Starting phenix.real_space_refine on Mon Aug 25 09:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3w_35160/08_2025/8i3w_35160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3w_35160/08_2025/8i3w_35160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3w_35160/08_2025/8i3w_35160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3w_35160/08_2025/8i3w_35160.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3w_35160/08_2025/8i3w_35160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3w_35160/08_2025/8i3w_35160.cif" } resolution = 2.8 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= 0.003 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 123 5.16 5 C 17127 2.51 5 N 4419 2.21 5 O 5331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27000 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8678 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 51, 'TRANS': 1063} Chain: "B" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8678 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 51, 'TRANS': 1063} Chain: "C" Number of atoms: 8678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8678 Classifications: {'peptide': 1115} Link IDs: {'PTRANS': 51, 'TRANS': 1063} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.02, per 1000 atoms: 0.22 Number of scatterers: 27000 At special positions: 0 Unit cell: (150.8, 144.56, 160.16, 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 123 16.00 O 5331 8.00 N 4419 7.00 C 17127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 297 " distance=2.02 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 428 " distance=2.05 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 484 " distance=2.02 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 730 " - pdb=" SG CYS A 752 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 832 " - pdb=" SG CYS A 843 " distance=2.03 Simple disulfide: pdb=" SG CYS A1024 " - pdb=" SG CYS A1035 " distance=2.03 Simple disulfide: pdb=" SG CYS A1074 " - pdb=" SG CYS A1118 " distance=1.68 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.02 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.02 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 730 " - pdb=" SG CYS B 752 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 832 " - pdb=" SG CYS B 843 " distance=2.03 Simple disulfide: pdb=" SG CYS B1024 " - pdb=" SG CYS B1035 " distance=2.03 Simple disulfide: pdb=" SG CYS B1074 " - pdb=" SG CYS B1118 " distance=1.15 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 165 " distance=2.04 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 297 " distance=2.02 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 357 " distance=2.04 Simple disulfide: pdb=" SG CYS C 375 " - pdb=" SG CYS C 428 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 484 " distance=2.02 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 730 " - pdb=" SG CYS C 752 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 832 " - pdb=" SG CYS C 843 " distance=2.03 Simple disulfide: pdb=" SG CYS C1024 " - pdb=" SG CYS C1035 " distance=2.03 Simple disulfide: pdb=" SG CYS C1074 " - pdb=" SG CYS C1118 " distance=1.43 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 18 " " NAG A1302 " - " ASN A 612 " " NAG A1303 " - " ASN A 327 " " NAG A1304 " - " ASN A 339 " " NAG A1305 " - " ASN A 366 " " NAG A1306 " - " ASN A 793 " " NAG A1307 " - " ASN A1066 " " NAG A1308 " - " ASN A 31 " " NAG A1309 " - " ASN A 62 " " NAG A1310 " - " ASN A 653 " " NAG A1311 " - " ASN A 701 " " NAG A1312 " - " ASN A1090 " " NAG A1313 " - " ASN A1126 " " NAG B1301 " - " ASN B 327 " " NAG B1302 " - " ASN B 793 " " NAG B1303 " - " ASN B 653 " " NAG B1304 " - " ASN B 701 " " NAG B1305 " - " ASN B1090 " " NAG B1306 " - " ASN B1126 " " NAG B1307 " - " ASN B 18 " " NAG B1308 " - " ASN B1066 " " NAG B1309 " - " ASN B 339 " " NAG B1310 " - " ASN B 62 " " NAG B1311 " - " ASN B 31 " " NAG B1312 " - " ASN B 612 " " NAG B1313 " - " ASN B 366 " " NAG C1301 " - " ASN C 62 " " NAG C1302 " - " ASN C 612 " " NAG C1303 " - " ASN C 701 " " NAG C1304 " - " ASN C1090 " " NAG C1305 " - " ASN C 653 " " NAG C1306 " - " ASN C 18 " " NAG C1307 " - " ASN C1066 " " NAG C1308 " - " ASN C 793 " " NAG C1309 " - " ASN C 366 " " NAG C1310 " - " ASN C 327 " " NAG C1311 " - " ASN C 31 " " NAG C1312 " - " ASN C1126 " " NAG C1313 " - " ASN C 339 " " NAG D 1 " - " ASN A 233 " " NAG E 1 " - " ASN A 164 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 278 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN B 164 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 233 " " NAG L 1 " - " ASN B 278 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN C 278 " " NAG O 1 " - " ASN C 122 " " NAG P 1 " - " ASN C 233 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 164 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 963.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6246 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 55 sheets defined 25.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 360 through 365 Processing helix chain 'A' and resid 379 through 385 removed outlier: 4.067A pdb=" N ASN A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.614A pdb=" N ARG A 404 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 729 through 735 removed outlier: 3.887A pdb=" N TYR A 733 " --> pdb=" O ASP A 729 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 734 " --> pdb=" O CYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 750 through 774 removed outlier: 4.258A pdb=" N GLN A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 Processing helix chain 'A' and resid 828 through 834 removed outlier: 3.557A pdb=" N CYS A 832 " --> pdb=" O GLN A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 848 Processing helix chain 'A' and resid 858 through 876 Processing helix chain 'A' and resid 878 through 882 removed outlier: 3.542A pdb=" N ALA A 882 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 900 Processing helix chain 'A' and resid 904 through 933 removed outlier: 4.434A pdb=" N LEU A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 957 removed outlier: 3.699A pdb=" N ASP A 942 " --> pdb=" O GLY A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 960 No H-bonds generated for 'chain 'A' and resid 958 through 960' Processing helix chain 'A' and resid 968 through 974 Processing helix chain 'A' and resid 977 through 1025 removed outlier: 3.952A pdb=" N VAL A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1076 No H-bonds generated for 'chain 'A' and resid 1074 through 1076' Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 401 through 406 removed outlier: 4.726A pdb=" N ARG B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 626 through 632 removed outlier: 4.180A pdb=" N TYR B 632 " --> pdb=" O THR B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 735 removed outlier: 3.729A pdb=" N TYR B 733 " --> pdb=" O ASP B 729 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 734 " --> pdb=" O CYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 750 through 775 removed outlier: 4.247A pdb=" N GLN B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 818 Processing helix chain 'B' and resid 828 through 834 Processing helix chain 'B' and resid 840 through 848 Processing helix chain 'B' and resid 858 through 876 Processing helix chain 'B' and resid 878 through 882 Processing helix chain 'B' and resid 889 through 900 removed outlier: 3.787A pdb=" N ALA B 895 " --> pdb=" O ALA B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 910 removed outlier: 4.913A pdb=" N TYR B 909 " --> pdb=" O ASN B 906 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 910 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 933 removed outlier: 3.622A pdb=" N LEU B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 957 removed outlier: 3.893A pdb=" N ASP B 942 " --> pdb=" O GLY B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 960 No H-bonds generated for 'chain 'B' and resid 958 through 960' Processing helix chain 'B' and resid 968 through 974 Processing helix chain 'B' and resid 977 through 1024 removed outlier: 4.033A pdb=" N VAL B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 984 " --> pdb=" O GLU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1076 No H-bonds generated for 'chain 'B' and resid 1074 through 1076' Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.911A pdb=" N ASN C 366 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 removed outlier: 4.138A pdb=" N ASN C 384 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.516A pdb=" N ARG C 404 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 622 through 625 Processing helix chain 'C' and resid 626 through 632 removed outlier: 4.162A pdb=" N TYR C 632 " --> pdb=" O THR C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 735 Processing helix chain 'C' and resid 738 through 749 Processing helix chain 'C' and resid 750 through 774 removed outlier: 4.188A pdb=" N GLN C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 818 Processing helix chain 'C' and resid 828 through 834 removed outlier: 3.503A pdb=" N CYS C 832 " --> pdb=" O GLN C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 848 Processing helix chain 'C' and resid 858 through 876 Processing helix chain 'C' and resid 878 through 882 Processing helix chain 'C' and resid 889 through 900 Processing helix chain 'C' and resid 907 through 933 removed outlier: 6.240A pdb=" N LYS C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 914 " --> pdb=" O GLU C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 957 removed outlier: 3.671A pdb=" N ASP C 942 " --> pdb=" O GLY C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 960 No H-bonds generated for 'chain 'C' and resid 958 through 960' Processing helix chain 'C' and resid 968 through 974 Processing helix chain 'C' and resid 977 through 1025 removed outlier: 3.936A pdb=" N VAL C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN C 984 " --> pdb=" O GLU C 980 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.740A pdb=" N ASN A 62 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TYR A 265 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 186 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 204 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 37 removed outlier: 5.880A pdb=" N SER A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.868A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.974A pdb=" N THR A 242 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 101 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N VAL A 126 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N GLU A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N ILE A 128 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 130 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN A 132 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 162 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 134 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.292A pdb=" N CYS A 357 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB4, first strand: chain 'A' and resid 650 through 651 Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 705 removed outlier: 3.796A pdb=" N THR A1068 " --> pdb=" O SER A1089 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 720 removed outlier: 6.798A pdb=" N VAL A1057 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 713 through 720 Processing sheet with id=AB9, first strand: chain 'A' and resid 726 through 728 Processing sheet with id=AC1, first strand: chain 'A' and resid 1078 through 1082 removed outlier: 4.456A pdb=" N ALA A1079 " --> pdb=" O SER A1115 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A1115 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.653A pdb=" N ASN B 62 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 265 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP B 186 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER B 204 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.902A pdb=" N ASP B 283 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.667A pdb=" N ARG B 245 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B 144 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.965A pdb=" N THR B 242 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 101 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N ILE B 128 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR B 166 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL B 130 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASN B 164 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN B 132 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR B 162 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN B 134 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 323 Processing sheet with id=AC9, first strand: chain 'B' and resid 344 through 345 removed outlier: 7.145A pdb=" N ALA B 344 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N ARG B 399 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 344 through 345 removed outlier: 7.145A pdb=" N ALA B 344 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N ARG B 399 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.382A pdb=" N CYS B 357 " --> pdb=" O CYS B 521 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AD4, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AD5, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AD6, first strand: chain 'B' and resid 703 through 705 removed outlier: 3.934A pdb=" N THR B1068 " --> pdb=" O SER B1089 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 713 through 720 Processing sheet with id=AD8, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AD9, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE1, first strand: chain 'B' and resid 1078 through 1082 removed outlier: 4.385A pdb=" N ALA B1079 " --> pdb=" O SER B1115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.534A pdb=" N ASN C 62 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR C 265 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP C 186 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER C 204 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 49 through 56 removed outlier: 3.862A pdb=" N ASP C 283 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.998A pdb=" N PHE C 237 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.078A pdb=" N TYR C 137 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N THR C 239 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU C 241 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLN C 134 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 158 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.979A pdb=" N THR C 242 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 101 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 126 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AE8, first strand: chain 'C' and resid 321 through 323 removed outlier: 5.610A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.399A pdb=" N CYS C 357 " --> pdb=" O CYS C 521 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AF2, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AF3, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AF4, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AF5, first strand: chain 'C' and resid 650 through 651 Processing sheet with id=AF6, first strand: chain 'C' and resid 703 through 705 removed outlier: 3.884A pdb=" N THR C1068 " --> pdb=" O SER C1089 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 713 through 720 removed outlier: 6.735A pdb=" N VAL C1057 " --> pdb=" O LEU C1041 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 713 through 720 Processing sheet with id=AF9, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AG1, first strand: chain 'C' and resid 1073 through 1075 removed outlier: 4.787A pdb=" N ALA C1079 " --> pdb=" O SER C1115 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2805 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: 5.79 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 8585 1.35 - 1.48: 7288 1.48 - 1.61: 11577 1.61 - 1.74: 0 1.74 - 1.87: 156 Bond restraints: 27606 Sorted by residual: bond pdb=" N VAL B1120 " pdb=" CA VAL B1120 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.10e+01 bond pdb=" N VAL A1120 " pdb=" CA VAL A1120 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ILE C1124 " pdb=" CA ILE C1124 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 9.86e+00 bond pdb=" N ILE A1124 " pdb=" CA ILE A1124 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.46e+00 bond pdb=" C SER B1115 " pdb=" N GLY B1116 " ideal model delta sigma weight residual 1.331 1.287 0.044 1.46e-02 4.69e+03 8.93e+00 ... (remaining 27601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 37415 3.30 - 6.60: 158 6.60 - 9.91: 9 9.91 - 13.21: 5 13.21 - 16.51: 3 Bond angle restraints: 37590 Sorted by residual: angle pdb=" N VAL A1120 " pdb=" CA VAL A1120 " pdb=" C VAL A1120 " ideal model delta sigma weight residual 111.90 95.39 16.51 8.10e-01 1.52e+00 4.15e+02 angle pdb=" N VAL B1120 " pdb=" CA VAL B1120 " pdb=" C VAL B1120 " ideal model delta sigma weight residual 111.90 96.45 15.45 8.10e-01 1.52e+00 3.64e+02 angle pdb=" N ILE C1122 " pdb=" CA ILE C1122 " pdb=" C ILE C1122 " ideal model delta sigma weight residual 110.53 121.58 -11.05 9.40e-01 1.13e+00 1.38e+02 angle pdb=" C SER B1115 " pdb=" N GLY B1116 " pdb=" CA GLY B1116 " ideal model delta sigma weight residual 121.41 104.99 16.42 1.96e+00 2.60e-01 7.02e+01 angle pdb=" C ILE C1122 " pdb=" CA ILE C1122 " pdb=" CB ILE C1122 " ideal model delta sigma weight residual 112.02 101.55 10.47 1.31e+00 5.83e-01 6.39e+01 ... (remaining 37585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 16002 20.28 - 40.56: 1066 40.56 - 60.84: 189 60.84 - 81.11: 34 81.11 - 101.39: 28 Dihedral angle restraints: 17319 sinusoidal: 7572 harmonic: 9747 Sorted by residual: dihedral pdb=" CB CYS A1074 " pdb=" SG CYS A1074 " pdb=" SG CYS A1118 " pdb=" CB CYS A1118 " ideal model delta sinusoidal sigma weight residual 93.00 15.03 77.97 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CA CYS C 375 " pdb=" C CYS C 375 " pdb=" N TYR C 376 " pdb=" CA TYR C 376 " ideal model delta harmonic sigma weight residual 180.00 -138.16 -41.84 0 5.00e+00 4.00e-02 7.00e+01 dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 428 " pdb=" CB CYS A 428 " ideal model delta sinusoidal sigma weight residual 93.00 34.08 58.92 1 1.00e+01 1.00e-02 4.64e+01 ... (remaining 17316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 4413 0.157 - 0.313: 28 0.313 - 0.470: 8 0.470 - 0.626: 2 0.626 - 0.783: 1 Chirality restraints: 4452 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.78e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.23e+01 ... (remaining 4449 not shown) Planarity restraints: 4836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " 0.351 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG B1304 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " 0.093 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.316 2.00e-02 2.50e+03 2.67e-01 8.89e+02 pdb=" C7 NAG C1303 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.461 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1313 " -0.243 2.00e-02 2.50e+03 2.03e-01 5.15e+02 pdb=" C7 NAG A1313 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A1313 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG A1313 " 0.338 2.00e-02 2.50e+03 pdb=" O7 NAG A1313 " 0.009 2.00e-02 2.50e+03 ... (remaining 4833 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 175 2.47 - 3.08: 19217 3.08 - 3.69: 40687 3.69 - 4.29: 64031 4.29 - 4.90: 104256 Nonbonded interactions: 228366 Sorted by model distance: nonbonded pdb=" OD1 ASN A1126 " pdb=" N ASN A1127 " model vdw 1.868 3.120 nonbonded pdb=" OD1 ASN C1126 " pdb=" N ASN C1127 " model vdw 1.868 3.120 nonbonded pdb=" OD1 ASN B1126 " pdb=" N ASN B1127 " model vdw 1.869 3.120 nonbonded pdb=" O CYS C1074 " pdb=" CB ASN C1126 " model vdw 2.031 3.440 nonbonded pdb=" OG1 THR C 549 " pdb=" OD1 ASP C 582 " model vdw 2.072 3.040 ... (remaining 228361 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.100 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 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 0.880 27719 Z= 0.409 Angle : 0.873 49.232 37885 Z= 0.469 Chirality : 0.055 0.783 4452 Planarity : 0.008 0.304 4782 Dihedral : 14.070 101.393 10941 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.71 (0.14), residues: 3339 helix: -0.38 (0.18), residues: 741 sheet: -0.02 (0.21), residues: 636 loop : -1.90 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1099 TYR 0.022 0.002 TYR B 262 PHE 0.038 0.002 PHE B 343 TRP 0.025 0.002 TRP C1094 HIS 0.005 0.001 HIS B1040 Details of bonding type rmsd covalent geometry : bond 0.00443 (27606) covalent geometry : angle 0.71310 (37590) SS BOND : bond 0.16956 ( 44) SS BOND : angle 8.23034 ( 88) hydrogen bonds : bond 0.12323 ( 1011) hydrogen bonds : angle 7.65125 ( 2805) link_BETA1-4 : bond 0.00409 ( 15) link_BETA1-4 : angle 2.02382 ( 45) link_NAG-ASN : bond 0.00810 ( 54) link_NAG-ASN : angle 4.73196 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0629 (mmp) cc_final: -0.0555 (mpp) REVERT: A 257 PHE cc_start: 0.7063 (m-80) cc_final: 0.6427 (m-80) REVERT: A 765 GLU cc_start: 0.7120 (tp30) cc_final: 0.6798 (tp30) REVERT: A 1114 VAL cc_start: 0.7195 (p) cc_final: 0.6975 (p) REVERT: B 765 GLU cc_start: 0.7033 (tp30) cc_final: 0.6804 (tp30) REVERT: B 878 TRP cc_start: 0.7503 (p90) cc_final: 0.6512 (p90) outliers start: 0 outliers final: 1 residues processed: 364 average time/residue: 0.5182 time to fit residues: 224.3836 Evaluate side-chains 257 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 436 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A 899 ASN A 905 GLN A1127 ASN B 53 GLN B 115 GLN B 410 GLN B1002 GLN B1127 ASN C 609 GLN C 754 GLN C 771 GLN C 776 GLN C1127 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149807 restraints weight = 36410.639| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.93 r_work: 0.3660 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27719 Z= 0.166 Angle : 0.708 20.809 37885 Z= 0.352 Chirality : 0.050 0.732 4452 Planarity : 0.005 0.043 4782 Dihedral : 8.026 81.468 5069 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.55 % Allowed : 8.22 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.46 (0.14), residues: 3339 helix: 0.22 (0.19), residues: 723 sheet: 0.00 (0.21), residues: 636 loop : -1.85 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 353 TYR 0.027 0.002 TYR C 896 PHE 0.025 0.002 PHE B 343 TRP 0.010 0.001 TRP A 254 HIS 0.005 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00370 (27606) covalent geometry : angle 0.63782 (37590) SS BOND : bond 0.00570 ( 44) SS BOND : angle 1.72517 ( 88) hydrogen bonds : bond 0.04188 ( 1011) hydrogen bonds : angle 6.37290 ( 2805) link_BETA1-4 : bond 0.00384 ( 15) link_BETA1-4 : angle 1.83987 ( 45) link_NAG-ASN : bond 0.00776 ( 54) link_NAG-ASN : angle 4.49581 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 294 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.0580 (mmp) cc_final: -0.0656 (mpp) REVERT: A 257 PHE cc_start: 0.6963 (m-80) cc_final: 0.6275 (m-80) REVERT: A 402 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 765 GLU cc_start: 0.7740 (tp30) cc_final: 0.7530 (tp30) REVERT: B 162 TYR cc_start: 0.6854 (p90) cc_final: 0.6625 (p90) REVERT: B 262 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: B 765 GLU cc_start: 0.7649 (tp30) cc_final: 0.7427 (tp30) REVERT: B 831 ASP cc_start: 0.7273 (m-30) cc_final: 0.7000 (m-30) REVERT: B 878 TRP cc_start: 0.7827 (p90) cc_final: 0.6580 (p90) REVERT: B 928 ASP cc_start: 0.7339 (m-30) cc_final: 0.7113 (m-30) REVERT: B 1042 MET cc_start: 0.7875 (ptm) cc_final: 0.7473 (ptp) REVERT: C 139 PRO cc_start: 0.6985 (Cg_endo) cc_final: 0.6722 (Cg_exo) REVERT: C 204 SER cc_start: 0.8538 (p) cc_final: 0.8249 (p) REVERT: C 737 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: C 740 GLU cc_start: 0.6645 (pm20) cc_final: 0.6344 (pm20) outliers start: 45 outliers final: 18 residues processed: 319 average time/residue: 0.4715 time to fit residues: 180.1186 Evaluate side-chains 289 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 737 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 188 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 chunk 254 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 214 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148780 restraints weight = 36381.646| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.15 r_work: 0.3655 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27719 Z= 0.158 Angle : 0.681 20.779 37885 Z= 0.337 Chirality : 0.050 0.738 4452 Planarity : 0.004 0.058 4782 Dihedral : 7.596 79.782 5069 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.21 % Allowed : 10.16 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.35 (0.14), residues: 3339 helix: 0.40 (0.19), residues: 741 sheet: -0.23 (0.21), residues: 690 loop : -1.74 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 35 TYR 0.014 0.001 TYR A1059 PHE 0.029 0.001 PHE B 809 TRP 0.011 0.001 TRP A1094 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00357 (27606) covalent geometry : angle 0.61231 (37590) SS BOND : bond 0.00475 ( 44) SS BOND : angle 1.68913 ( 88) hydrogen bonds : bond 0.04014 ( 1011) hydrogen bonds : angle 6.13719 ( 2805) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.78237 ( 45) link_NAG-ASN : bond 0.00783 ( 54) link_NAG-ASN : angle 4.36317 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.0397 (mmp) cc_final: -0.0787 (mpp) REVERT: A 257 PHE cc_start: 0.6921 (m-80) cc_final: 0.6330 (m-80) REVERT: A 402 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 740 GLU cc_start: 0.7000 (pm20) cc_final: 0.6671 (pm20) REVERT: A 765 GLU cc_start: 0.7757 (tp30) cc_final: 0.7535 (tp30) REVERT: B 162 TYR cc_start: 0.6955 (p90) cc_final: 0.6730 (p90) REVERT: B 262 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: B 550 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: B 582 ASP cc_start: 0.7877 (p0) cc_final: 0.7428 (p0) REVERT: B 751 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6720 (m-80) REVERT: B 765 GLU cc_start: 0.7643 (tp30) cc_final: 0.7429 (tp30) REVERT: B 831 ASP cc_start: 0.7156 (m-30) cc_final: 0.6939 (m-30) REVERT: B 878 TRP cc_start: 0.7840 (p90) cc_final: 0.6570 (p90) REVERT: B 896 TYR cc_start: 0.6583 (m-80) cc_final: 0.6352 (m-80) REVERT: B 928 ASP cc_start: 0.7414 (m-30) cc_final: 0.7147 (m-30) REVERT: B 1042 MET cc_start: 0.7893 (ptm) cc_final: 0.7615 (ptp) REVERT: C 139 PRO cc_start: 0.6957 (Cg_endo) cc_final: 0.6597 (Cg_exo) REVERT: C 740 GLU cc_start: 0.6845 (pm20) cc_final: 0.6611 (pm20) REVERT: C 768 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7690 (tttt) REVERT: C 1002 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7446 (mp10) outliers start: 64 outliers final: 31 residues processed: 326 average time/residue: 0.4519 time to fit residues: 177.8064 Evaluate side-chains 298 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN C 769 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150629 restraints weight = 36293.991| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.96 r_work: 0.3666 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 27719 Z= 0.145 Angle : 0.665 20.558 37885 Z= 0.329 Chirality : 0.049 0.718 4452 Planarity : 0.004 0.049 4782 Dihedral : 7.280 78.573 5069 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.28 % Allowed : 11.85 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.28 (0.14), residues: 3339 helix: 0.53 (0.20), residues: 741 sheet: -0.03 (0.21), residues: 636 loop : -1.77 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 839 TYR 0.013 0.001 TYR B 261 PHE 0.030 0.001 PHE B 809 TRP 0.011 0.001 TRP B1094 HIS 0.004 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00327 (27606) covalent geometry : angle 0.59671 (37590) SS BOND : bond 0.00460 ( 44) SS BOND : angle 2.06198 ( 88) hydrogen bonds : bond 0.03806 ( 1011) hydrogen bonds : angle 6.01128 ( 2805) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.76713 ( 45) link_NAG-ASN : bond 0.00826 ( 54) link_NAG-ASN : angle 4.21155 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 285 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0587 (mmp) cc_final: -0.0722 (mpp) REVERT: A 257 PHE cc_start: 0.6983 (m-80) cc_final: 0.6388 (m-80) REVERT: A 402 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7930 (mt-10) REVERT: A 765 GLU cc_start: 0.7772 (tp30) cc_final: 0.7236 (tp30) REVERT: A 769 ASN cc_start: 0.8468 (m110) cc_final: 0.8131 (m-40) REVERT: B 550 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: B 751 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: B 765 GLU cc_start: 0.7601 (tp30) cc_final: 0.7380 (tp30) REVERT: B 878 TRP cc_start: 0.7837 (p90) cc_final: 0.6578 (p90) REVERT: B 928 ASP cc_start: 0.7316 (m-30) cc_final: 0.7043 (m-30) REVERT: B 1042 MET cc_start: 0.7806 (ptm) cc_final: 0.7493 (ptp) REVERT: C 139 PRO cc_start: 0.7026 (Cg_endo) cc_final: 0.6624 (Cg_exo) REVERT: C 204 SER cc_start: 0.8515 (p) cc_final: 0.8201 (p) REVERT: C 331 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6851 (mm) REVERT: C 737 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: C 751 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6105 (m-80) REVERT: C 1002 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: C 1042 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7738 (ptp) outliers start: 66 outliers final: 25 residues processed: 323 average time/residue: 0.4654 time to fit residues: 179.7078 Evaluate side-chains 295 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 57 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A 947 ASN A1100 ASN B 918 GLN B1002 GLN C 34 HIS ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.170429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144576 restraints weight = 36274.766| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.08 r_work: 0.3588 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 27719 Z= 0.275 Angle : 0.781 20.749 37885 Z= 0.391 Chirality : 0.053 0.708 4452 Planarity : 0.005 0.048 4782 Dihedral : 7.721 76.683 5067 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.87 % Allowed : 12.75 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.56 (0.14), residues: 3339 helix: 0.20 (0.19), residues: 723 sheet: -0.37 (0.21), residues: 612 loop : -1.80 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 404 TYR 0.023 0.002 TYR B 419 PHE 0.029 0.002 PHE B 794 TRP 0.019 0.002 TRP B1094 HIS 0.009 0.002 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00646 (27606) covalent geometry : angle 0.71795 (37590) SS BOND : bond 0.00793 ( 44) SS BOND : angle 2.41624 ( 88) hydrogen bonds : bond 0.04499 ( 1011) hydrogen bonds : angle 6.35092 ( 2805) link_BETA1-4 : bond 0.00411 ( 15) link_BETA1-4 : angle 1.86751 ( 45) link_NAG-ASN : bond 0.00881 ( 54) link_NAG-ASN : angle 4.36297 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 272 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7910 (mt) REVERT: A 175 MET cc_start: 0.0256 (mmp) cc_final: -0.0895 (mpp) REVERT: A 257 PHE cc_start: 0.6901 (m-80) cc_final: 0.6319 (m-80) REVERT: A 402 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8130 (mt-10) REVERT: A 740 GLU cc_start: 0.7262 (pm20) cc_final: 0.6970 (pm20) REVERT: A 765 GLU cc_start: 0.7968 (tp30) cc_final: 0.7702 (tp30) REVERT: A 980 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: A 1064 GLU cc_start: 0.7799 (mp0) cc_final: 0.7597 (mp0) REVERT: B 204 SER cc_start: 0.8501 (p) cc_final: 0.8281 (p) REVERT: B 582 ASP cc_start: 0.8130 (p0) cc_final: 0.7738 (p0) REVERT: B 751 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: B 765 GLU cc_start: 0.7767 (tp30) cc_final: 0.7523 (tp30) REVERT: B 768 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8101 (ttpt) REVERT: B 878 TRP cc_start: 0.7915 (p90) cc_final: 0.6689 (p90) REVERT: B 896 TYR cc_start: 0.6778 (m-80) cc_final: 0.6552 (m-80) REVERT: B 1042 MET cc_start: 0.8032 (ptm) cc_final: 0.7795 (ptp) REVERT: C 85 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: C 204 SER cc_start: 0.8565 (p) cc_final: 0.8306 (p) REVERT: C 768 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8021 (tttt) REVERT: C 1002 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7437 (mp10) outliers start: 83 outliers final: 46 residues processed: 319 average time/residue: 0.5254 time to fit residues: 200.4320 Evaluate side-chains 303 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 861 MET Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 436 ASN Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 195 optimal weight: 0.9980 chunk 277 optimal weight: 8.9990 chunk 291 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.173871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148719 restraints weight = 36394.052| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.02 r_work: 0.3649 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27719 Z= 0.154 Angle : 0.685 20.550 37885 Z= 0.341 Chirality : 0.049 0.689 4452 Planarity : 0.004 0.049 4782 Dihedral : 7.294 77.612 5067 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.73 % Allowed : 14.27 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.41 (0.14), residues: 3339 helix: 0.35 (0.19), residues: 747 sheet: -0.12 (0.21), residues: 636 loop : -1.82 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 839 TYR 0.015 0.001 TYR A 419 PHE 0.028 0.001 PHE B 809 TRP 0.016 0.001 TRP B1094 HIS 0.003 0.001 HIS B 244 Details of bonding type rmsd covalent geometry : bond 0.00348 (27606) covalent geometry : angle 0.61816 (37590) SS BOND : bond 0.00565 ( 44) SS BOND : angle 2.17762 ( 88) hydrogen bonds : bond 0.03913 ( 1011) hydrogen bonds : angle 6.04891 ( 2805) link_BETA1-4 : bond 0.00404 ( 15) link_BETA1-4 : angle 1.80884 ( 45) link_NAG-ASN : bond 0.00798 ( 54) link_NAG-ASN : angle 4.20437 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 269 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.5467 (tm-30) cc_final: 0.5261 (tm-30) REVERT: A 175 MET cc_start: 0.0768 (mmp) cc_final: -0.0652 (mpp) REVERT: A 257 PHE cc_start: 0.6942 (m-80) cc_final: 0.6345 (m-80) REVERT: A 740 GLU cc_start: 0.7123 (pm20) cc_final: 0.6787 (pm20) REVERT: A 765 GLU cc_start: 0.7748 (tp30) cc_final: 0.7493 (tp30) REVERT: A 980 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: A 1064 GLU cc_start: 0.7697 (mp0) cc_final: 0.7470 (mp0) REVERT: B 751 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: B 765 GLU cc_start: 0.7601 (tp30) cc_final: 0.7395 (tp30) REVERT: B 806 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6948 (tttm) REVERT: B 878 TRP cc_start: 0.7912 (p90) cc_final: 0.6665 (p90) REVERT: B 1042 MET cc_start: 0.7859 (ptm) cc_final: 0.7495 (ptp) REVERT: C 115 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: C 204 SER cc_start: 0.8569 (p) cc_final: 0.8257 (p) REVERT: C 331 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6880 (mm) REVERT: C 737 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: C 751 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6348 (m-80) REVERT: C 1002 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7337 (mp10) outliers start: 79 outliers final: 41 residues processed: 314 average time/residue: 0.4978 time to fit residues: 186.8192 Evaluate side-chains 302 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 1037 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN A1100 ASN B1002 GLN C 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.173438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.147138 restraints weight = 36136.095| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.12 r_work: 0.3634 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27719 Z= 0.169 Angle : 0.688 20.433 37885 Z= 0.341 Chirality : 0.049 0.671 4452 Planarity : 0.004 0.048 4782 Dihedral : 7.191 76.697 5067 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.69 % Allowed : 14.99 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.39 (0.14), residues: 3339 helix: 0.35 (0.19), residues: 759 sheet: -0.36 (0.20), residues: 690 loop : -1.74 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 839 TYR 0.014 0.002 TYR C 419 PHE 0.032 0.002 PHE B 809 TRP 0.020 0.002 TRP B1094 HIS 0.004 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00386 (27606) covalent geometry : angle 0.62318 (37590) SS BOND : bond 0.00598 ( 44) SS BOND : angle 2.00926 ( 88) hydrogen bonds : bond 0.03922 ( 1011) hydrogen bonds : angle 6.01049 ( 2805) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.80071 ( 45) link_NAG-ASN : bond 0.00807 ( 54) link_NAG-ASN : angle 4.17668 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 263 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0828 (mmp) cc_final: -0.0638 (mpp) REVERT: A 257 PHE cc_start: 0.6925 (m-80) cc_final: 0.6286 (m-80) REVERT: A 740 GLU cc_start: 0.7174 (pm20) cc_final: 0.6837 (pm20) REVERT: A 765 GLU cc_start: 0.7859 (tp30) cc_final: 0.7524 (tp30) REVERT: A 980 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: A 1002 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: A 1064 GLU cc_start: 0.7736 (mp0) cc_final: 0.7513 (mp0) REVERT: B 204 SER cc_start: 0.8669 (p) cc_final: 0.8403 (p) REVERT: B 751 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: B 765 GLU cc_start: 0.7624 (tp30) cc_final: 0.7412 (tp30) REVERT: B 768 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7865 (tmmt) REVERT: B 878 TRP cc_start: 0.7946 (p90) cc_final: 0.6696 (p90) REVERT: B 896 TYR cc_start: 0.6705 (m-80) cc_final: 0.6473 (m-80) REVERT: B 1042 MET cc_start: 0.7922 (ptm) cc_final: 0.7561 (ptp) REVERT: C 85 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: C 115 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: C 331 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6921 (mm) REVERT: C 737 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: C 751 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: C 768 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8402 (tmmt) REVERT: C 1002 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7385 (mp10) outliers start: 78 outliers final: 43 residues processed: 310 average time/residue: 0.5036 time to fit residues: 187.6358 Evaluate side-chains 304 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 1037 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 297 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 275 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 326 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 HIS B1002 GLN C 754 GLN C 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.174283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149623 restraints weight = 36334.337| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.01 r_work: 0.3646 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27719 Z= 0.151 Angle : 0.669 20.354 37885 Z= 0.332 Chirality : 0.049 0.659 4452 Planarity : 0.004 0.048 4782 Dihedral : 7.006 76.281 5067 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.42 % Allowed : 15.89 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.31 (0.14), residues: 3339 helix: 0.40 (0.19), residues: 765 sheet: -0.19 (0.21), residues: 642 loop : -1.71 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 839 TYR 0.013 0.001 TYR A 419 PHE 0.030 0.001 PHE B 809 TRP 0.022 0.002 TRP B1094 HIS 0.004 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00341 (27606) covalent geometry : angle 0.60512 (37590) SS BOND : bond 0.00525 ( 44) SS BOND : angle 1.86921 ( 88) hydrogen bonds : bond 0.03774 ( 1011) hydrogen bonds : angle 5.92976 ( 2805) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.78951 ( 45) link_NAG-ASN : bond 0.00790 ( 54) link_NAG-ASN : angle 4.11180 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0970 (mmp) cc_final: -0.0521 (mpp) REVERT: A 257 PHE cc_start: 0.7031 (m-80) cc_final: 0.6388 (m-80) REVERT: A 740 GLU cc_start: 0.7166 (pm20) cc_final: 0.6829 (pm20) REVERT: A 765 GLU cc_start: 0.7861 (tp30) cc_final: 0.7512 (tp30) REVERT: A 980 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: A 1002 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8031 (mp10) REVERT: A 1064 GLU cc_start: 0.7687 (mp0) cc_final: 0.7462 (mp0) REVERT: B 204 SER cc_start: 0.8652 (p) cc_final: 0.8375 (p) REVERT: B 353 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7888 (ttm110) REVERT: B 402 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 582 ASP cc_start: 0.8034 (p0) cc_final: 0.7548 (p0) REVERT: B 751 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: B 765 GLU cc_start: 0.7609 (tp30) cc_final: 0.7363 (tp30) REVERT: B 768 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8186 (tptt) REVERT: B 772 GLU cc_start: 0.7717 (pt0) cc_final: 0.7297 (pt0) REVERT: B 878 TRP cc_start: 0.7878 (p90) cc_final: 0.6693 (p90) REVERT: B 1042 MET cc_start: 0.7875 (ptm) cc_final: 0.7496 (ptp) REVERT: C 85 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: C 115 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: C 204 SER cc_start: 0.8553 (p) cc_final: 0.8240 (p) REVERT: C 244 HIS cc_start: 0.6092 (t-90) cc_final: 0.5760 (t70) REVERT: C 331 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6901 (mm) REVERT: C 737 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: C 751 PHE cc_start: 0.6508 (OUTLIER) cc_final: 0.6158 (m-80) REVERT: C 768 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8406 (tmmt) REVERT: C 878 TRP cc_start: 0.7736 (p90) cc_final: 0.6609 (p90) outliers start: 70 outliers final: 42 residues processed: 307 average time/residue: 0.5047 time to fit residues: 186.0526 Evaluate side-chains 303 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 831 ASP Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 642 ARG Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 86 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 270 optimal weight: 0.0070 chunk 256 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.174090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148983 restraints weight = 36391.792| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.03 r_work: 0.3649 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27719 Z= 0.166 Angle : 0.778 51.108 37885 Z= 0.407 Chirality : 0.049 0.653 4452 Planarity : 0.004 0.050 4782 Dihedral : 7.309 79.038 5067 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.49 % Allowed : 16.23 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.14), residues: 3339 helix: 0.41 (0.19), residues: 759 sheet: -0.42 (0.20), residues: 696 loop : -1.65 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 839 TYR 0.027 0.002 TYR A1059 PHE 0.020 0.001 PHE B 809 TRP 0.033 0.002 TRP A1094 HIS 0.004 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00378 (27606) covalent geometry : angle 0.72498 (37590) SS BOND : bond 0.00562 ( 44) SS BOND : angle 1.88153 ( 88) hydrogen bonds : bond 0.03842 ( 1011) hydrogen bonds : angle 5.95591 ( 2805) link_BETA1-4 : bond 0.00388 ( 15) link_BETA1-4 : angle 1.78456 ( 45) link_NAG-ASN : bond 0.00787 ( 54) link_NAG-ASN : angle 4.11575 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0929 (mmp) cc_final: -0.0583 (mpp) REVERT: A 257 PHE cc_start: 0.6978 (m-80) cc_final: 0.6329 (m-80) REVERT: A 737 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7526 (m-30) REVERT: A 740 GLU cc_start: 0.7169 (pm20) cc_final: 0.6893 (pm20) REVERT: A 765 GLU cc_start: 0.7854 (tp30) cc_final: 0.7503 (tp30) REVERT: A 980 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: A 1002 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: A 1064 GLU cc_start: 0.7694 (mp0) cc_final: 0.7476 (mp0) REVERT: B 204 SER cc_start: 0.8659 (p) cc_final: 0.8387 (p) REVERT: B 353 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (ttm110) REVERT: B 402 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7802 (mt-10) REVERT: B 582 ASP cc_start: 0.7942 (p0) cc_final: 0.7451 (p0) REVERT: B 751 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: B 765 GLU cc_start: 0.7572 (tp30) cc_final: 0.7351 (tp30) REVERT: B 768 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8259 (tptt) REVERT: B 878 TRP cc_start: 0.7956 (p90) cc_final: 0.6716 (p90) REVERT: B 1042 MET cc_start: 0.7964 (ptm) cc_final: 0.7645 (ptp) REVERT: C 85 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: C 115 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: C 204 SER cc_start: 0.8557 (p) cc_final: 0.8236 (p) REVERT: C 331 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.6908 (mm) REVERT: C 737 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: C 751 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.6139 (m-80) REVERT: C 768 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8409 (tmmt) REVERT: C 1002 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7396 (mp10) outliers start: 72 outliers final: 42 residues processed: 299 average time/residue: 0.4725 time to fit residues: 170.0869 Evaluate side-chains 303 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.174530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149546 restraints weight = 36266.643| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.99 r_work: 0.3644 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27719 Z= 0.151 Angle : 0.694 20.294 37885 Z= 0.344 Chirality : 0.048 0.643 4452 Planarity : 0.004 0.078 4782 Dihedral : 7.456 105.702 5067 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.93 % Allowed : 16.75 % Favored : 81.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.27 (0.14), residues: 3339 helix: 0.50 (0.19), residues: 759 sheet: -0.43 (0.20), residues: 696 loop : -1.62 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 453 TYR 0.023 0.001 TYR A 699 PHE 0.019 0.001 PHE B 809 TRP 0.037 0.002 TRP A1094 HIS 0.003 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00338 (27606) covalent geometry : angle 0.63257 (37590) SS BOND : bond 0.00492 ( 44) SS BOND : angle 1.80499 ( 88) hydrogen bonds : bond 0.03773 ( 1011) hydrogen bonds : angle 5.88102 ( 2805) link_BETA1-4 : bond 0.00392 ( 15) link_BETA1-4 : angle 1.79431 ( 45) link_NAG-ASN : bond 0.00815 ( 54) link_NAG-ASN : angle 4.13665 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6678 Ramachandran restraints generated. 3339 Oldfield, 0 Emsley, 3339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0611 (mmp) cc_final: -0.0677 (mpp) REVERT: A 257 PHE cc_start: 0.7009 (m-80) cc_final: 0.6359 (m-80) REVERT: A 740 GLU cc_start: 0.7160 (pm20) cc_final: 0.6878 (pm20) REVERT: A 765 GLU cc_start: 0.7842 (tp30) cc_final: 0.7493 (tp30) REVERT: A 980 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: A 1002 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: A 1064 GLU cc_start: 0.7717 (mp0) cc_final: 0.7507 (mp0) REVERT: B 204 SER cc_start: 0.8661 (p) cc_final: 0.8387 (p) REVERT: B 353 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7900 (ttm110) REVERT: B 402 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7787 (mt-10) REVERT: B 582 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7510 (p0) REVERT: B 751 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: B 765 GLU cc_start: 0.7595 (tp30) cc_final: 0.6830 (tp30) REVERT: B 768 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7992 (tmmt) REVERT: B 878 TRP cc_start: 0.7947 (p90) cc_final: 0.6688 (p90) REVERT: B 1042 MET cc_start: 0.7910 (ptm) cc_final: 0.7586 (ptp) REVERT: C 85 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: C 204 SER cc_start: 0.8569 (p) cc_final: 0.8254 (p) REVERT: C 331 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6894 (mm) REVERT: C 737 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: C 751 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: C 768 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8417 (tmmt) REVERT: C 1002 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7422 (mp10) outliers start: 56 outliers final: 40 residues processed: 290 average time/residue: 0.4743 time to fit residues: 165.7179 Evaluate side-chains 300 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 796 GLN Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 360 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 751 PHE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 768 LYS Chi-restraints excluded: chain C residue 861 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1100 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 256 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 262 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 330 optimal weight: 0.6980 chunk 179 optimal weight: 0.0070 chunk 276 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B1002 GLN ** B1040 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1075 HIS C 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.177123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150901 restraints weight = 36002.457| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.14 r_work: 0.3679 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27719 Z= 0.125 Angle : 0.660 20.151 37885 Z= 0.326 Chirality : 0.047 0.626 4452 Planarity : 0.004 0.050 4782 Dihedral : 7.139 101.150 5067 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.66 % Allowed : 17.34 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.18 (0.15), residues: 3339 helix: 0.64 (0.19), residues: 759 sheet: -0.45 (0.20), residues: 708 loop : -1.56 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 563 TYR 0.023 0.001 TYR A 699 PHE 0.016 0.001 PHE B 809 TRP 0.026 0.001 TRP A1094 HIS 0.003 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00272 (27606) covalent geometry : angle 0.59864 (37590) SS BOND : bond 0.00511 ( 44) SS BOND : angle 1.73345 ( 88) hydrogen bonds : bond 0.03534 ( 1011) hydrogen bonds : angle 5.74476 ( 2805) link_BETA1-4 : bond 0.00407 ( 15) link_BETA1-4 : angle 1.77629 ( 45) link_NAG-ASN : bond 0.00739 ( 54) link_NAG-ASN : angle 4.02470 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8670.99 seconds wall clock time: 148 minutes 39.19 seconds (8919.19 seconds total)