: B 314 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: B 355 ARG cc_start: 0.6327 (mmt-90) cc_final: 0.5868 (mmt-90) REVERT: B 646 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7616 (mpp80) REVERT: B 1010 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: B 1017 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: B 1038 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8720 (mptt) REVERT: B 1092 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8114 (mt-10) REVERT: B 1119 ASN cc_start: 0.7965 (m-40) cc_final: 0.7637 (m-40) REVERT: B 1142 GLN cc_start: 0.6752 (mm110) cc_final: 0.6055 (tp40) REVERT: C 234 ASN cc_start: 0.6770 (t0) cc_final: 0.6517 (t0) REVERT: C 1010 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8129 (mp10) outliers start: 61 outliers final: 20 residues processed: 333 average time/residue: 0.4704 time to fit residues: 190.5106 Evaluate side-chains 285 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 269 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A1071 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 779 GLN C 26 GLN C 271 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118786 restraints weight = 30854.945| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.44 r_work: 0.3159 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 26199 Z= 0.200 Angle : 0.675 14.286 35752 Z= 0.337 Chirality : 0.049 0.490 4176 Planarity : 0.004 0.050 4499 Dihedral : 6.480 48.735 4595 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.54 % Allowed : 10.66 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.15), residues: 3104 helix: 2.40 (0.19), residues: 680 sheet: 0.48 (0.19), residues: 680 loop : -0.59 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 815 TYR 0.023 0.001 TYR B1067 PHE 0.021 0.002 PHE C 562 TRP 0.035 0.002 TRP A 452 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00481 (26102) covalent geometry : angle 0.63417 (35499) SS BOND : bond 0.00434 ( 38) SS BOND : angle 1.61372 ( 76) hydrogen bonds : bond 0.04843 ( 1028) hydrogen bonds : angle 5.75874 ( 2970) link_BETA1-4 : bond 0.00663 ( 21) link_BETA1-4 : angle 2.08916 ( 63) link_NAG-ASN : bond 0.00657 ( 38) link_NAG-ASN : angle 3.66202 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 285 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8611 (p) cc_final: 0.8274 (m) REVERT: A 200 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6610 (m-80) REVERT: A 237 ARG cc_start: 0.7363 (mtp-110) cc_final: 0.6838 (mtt90) REVERT: A 269 TYR cc_start: 0.8478 (m-80) cc_final: 0.8272 (m-80) REVERT: A 271 GLN cc_start: 0.8527 (mt0) cc_final: 0.8229 (mt0) REVERT: A 493 GLU cc_start: 0.5042 (pp20) cc_final: 0.4546 (pp20) REVERT: A 529 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8525 (mtpt) REVERT: A 574 ASP cc_start: 0.8581 (t0) cc_final: 0.8318 (t0) REVERT: A 577 ARG cc_start: 0.8443 (ttp80) cc_final: 0.7486 (ttt-90) REVERT: A 618 THR cc_start: 0.8453 (m) cc_final: 0.8181 (p) REVERT: A 765 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7502 (ttm110) REVERT: A 779 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: A 794 ILE cc_start: 0.8695 (mp) cc_final: 0.8375 (mm) REVERT: A 974 SER cc_start: 0.8531 (t) cc_final: 0.8317 (p) REVERT: A 994 ASP cc_start: 0.7661 (m-30) cc_final: 0.7371 (t70) REVERT: A 995 ARG cc_start: 0.7810 (mtt180) cc_final: 0.6984 (mtp180) REVERT: A 1010 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: A 1092 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8684 (mt-10) REVERT: A 1142 GLN cc_start: 0.7157 (mm110) cc_final: 0.6842 (mm-40) REVERT: B 41 LYS cc_start: 0.7495 (mmtp) cc_final: 0.7023 (mmpt) REVERT: B 128 ILE cc_start: 0.7674 (mt) cc_final: 0.7405 (mp) REVERT: B 202 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7230 (mptt) REVERT: B 233 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7092 (tp) REVERT: B 355 ARG cc_start: 0.6511 (mmt-90) cc_final: 0.5995 (mmt-90) REVERT: B 574 ASP cc_start: 0.8210 (p0) cc_final: 0.7951 (p0) REVERT: B 646 ARG cc_start: 0.8271 (tpp-160) cc_final: 0.7538 (mtm180) REVERT: B 735 SER cc_start: 0.8745 (t) cc_final: 0.8364 (p) REVERT: B 1010 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.6851 (mp10) REVERT: B 1038 LYS cc_start: 0.8983 (mmtp) cc_final: 0.8621 (mptt) REVERT: B 1092 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 1142 GLN cc_start: 0.6777 (mm110) cc_final: 0.6117 (tp40) REVERT: C 94 SER cc_start: 0.8061 (p) cc_final: 0.7678 (m) REVERT: C 234 ASN cc_start: 0.6955 (t0) cc_final: 0.6672 (t0) REVERT: C 237 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7700 (mtm110) REVERT: C 408 SER cc_start: 0.5669 (OUTLIER) cc_final: 0.5296 (p) REVERT: C 1010 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8173 (mp10) REVERT: C 1086 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8229 (mtpp) outliers start: 70 outliers final: 36 residues processed: 334 average time/residue: 0.4799 time to fit residues: 192.8263 Evaluate side-chains 298 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 177 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 54 optimal weight: 0.0970 chunk 300 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 286 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 779 GLN C 26 GLN C 271 GLN C 280 ASN C 409 GLN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.171596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119189 restraints weight = 30779.412| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.46 r_work: 0.3158 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26199 Z= 0.160 Angle : 0.633 12.868 35752 Z= 0.316 Chirality : 0.048 0.437 4176 Planarity : 0.004 0.053 4499 Dihedral : 5.929 81.815 4595 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.50 % Allowed : 12.32 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.15), residues: 3104 helix: 2.29 (0.19), residues: 699 sheet: 0.42 (0.19), residues: 688 loop : -0.67 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.058 0.001 TYR C 28 PHE 0.023 0.001 PHE C 562 TRP 0.036 0.002 TRP A 452 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00376 (26102) covalent geometry : angle 0.59474 (35499) SS BOND : bond 0.00324 ( 38) SS BOND : angle 1.43390 ( 76) hydrogen bonds : bond 0.04427 ( 1028) hydrogen bonds : angle 5.59798 ( 2970) link_BETA1-4 : bond 0.00630 ( 21) link_BETA1-4 : angle 1.87151 ( 63) link_NAG-ASN : bond 0.00885 ( 38) link_NAG-ASN : angle 3.48488 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 270 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8629 (p) cc_final: 0.8323 (m) REVERT: A 200 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: A 237 ARG cc_start: 0.7350 (mtp-110) cc_final: 0.6863 (mtt90) REVERT: A 271 GLN cc_start: 0.8517 (mt0) cc_final: 0.8214 (mt0) REVERT: A 465 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7892 (tt0) REVERT: A 493 GLU cc_start: 0.5083 (pp20) cc_final: 0.4499 (pp20) REVERT: A 529 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8535 (mtpt) REVERT: A 574 ASP cc_start: 0.8484 (t0) cc_final: 0.8205 (t0) REVERT: A 765 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7455 (ttm110) REVERT: A 779 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: A 794 ILE cc_start: 0.8662 (mp) cc_final: 0.8366 (mm) REVERT: A 974 SER cc_start: 0.8516 (t) cc_final: 0.8304 (p) REVERT: A 994 ASP cc_start: 0.7651 (m-30) cc_final: 0.7368 (t70) REVERT: A 1010 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: A 1092 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8662 (mt-10) REVERT: A 1142 GLN cc_start: 0.7179 (mm110) cc_final: 0.6867 (mm-40) REVERT: B 41 LYS cc_start: 0.7411 (mmtp) cc_final: 0.7000 (mmpt) REVERT: B 128 ILE cc_start: 0.7630 (mt) cc_final: 0.7389 (mp) REVERT: B 202 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7091 (mptt) REVERT: B 233 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7122 (tp) REVERT: B 355 ARG cc_start: 0.6599 (mmt-90) cc_final: 0.6091 (mmt-90) REVERT: B 574 ASP cc_start: 0.8271 (p0) cc_final: 0.7982 (p0) REVERT: B 646 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7584 (mtm180) REVERT: B 735 SER cc_start: 0.8740 (t) cc_final: 0.8344 (p) REVERT: B 904 TYR cc_start: 0.8205 (m-80) cc_final: 0.7079 (m-80) REVERT: B 1010 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: B 1038 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8620 (mptt) REVERT: B 1092 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 1142 GLN cc_start: 0.6736 (mm110) cc_final: 0.6075 (tp40) REVERT: C 94 SER cc_start: 0.8018 (p) cc_final: 0.7706 (m) REVERT: C 102 ARG cc_start: 0.6652 (ptm160) cc_final: 0.5783 (mmt-90) REVERT: C 234 ASN cc_start: 0.6867 (t0) cc_final: 0.6616 (t0) REVERT: C 237 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7745 (mtp-110) REVERT: C 377 PHE cc_start: 0.5991 (OUTLIER) cc_final: 0.5390 (m-80) REVERT: C 408 SER cc_start: 0.5801 (OUTLIER) cc_final: 0.5470 (p) REVERT: C 581 THR cc_start: 0.8288 (p) cc_final: 0.8078 (t) REVERT: C 646 ARG cc_start: 0.8319 (mmt180) cc_final: 0.7994 (tpp80) REVERT: C 854 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5734 (mtmt) REVERT: C 990 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: C 1010 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: C 1086 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8133 (mtpp) REVERT: C 1119 ASN cc_start: 0.8013 (m110) cc_final: 0.7748 (m110) outliers start: 69 outliers final: 33 residues processed: 319 average time/residue: 0.4859 time to fit residues: 188.2701 Evaluate side-chains 294 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 145 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 143 optimal weight: 0.0370 chunk 2 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 506 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 26 GLN C 271 GLN C 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118465 restraints weight = 30529.583| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.46 r_work: 0.3162 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26199 Z= 0.154 Angle : 0.606 11.940 35752 Z= 0.303 Chirality : 0.046 0.358 4176 Planarity : 0.004 0.053 4499 Dihedral : 5.408 63.905 4595 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.94 % Allowed : 12.43 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3104 helix: 2.37 (0.19), residues: 699 sheet: 0.40 (0.19), residues: 676 loop : -0.72 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 577 TYR 0.022 0.001 TYR B1067 PHE 0.017 0.001 PHE C 562 TRP 0.040 0.002 TRP A 452 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00364 (26102) covalent geometry : angle 0.57368 (35499) SS BOND : bond 0.00312 ( 38) SS BOND : angle 1.42880 ( 76) hydrogen bonds : bond 0.04313 ( 1028) hydrogen bonds : angle 5.48278 ( 2970) link_BETA1-4 : bond 0.00569 ( 21) link_BETA1-4 : angle 1.61376 ( 63) link_NAG-ASN : bond 0.00594 ( 38) link_NAG-ASN : angle 3.16133 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 261 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8662 (p) cc_final: 0.8354 (m) REVERT: A 237 ARG cc_start: 0.7371 (mtp-110) cc_final: 0.6899 (mtt90) REVERT: A 269 TYR cc_start: 0.8472 (m-80) cc_final: 0.8262 (m-80) REVERT: A 271 GLN cc_start: 0.8514 (mt0) cc_final: 0.8187 (mt0) REVERT: A 465 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7954 (tt0) REVERT: A 493 GLU cc_start: 0.5111 (pp20) cc_final: 0.4554 (pp20) REVERT: A 529 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8461 (mtpt) REVERT: A 574 ASP cc_start: 0.8479 (t0) cc_final: 0.8192 (t0) REVERT: A 765 ARG cc_start: 0.8045 (mtp-110) cc_final: 0.7467 (ttm110) REVERT: A 779 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8235 (tp40) REVERT: A 794 ILE cc_start: 0.8647 (mp) cc_final: 0.8362 (mm) REVERT: A 974 SER cc_start: 0.8549 (t) cc_final: 0.8330 (p) REVERT: A 994 ASP cc_start: 0.7659 (m-30) cc_final: 0.7388 (t70) REVERT: A 1010 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: A 1092 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8678 (mt-10) REVERT: A 1142 GLN cc_start: 0.7206 (mm110) cc_final: 0.6912 (mm-40) REVERT: B 41 LYS cc_start: 0.7429 (mmtp) cc_final: 0.6931 (mmpt) REVERT: B 61 ASN cc_start: 0.7090 (t0) cc_final: 0.6782 (m110) REVERT: B 169 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7370 (tp30) REVERT: B 202 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7129 (mptt) REVERT: B 233 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7090 (tp) REVERT: B 310 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8753 (tttm) REVERT: B 335 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7074 (tp) REVERT: B 574 ASP cc_start: 0.8276 (p0) cc_final: 0.7971 (p0) REVERT: B 646 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.7664 (mtm180) REVERT: B 735 SER cc_start: 0.8741 (t) cc_final: 0.8353 (p) REVERT: B 904 TYR cc_start: 0.8185 (m-80) cc_final: 0.7096 (m-80) REVERT: B 1010 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.6908 (mp10) REVERT: B 1038 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8613 (mptt) REVERT: B 1092 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 1142 GLN cc_start: 0.6705 (mm110) cc_final: 0.6043 (tp40) REVERT: C 102 ARG cc_start: 0.6645 (ptm160) cc_final: 0.5766 (mmt-90) REVERT: C 234 ASN cc_start: 0.6908 (t0) cc_final: 0.6664 (t0) REVERT: C 237 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7735 (mtm110) REVERT: C 377 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.5436 (m-80) REVERT: C 408 SER cc_start: 0.5859 (OUTLIER) cc_final: 0.5527 (p) REVERT: C 554 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7260 (mtpt) REVERT: C 646 ARG cc_start: 0.8316 (mmt180) cc_final: 0.7974 (mpp-170) REVERT: C 690 GLN cc_start: 0.7730 (mt0) cc_final: 0.7320 (mm110) REVERT: C 854 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5746 (mtmt) REVERT: C 934 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 990 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: C 1010 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8124 (mp10) REVERT: C 1119 ASN cc_start: 0.8140 (m110) cc_final: 0.7863 (m110) outliers start: 81 outliers final: 40 residues processed: 321 average time/residue: 0.4945 time to fit residues: 192.4942 Evaluate side-chains 298 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 128 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 304 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 26 GLN C 271 GLN C 280 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116553 restraints weight = 30914.993| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.43 r_work: 0.3141 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26199 Z= 0.194 Angle : 0.636 15.725 35752 Z= 0.318 Chirality : 0.048 0.344 4176 Planarity : 0.004 0.054 4499 Dihedral : 5.421 62.122 4595 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 3.19 % Allowed : 12.40 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.15), residues: 3104 helix: 2.25 (0.19), residues: 698 sheet: 0.40 (0.19), residues: 660 loop : -0.83 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 577 TYR 0.022 0.001 TYR B1067 PHE 0.018 0.002 PHE B 562 TRP 0.040 0.002 TRP A 452 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00467 (26102) covalent geometry : angle 0.60057 (35499) SS BOND : bond 0.00397 ( 38) SS BOND : angle 1.45864 ( 76) hydrogen bonds : bond 0.04584 ( 1028) hydrogen bonds : angle 5.55010 ( 2970) link_BETA1-4 : bond 0.00567 ( 21) link_BETA1-4 : angle 1.55155 ( 63) link_NAG-ASN : bond 0.00787 ( 38) link_NAG-ASN : angle 3.44306 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 250 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8739 (p) cc_final: 0.8304 (m) REVERT: A 237 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.6953 (mtt90) REVERT: A 269 TYR cc_start: 0.8442 (m-80) cc_final: 0.8127 (m-80) REVERT: A 271 GLN cc_start: 0.8500 (mt0) cc_final: 0.8194 (mt0) REVERT: A 465 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8059 (tt0) REVERT: A 493 GLU cc_start: 0.5138 (pp20) cc_final: 0.4545 (pp20) REVERT: A 529 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8425 (mtpt) REVERT: A 574 ASP cc_start: 0.8495 (t0) cc_final: 0.8194 (t0) REVERT: A 765 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.7506 (ttm110) REVERT: A 779 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8260 (tp40) REVERT: A 794 ILE cc_start: 0.8689 (mp) cc_final: 0.8410 (mm) REVERT: A 994 ASP cc_start: 0.7678 (m-30) cc_final: 0.7429 (t70) REVERT: A 1010 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7570 (mp10) REVERT: A 1092 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8683 (mt-10) REVERT: A 1142 GLN cc_start: 0.7357 (mm110) cc_final: 0.6992 (mm110) REVERT: B 41 LYS cc_start: 0.7529 (mmtp) cc_final: 0.6939 (mmpt) REVERT: B 61 ASN cc_start: 0.7085 (t0) cc_final: 0.6822 (m110) REVERT: B 129 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6733 (ttpt) REVERT: B 169 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: B 202 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7229 (mptt) REVERT: B 233 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7101 (tp) REVERT: B 310 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8805 (tttm) REVERT: B 574 ASP cc_start: 0.8383 (p0) cc_final: 0.8086 (p0) REVERT: B 646 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.7742 (mtm180) REVERT: B 735 SER cc_start: 0.8763 (t) cc_final: 0.8383 (p) REVERT: B 904 TYR cc_start: 0.8151 (m-80) cc_final: 0.7082 (m-80) REVERT: B 1010 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 1038 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8629 (mptt) REVERT: B 1092 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 1142 GLN cc_start: 0.6743 (mm110) cc_final: 0.6080 (tp40) REVERT: C 102 ARG cc_start: 0.6684 (ptm160) cc_final: 0.5785 (mmt-90) REVERT: C 197 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 205 SER cc_start: 0.9343 (p) cc_final: 0.8992 (t) REVERT: C 234 ASN cc_start: 0.7068 (t0) cc_final: 0.6843 (t0) REVERT: C 377 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5564 (m-80) REVERT: C 408 SER cc_start: 0.5952 (OUTLIER) cc_final: 0.5644 (p) REVERT: C 554 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7237 (mtpt) REVERT: C 646 ARG cc_start: 0.8356 (mmt180) cc_final: 0.8041 (mpp-170) REVERT: C 854 LYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5856 (mtmt) REVERT: C 934 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7727 (mp) REVERT: C 1010 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: C 1143 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6877 (mp) outliers start: 88 outliers final: 46 residues processed: 320 average time/residue: 0.4874 time to fit residues: 189.5307 Evaluate side-chains 296 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 37 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 26 GLN C 271 GLN C 280 ASN C 564 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.170129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118450 restraints weight = 30520.462| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.40 r_work: 0.3170 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26199 Z= 0.130 Angle : 0.594 13.018 35752 Z= 0.297 Chirality : 0.046 0.352 4176 Planarity : 0.004 0.056 4499 Dihedral : 5.244 71.048 4595 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 2.46 % Allowed : 13.45 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.15), residues: 3104 helix: 2.41 (0.19), residues: 697 sheet: 0.35 (0.19), residues: 674 loop : -0.80 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 577 TYR 0.021 0.001 TYR B1067 PHE 0.015 0.001 PHE B 562 TRP 0.031 0.001 TRP A 452 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00301 (26102) covalent geometry : angle 0.56026 (35499) SS BOND : bond 0.00263 ( 38) SS BOND : angle 1.33663 ( 76) hydrogen bonds : bond 0.04090 ( 1028) hydrogen bonds : angle 5.39214 ( 2970) link_BETA1-4 : bond 0.00551 ( 21) link_BETA1-4 : angle 1.43470 ( 63) link_NAG-ASN : bond 0.00501 ( 38) link_NAG-ASN : angle 3.25755 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 253 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8738 (p) cc_final: 0.8352 (m) REVERT: A 237 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6889 (mtt90) REVERT: A 269 TYR cc_start: 0.8377 (m-80) cc_final: 0.7998 (m-80) REVERT: A 271 GLN cc_start: 0.8470 (mt0) cc_final: 0.8167 (mt0) REVERT: A 465 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8012 (tt0) REVERT: A 493 GLU cc_start: 0.5089 (pp20) cc_final: 0.4502 (pp20) REVERT: A 529 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8443 (mtpt) REVERT: A 574 ASP cc_start: 0.8451 (t0) cc_final: 0.8096 (t0) REVERT: A 765 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7542 (ttp-110) REVERT: A 779 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8220 (tp40) REVERT: A 794 ILE cc_start: 0.8636 (mp) cc_final: 0.8369 (mm) REVERT: A 994 ASP cc_start: 0.7573 (m-30) cc_final: 0.7318 (t70) REVERT: A 1010 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 1092 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8668 (mt-10) REVERT: A 1142 GLN cc_start: 0.7286 (mm110) cc_final: 0.6915 (mm110) REVERT: B 41 LYS cc_start: 0.7483 (mmtp) cc_final: 0.6916 (mmpt) REVERT: B 61 ASN cc_start: 0.7025 (t0) cc_final: 0.6783 (m110) REVERT: B 202 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7124 (mptt) REVERT: B 233 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7084 (tp) REVERT: B 310 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8717 (tttm) REVERT: B 335 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7139 (tp) REVERT: B 574 ASP cc_start: 0.8269 (p0) cc_final: 0.7997 (p0) REVERT: B 646 ARG cc_start: 0.8342 (tpp-160) cc_final: 0.7732 (mtm180) REVERT: B 735 SER cc_start: 0.8742 (t) cc_final: 0.8345 (p) REVERT: B 904 TYR cc_start: 0.8058 (m-80) cc_final: 0.7012 (m-80) REVERT: B 1010 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.6869 (mp10) REVERT: B 1038 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8591 (mptt) REVERT: B 1092 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8223 (mt-10) REVERT: B 1142 GLN cc_start: 0.6696 (mm110) cc_final: 0.6032 (tp40) REVERT: C 102 ARG cc_start: 0.6598 (ptm160) cc_final: 0.5735 (mmt-90) REVERT: C 205 SER cc_start: 0.9321 (p) cc_final: 0.9006 (t) REVERT: C 234 ASN cc_start: 0.6982 (t0) cc_final: 0.6732 (t0) REVERT: C 377 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5569 (m-80) REVERT: C 408 SER cc_start: 0.5979 (OUTLIER) cc_final: 0.5696 (p) REVERT: C 501 TYR cc_start: 0.4813 (OUTLIER) cc_final: 0.2892 (m-80) REVERT: C 646 ARG cc_start: 0.8316 (mmt180) cc_final: 0.8000 (mpp-170) REVERT: C 934 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 1010 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8109 (mp10) outliers start: 68 outliers final: 36 residues processed: 306 average time/residue: 0.5063 time to fit residues: 187.6089 Evaluate side-chains 285 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 293 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 313 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 283 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 26 GLN C 271 GLN C 280 ASN C 564 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117116 restraints weight = 30731.565| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.38 r_work: 0.3149 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26199 Z= 0.171 Angle : 0.628 18.032 35752 Z= 0.313 Chirality : 0.047 0.472 4176 Planarity : 0.004 0.056 4499 Dihedral : 5.612 97.050 4595 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 2.72 % Allowed : 13.34 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.15), residues: 3104 helix: 2.37 (0.19), residues: 697 sheet: 0.28 (0.19), residues: 674 loop : -0.88 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 995 TYR 0.022 0.001 TYR B1067 PHE 0.017 0.001 PHE B 898 TRP 0.035 0.002 TRP A 452 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00413 (26102) covalent geometry : angle 0.58524 (35499) SS BOND : bond 0.00474 ( 38) SS BOND : angle 1.48892 ( 76) hydrogen bonds : bond 0.04318 ( 1028) hydrogen bonds : angle 5.42448 ( 2970) link_BETA1-4 : bond 0.00535 ( 21) link_BETA1-4 : angle 1.44127 ( 63) link_NAG-ASN : bond 0.00496 ( 38) link_NAG-ASN : angle 3.80006 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 245 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8765 (p) cc_final: 0.8346 (m) REVERT: A 200 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: A 237 ARG cc_start: 0.7351 (mtp-110) cc_final: 0.6960 (mtt90) REVERT: A 269 TYR cc_start: 0.8438 (m-80) cc_final: 0.8097 (m-80) REVERT: A 271 GLN cc_start: 0.8472 (mt0) cc_final: 0.8213 (mt0) REVERT: A 357 ARG cc_start: 0.8150 (ttt-90) cc_final: 0.7765 (ttt90) REVERT: A 465 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8103 (tt0) REVERT: A 493 GLU cc_start: 0.5204 (pp20) cc_final: 0.4583 (pp20) REVERT: A 529 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8446 (mtpt) REVERT: A 574 ASP cc_start: 0.8485 (t0) cc_final: 0.8122 (t0) REVERT: A 577 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7750 (ttp80) REVERT: A 765 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7652 (ttp-110) REVERT: A 779 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8271 (tp40) REVERT: A 794 ILE cc_start: 0.8688 (mp) cc_final: 0.8417 (mm) REVERT: A 994 ASP cc_start: 0.7650 (m-30) cc_final: 0.7399 (t70) REVERT: A 1010 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: A 1092 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 1142 GLN cc_start: 0.7419 (mm110) cc_final: 0.7082 (mm110) REVERT: B 41 LYS cc_start: 0.7548 (mmtp) cc_final: 0.6947 (mmpt) REVERT: B 61 ASN cc_start: 0.6987 (t0) cc_final: 0.6772 (m110) REVERT: B 202 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7175 (mptt) REVERT: B 233 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7086 (tp) REVERT: B 310 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8776 (tttm) REVERT: B 574 ASP cc_start: 0.8289 (p0) cc_final: 0.8026 (p0) REVERT: B 646 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.7778 (mtm180) REVERT: B 735 SER cc_start: 0.8767 (t) cc_final: 0.8336 (p) REVERT: B 759 PHE cc_start: 0.8161 (t80) cc_final: 0.7370 (m-80) REVERT: B 904 TYR cc_start: 0.8105 (m-80) cc_final: 0.7044 (m-80) REVERT: B 929 SER cc_start: 0.8512 (t) cc_final: 0.8226 (p) REVERT: B 1010 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: B 1038 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8618 (mptt) REVERT: B 1092 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 1142 GLN cc_start: 0.6758 (mm110) cc_final: 0.6076 (tp40) REVERT: C 102 ARG cc_start: 0.6669 (ptm160) cc_final: 0.5784 (mmt-90) REVERT: C 197 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 205 SER cc_start: 0.9334 (p) cc_final: 0.9031 (t) REVERT: C 234 ASN cc_start: 0.7004 (t0) cc_final: 0.6768 (t0) REVERT: C 377 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5687 (m-80) REVERT: C 408 SER cc_start: 0.5998 (OUTLIER) cc_final: 0.5765 (p) REVERT: C 501 TYR cc_start: 0.4977 (OUTLIER) cc_final: 0.3008 (m-80) REVERT: C 646 ARG cc_start: 0.8350 (mmt180) cc_final: 0.8049 (mpp-170) REVERT: C 934 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7681 (mp) REVERT: C 1010 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8154 (mp10) outliers start: 75 outliers final: 45 residues processed: 303 average time/residue: 0.5020 time to fit residues: 184.1641 Evaluate side-chains 295 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 142 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 276 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN C 271 GLN C 280 ASN C 556 ASN C 564 GLN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118274 restraints weight = 30701.150| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.36 r_work: 0.3167 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26199 Z= 0.141 Angle : 0.597 14.551 35752 Z= 0.299 Chirality : 0.047 0.664 4176 Planarity : 0.004 0.057 4499 Dihedral : 5.915 117.543 4595 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.57 % Allowed : 13.99 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.15), residues: 3104 helix: 2.50 (0.19), residues: 695 sheet: 0.28 (0.19), residues: 675 loop : -0.86 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 995 TYR 0.021 0.001 TYR B1067 PHE 0.015 0.001 PHE B 562 TRP 0.037 0.002 TRP A 452 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00334 (26102) covalent geometry : angle 0.56100 (35499) SS BOND : bond 0.00344 ( 38) SS BOND : angle 1.49719 ( 76) hydrogen bonds : bond 0.04076 ( 1028) hydrogen bonds : angle 5.35657 ( 2970) link_BETA1-4 : bond 0.00525 ( 21) link_BETA1-4 : angle 1.38645 ( 63) link_NAG-ASN : bond 0.00526 ( 38) link_NAG-ASN : angle 3.32882 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 248 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8751 (p) cc_final: 0.8305 (m) REVERT: A 237 ARG cc_start: 0.7257 (mtp-110) cc_final: 0.6857 (mtt90) REVERT: A 269 TYR cc_start: 0.8371 (m-80) cc_final: 0.7962 (m-80) REVERT: A 271 GLN cc_start: 0.8422 (mt0) cc_final: 0.8169 (mt0) REVERT: A 357 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7741 (ttt90) REVERT: A 465 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8064 (tt0) REVERT: A 493 GLU cc_start: 0.5125 (pp20) cc_final: 0.4539 (pp20) REVERT: A 529 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8418 (mtpt) REVERT: A 574 ASP cc_start: 0.8455 (t0) cc_final: 0.8159 (t0) REVERT: A 577 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7701 (ttp80) REVERT: A 765 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7562 (ttp-110) REVERT: A 779 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: A 794 ILE cc_start: 0.8636 (mp) cc_final: 0.8368 (mm) REVERT: A 994 ASP cc_start: 0.7570 (m-30) cc_final: 0.7304 (t70) REVERT: A 1010 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: A 1092 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 1142 GLN cc_start: 0.7364 (mm110) cc_final: 0.7032 (mm110) REVERT: B 41 LYS cc_start: 0.7498 (mmtp) cc_final: 0.6912 (mmpt) REVERT: B 61 ASN cc_start: 0.6910 (t0) cc_final: 0.6705 (m110) REVERT: B 202 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7279 (mptt) REVERT: B 233 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7046 (tp) REVERT: B 310 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8715 (tttm) REVERT: B 355 ARG cc_start: 0.6414 (mmt-90) cc_final: 0.6206 (mmt-90) REVERT: B 646 ARG cc_start: 0.8332 (tpp-160) cc_final: 0.7742 (mtm180) REVERT: B 735 SER cc_start: 0.8747 (t) cc_final: 0.8290 (p) REVERT: B 904 TYR cc_start: 0.8042 (m-80) cc_final: 0.6993 (m-80) REVERT: B 1010 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: B 1092 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8215 (mt-10) REVERT: C 102 ARG cc_start: 0.6579 (ptm160) cc_final: 0.5713 (mmt-90) REVERT: C 205 SER cc_start: 0.9309 (p) cc_final: 0.9025 (t) REVERT: C 234 ASN cc_start: 0.6953 (t0) cc_final: 0.6719 (t0) REVERT: C 377 PHE cc_start: 0.5984 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: C 501 TYR cc_start: 0.4953 (OUTLIER) cc_final: 0.2996 (m-80) REVERT: C 646 ARG cc_start: 0.8320 (mmt180) cc_final: 0.8029 (mpp-170) REVERT: C 934 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7596 (mp) REVERT: C 990 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: C 1010 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8101 (mp10) outliers start: 71 outliers final: 45 residues processed: 303 average time/residue: 0.4946 time to fit residues: 181.5836 Evaluate side-chains 288 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 116 optimal weight: 5.9990 chunk 274 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN C 26 GLN C 271 GLN C 280 ASN C 556 ASN C 564 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117746 restraints weight = 30738.206| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.38 r_work: 0.3160 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26199 Z= 0.153 Angle : 0.628 20.299 35752 Z= 0.311 Chirality : 0.050 0.947 4176 Planarity : 0.004 0.056 4499 Dihedral : 5.895 118.280 4595 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 2.43 % Allowed : 14.39 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 3104 helix: 2.47 (0.19), residues: 696 sheet: 0.27 (0.19), residues: 673 loop : -0.89 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 995 TYR 0.021 0.001 TYR B1067 PHE 0.016 0.001 PHE B 562 TRP 0.039 0.002 TRP A 452 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00363 (26102) covalent geometry : angle 0.57820 (35499) SS BOND : bond 0.00368 ( 38) SS BOND : angle 1.51552 ( 76) hydrogen bonds : bond 0.04160 ( 1028) hydrogen bonds : angle 5.36647 ( 2970) link_BETA1-4 : bond 0.00528 ( 21) link_BETA1-4 : angle 1.38542 ( 63) link_NAG-ASN : bond 0.00623 ( 38) link_NAG-ASN : angle 4.12055 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 236 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8756 (p) cc_final: 0.8299 (m) REVERT: A 237 ARG cc_start: 0.7300 (mtp-110) cc_final: 0.6904 (mtt90) REVERT: A 269 TYR cc_start: 0.8372 (m-80) cc_final: 0.8022 (m-80) REVERT: A 271 GLN cc_start: 0.8426 (mt0) cc_final: 0.8174 (mt0) REVERT: A 357 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.7718 (ttt90) REVERT: A 465 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8069 (tt0) REVERT: A 493 GLU cc_start: 0.5177 (pp20) cc_final: 0.4554 (pp20) REVERT: A 529 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8424 (mtpt) REVERT: A 574 ASP cc_start: 0.8446 (t0) cc_final: 0.8149 (t0) REVERT: A 577 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7685 (ttp80) REVERT: A 765 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7562 (ttp-110) REVERT: A 779 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8197 (tp40) REVERT: A 794 ILE cc_start: 0.8644 (mp) cc_final: 0.8368 (mm) REVERT: A 994 ASP cc_start: 0.7571 (m-30) cc_final: 0.7319 (t70) REVERT: A 1010 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: A 1092 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8682 (mt-10) REVERT: A 1142 GLN cc_start: 0.7366 (mm110) cc_final: 0.7039 (mm110) REVERT: B 41 LYS cc_start: 0.7495 (mmtp) cc_final: 0.6912 (mmpt) REVERT: B 61 ASN cc_start: 0.6921 (t0) cc_final: 0.6693 (m110) REVERT: B 202 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7275 (mptt) REVERT: B 233 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7045 (tp) REVERT: B 310 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8767 (tttm) REVERT: B 646 ARG cc_start: 0.8350 (tpp-160) cc_final: 0.7756 (mtm180) REVERT: B 735 SER cc_start: 0.8766 (t) cc_final: 0.8310 (p) REVERT: B 759 PHE cc_start: 0.8060 (t80) cc_final: 0.7245 (m-80) REVERT: B 904 TYR cc_start: 0.8052 (m-80) cc_final: 0.6997 (m-80) REVERT: B 929 SER cc_start: 0.8464 (t) cc_final: 0.8177 (p) REVERT: B 1010 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.6871 (mp10) REVERT: B 1092 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8233 (mt-10) REVERT: C 102 ARG cc_start: 0.6597 (ptm160) cc_final: 0.5719 (mmt-90) REVERT: C 205 SER cc_start: 0.9308 (p) cc_final: 0.9026 (t) REVERT: C 234 ASN cc_start: 0.7001 (t0) cc_final: 0.6775 (t0) REVERT: C 377 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5692 (m-80) REVERT: C 501 TYR cc_start: 0.4996 (OUTLIER) cc_final: 0.3036 (m-80) REVERT: C 646 ARG cc_start: 0.8321 (mmt180) cc_final: 0.8016 (mpp-170) REVERT: C 934 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7592 (mp) REVERT: C 1010 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8104 (mp10) outliers start: 67 outliers final: 47 residues processed: 288 average time/residue: 0.4846 time to fit residues: 168.6733 Evaluate side-chains 290 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 280 ASN C 564 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117000 restraints weight = 30684.490| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.41 r_work: 0.3154 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26199 Z= 0.161 Angle : 0.621 18.149 35752 Z= 0.309 Chirality : 0.049 0.821 4176 Planarity : 0.004 0.057 4499 Dihedral : 5.871 117.481 4595 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 2.43 % Allowed : 14.39 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3104 helix: 2.43 (0.19), residues: 699 sheet: 0.26 (0.19), residues: 673 loop : -0.90 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 995 TYR 0.021 0.001 TYR B1067 PHE 0.016 0.001 PHE B 562 TRP 0.041 0.002 TRP A 452 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00386 (26102) covalent geometry : angle 0.57668 (35499) SS BOND : bond 0.00370 ( 38) SS BOND : angle 1.49669 ( 76) hydrogen bonds : bond 0.04225 ( 1028) hydrogen bonds : angle 5.38715 ( 2970) link_BETA1-4 : bond 0.00529 ( 21) link_BETA1-4 : angle 1.38575 ( 63) link_NAG-ASN : bond 0.00570 ( 38) link_NAG-ASN : angle 3.83309 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9235.77 seconds wall clock time: 158 minutes 22.15 seconds (9502.15 seconds total)