Starting phenix.real_space_refine on Sun May 25 16:04:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3w_35160/05_2025/8i3w_35160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3w_35160/05_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_35160/05_2025/8i3w_35160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3w_35160/05_2025/8i3w_35160.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3w_35160/05_2025/8i3w_35160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3w_35160/05_2025/8i3w_35160.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.67s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.93, per 1000 atoms: 0.55 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: 7.49 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 4.05 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: 12.14 Time building geometry restraints manager: 8.75 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: 0.00 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 62.260 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.850 ------------------------------------------------------------------------------- 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 : 13.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.002 TRP C1094 HIS 0.005 0.001 HIS B1040 PHE 0.038 0.002 PHE B 343 TYR 0.022 0.002 TYR B 262 ARG 0.005 0.000 ARG C1099 Details of bonding type rmsd link_NAG-ASN : bond 0.00810 ( 54) link_NAG-ASN : angle 4.73196 ( 162) link_BETA1-4 : bond 0.00409 ( 15) link_BETA1-4 : angle 2.02382 ( 45) hydrogen bonds : bond 0.12323 ( 1011) hydrogen bonds : angle 7.65125 ( 2805) SS BOND : bond 0.16956 ( 44) SS BOND : angle 8.23034 ( 88) covalent geometry : bond 0.00443 (27606) covalent geometry : angle 0.71310 (37590) *********************** 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 : 2.867 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: 0.6799 (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: 1.1183 time to fit residues: 488.9635 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 : 2.711 ------------------------------------------------------------------------------- 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 281 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 302 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 115 GLN B1002 GLN B1127 ASN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN C 754 GLN C 776 GLN C1100 ASN C1127 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.172011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146625 restraints weight = 36147.503| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.16 r_work: 0.3623 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 27719 Z= 0.226 Angle : 0.759 20.952 37885 Z= 0.380 Chirality : 0.052 0.745 4452 Planarity : 0.005 0.046 4782 Dihedral : 8.233 81.540 5069 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.83 % Allowed : 8.57 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3339 helix: -0.00 (0.19), residues: 723 sheet: -0.22 (0.21), residues: 678 loop : -1.86 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1094 HIS 0.007 0.001 HIS A 34 PHE 0.033 0.002 PHE B 343 TYR 0.024 0.002 TYR C 896 ARG 0.006 0.001 ARG A 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 54) link_NAG-ASN : angle 4.63469 ( 162) link_BETA1-4 : bond 0.00477 ( 15) link_BETA1-4 : angle 1.84825 ( 45) hydrogen bonds : bond 0.04523 ( 1011) hydrogen bonds : angle 6.52481 ( 2805) SS BOND : bond 0.00650 ( 44) SS BOND : angle 1.99237 ( 88) covalent geometry : bond 0.00521 (27606) covalent geometry : angle 0.68931 (37590) *********************** 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 341 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 2.809 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.0622 (mmp) cc_final: -0.0659 (mpp) REVERT: A 257 PHE cc_start: 0.6905 (m-80) cc_final: 0.6205 (m-80) REVERT: A 740 GLU cc_start: 0.7159 (pm20) cc_final: 0.6885 (pm20) REVERT: A 765 GLU cc_start: 0.7774 (tp30) cc_final: 0.7559 (tp30) REVERT: A 1002 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7850 (mp-120) REVERT: B 35 ARG cc_start: 0.7844 (mtt-85) cc_final: 0.7621 (mtt90) REVERT: B 162 TYR cc_start: 0.6932 (p90) cc_final: 0.6691 (p90) REVERT: B 262 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: B 751 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: B 765 GLU cc_start: 0.7733 (tp30) cc_final: 0.7512 (tp30) REVERT: B 831 ASP cc_start: 0.7265 (m-30) cc_final: 0.6981 (m-30) REVERT: B 1042 MET cc_start: 0.7981 (ptm) cc_final: 0.7437 (ptp) REVERT: C 139 PRO cc_start: 0.7006 (Cg_endo) cc_final: 0.6710 (Cg_exo) REVERT: C 204 SER cc_start: 0.8590 (p) cc_final: 0.8322 (p) REVERT: C 740 GLU cc_start: 0.6894 (pm20) cc_final: 0.6555 (pm20) outliers start: 53 outliers final: 26 residues processed: 316 average time/residue: 1.1005 time to fit residues: 420.0351 Evaluate side-chains 291 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 3.140 ------------------------------------------------------------------------------- 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 642 ARG Chi-restraints excluded: chain A residue 727 SER 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 B residue 63 ILE 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 542 LEU Chi-restraints excluded: chain B residue 582 ASP Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 751 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain C residue 63 ILE 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 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 858 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 171 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 159 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 295 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 233 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 53 GLN B 410 GLN B1002 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN C 769 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150196 restraints weight = 36171.108| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.03 r_work: 0.3671 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27719 Z= 0.137 Angle : 0.672 20.703 37885 Z= 0.332 Chirality : 0.049 0.735 4452 Planarity : 0.004 0.045 4782 Dihedral : 7.554 80.630 5069 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.97 % Allowed : 10.57 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3339 helix: 0.34 (0.19), residues: 738 sheet: -0.03 (0.21), residues: 636 loop : -1.82 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1094 HIS 0.003 0.001 HIS C1080 PHE 0.027 0.001 PHE B 809 TYR 0.013 0.001 TYR C 501 ARG 0.005 0.000 ARG C 839 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 54) link_NAG-ASN : angle 4.38882 ( 162) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 1.79473 ( 45) hydrogen bonds : bond 0.03901 ( 1011) hydrogen bonds : angle 6.11682 ( 2805) SS BOND : bond 0.00541 ( 44) SS BOND : angle 1.79512 ( 88) covalent geometry : bond 0.00302 (27606) covalent geometry : angle 0.60040 (37590) *********************** 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 359 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 302 time to evaluate : 3.046 Fit side-chains revert: symmetry clash REVERT: A 175 MET cc_start: 0.0561 (mmp) cc_final: -0.0715 (mpp) REVERT: A 257 PHE cc_start: 0.6945 (m-80) cc_final: 0.6343 (m-80) REVERT: A 765 GLU cc_start: 0.7741 (tp30) cc_final: 0.7525 (tp30) REVERT: B 162 TYR cc_start: 0.7000 (p90) cc_final: 0.6791 (p90) REVERT: B 550 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: B 582 ASP cc_start: 0.7916 (p0) cc_final: 0.7469 (p0) REVERT: B 765 GLU cc_start: 0.7609 (tp30) cc_final: 0.7397 (tp30) REVERT: B 878 TRP cc_start: 0.7814 (p90) cc_final: 0.6581 (p90) REVERT: B 1042 MET cc_start: 0.7835 (ptm) cc_final: 0.7538 (ptp) REVERT: C 139 PRO cc_start: 0.7029 (Cg_endo) cc_final: 0.6677 (Cg_exo) REVERT: C 331 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6740 (mm) REVERT: C 737 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: C 768 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7710 (tttt) REVERT: C 1002 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7402 (mp10) outliers start: 57 outliers final: 19 residues processed: 337 average time/residue: 1.1184 time to fit residues: 457.3966 Evaluate side-chains 290 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE 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 727 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 1100 ASN 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 752 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 69 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 23 optimal weight: 8.9990 chunk 272 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 306 optimal weight: 0.0980 chunk 120 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 282 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** A 947 ASN B1002 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.151004 restraints weight = 36467.267| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.08 r_work: 0.3680 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27719 Z= 0.132 Angle : 0.656 20.475 37885 Z= 0.323 Chirality : 0.049 0.708 4452 Planarity : 0.004 0.048 4782 Dihedral : 7.187 79.098 5069 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.07 % Allowed : 12.57 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3339 helix: 0.57 (0.20), residues: 741 sheet: -0.18 (0.21), residues: 654 loop : -1.72 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1094 HIS 0.004 0.001 HIS B1080 PHE 0.029 0.001 PHE B 809 TYR 0.013 0.001 TYR B 261 ARG 0.008 0.000 ARG B 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00791 ( 54) link_NAG-ASN : angle 4.18736 ( 162) link_BETA1-4 : bond 0.00402 ( 15) link_BETA1-4 : angle 1.77283 ( 45) hydrogen bonds : bond 0.03717 ( 1011) hydrogen bonds : angle 5.95240 ( 2805) SS BOND : bond 0.00435 ( 44) SS BOND : angle 2.03240 ( 88) covalent geometry : bond 0.00294 (27606) covalent geometry : angle 0.58741 (37590) *********************** 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 342 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0736 (mmp) cc_final: -0.0670 (mpp) REVERT: A 257 PHE cc_start: 0.6928 (m-80) cc_final: 0.6308 (m-80) REVERT: A 740 GLU cc_start: 0.6993 (pm20) cc_final: 0.6713 (pm20) REVERT: A 765 GLU cc_start: 0.7726 (tp30) cc_final: 0.7284 (tp30) REVERT: B 402 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 550 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6446 (tm-30) REVERT: B 582 ASP cc_start: 0.7871 (p0) cc_final: 0.7477 (p0) REVERT: B 765 GLU cc_start: 0.7582 (tp30) cc_final: 0.7355 (tp30) REVERT: B 878 TRP cc_start: 0.7781 (p90) cc_final: 0.6516 (p90) REVERT: B 1042 MET cc_start: 0.7781 (ptm) cc_final: 0.7453 (ptp) REVERT: C 139 PRO cc_start: 0.7007 (Cg_endo) cc_final: 0.6607 (Cg_exo) REVERT: C 204 SER cc_start: 0.8509 (p) cc_final: 0.8200 (p) REVERT: C 241 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7038 (mt) REVERT: C 244 HIS cc_start: 0.6160 (t-90) cc_final: 0.5690 (t70) REVERT: C 331 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6744 (mm) REVERT: C 737 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: C 751 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: C 1002 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: C 1122 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6327 (pp) outliers start: 60 outliers final: 24 residues processed: 318 average time/residue: 1.1246 time to fit residues: 430.9332 Evaluate side-chains 292 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 2.796 ------------------------------------------------------------------------------- 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 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 316 VAL Chi-restraints excluded: chain B residue 331 LEU 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 752 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 241 LEU 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 672 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 740 GLU 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 1122 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 28 optimal weight: 0.0980 chunk 305 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 B1002 GLN ** C 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146341 restraints weight = 36254.240| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.05 r_work: 0.3610 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 27719 Z= 0.223 Angle : 0.730 20.629 37885 Z= 0.364 Chirality : 0.051 0.697 4452 Planarity : 0.005 0.049 4782 Dihedral : 7.398 77.235 5067 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.73 % Allowed : 13.13 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3339 helix: 0.34 (0.19), residues: 741 sheet: -0.06 (0.21), residues: 630 loop : -1.82 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1094 HIS 0.007 0.001 HIS A 34 PHE 0.025 0.002 PHE B 794 TYR 0.019 0.002 TYR A 419 ARG 0.005 0.001 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00846 ( 54) link_NAG-ASN : angle 4.26222 ( 162) link_BETA1-4 : bond 0.00406 ( 15) link_BETA1-4 : angle 1.81122 ( 45) hydrogen bonds : bond 0.04195 ( 1011) hydrogen bonds : angle 6.16427 ( 2805) SS BOND : bond 0.00745 ( 44) SS BOND : angle 2.13476 ( 88) covalent geometry : bond 0.00520 (27606) covalent geometry : angle 0.66686 (37590) *********************** 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 348 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 269 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7794 (mt) REVERT: A 175 MET cc_start: 0.0514 (mmp) cc_final: -0.0802 (mpp) REVERT: A 257 PHE cc_start: 0.6965 (m-80) cc_final: 0.6365 (m-80) REVERT: A 737 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: A 740 GLU cc_start: 0.7260 (pm20) cc_final: 0.6975 (pm20) REVERT: A 765 GLU cc_start: 0.7886 (tp30) cc_final: 0.7641 (tp30) REVERT: A 980 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: A 1002 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8372 (mp10) REVERT: A 1064 GLU cc_start: 0.7786 (mp0) cc_final: 0.7574 (mp0) REVERT: B 204 SER cc_start: 0.8549 (p) cc_final: 0.8298 (p) REVERT: B 353 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7933 (ttm110) REVERT: B 550 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: B 582 ASP cc_start: 0.8077 (p0) cc_final: 0.7755 (p0) REVERT: B 731 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 751 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: B 765 GLU cc_start: 0.7688 (tp30) cc_final: 0.7481 (tp30) REVERT: B 806 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6982 (tttm) REVERT: B 878 TRP cc_start: 0.7935 (p90) cc_final: 0.6716 (p90) REVERT: B 1042 MET cc_start: 0.7968 (ptm) cc_final: 0.7691 (ptp) REVERT: C 85 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: C 204 SER cc_start: 0.8577 (p) cc_final: 0.8290 (p) REVERT: C 331 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6929 (mm) REVERT: C 751 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: C 1002 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7358 (mp10) outliers start: 79 outliers final: 38 residues processed: 308 average time/residue: 1.1167 time to fit residues: 415.1955 Evaluate side-chains 304 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 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 642 ARG Chi-restraints excluded: chain A residue 672 THR 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 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 542 LEU 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 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 305 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 436 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 321 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 300 optimal weight: 0.0030 chunk 93 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 210 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.175012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149366 restraints weight = 36265.830| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.17 r_work: 0.3658 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27719 Z= 0.141 Angle : 0.665 20.504 37885 Z= 0.330 Chirality : 0.049 0.676 4452 Planarity : 0.004 0.050 4782 Dihedral : 7.057 77.761 5067 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.45 % Allowed : 14.58 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3339 helix: 0.54 (0.20), residues: 741 sheet: -0.09 (0.21), residues: 636 loop : -1.77 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1094 HIS 0.003 0.001 HIS C1080 PHE 0.032 0.001 PHE B 809 TYR 0.012 0.001 TYR A 419 ARG 0.005 0.000 ARG B 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 54) link_NAG-ASN : angle 4.15030 ( 162) link_BETA1-4 : bond 0.00400 ( 15) link_BETA1-4 : angle 1.79426 ( 45) hydrogen bonds : bond 0.03780 ( 1011) hydrogen bonds : angle 5.93561 ( 2805) SS BOND : bond 0.00558 ( 44) SS BOND : angle 2.01791 ( 88) covalent geometry : bond 0.00315 (27606) covalent geometry : angle 0.59877 (37590) *********************** 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 349 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0829 (mmp) cc_final: -0.0623 (mpp) REVERT: A 257 PHE cc_start: 0.6944 (m-80) cc_final: 0.6342 (m-80) REVERT: A 740 GLU cc_start: 0.7182 (pm20) cc_final: 0.6916 (pm20) REVERT: A 765 GLU cc_start: 0.7914 (tp30) cc_final: 0.7608 (tp30) REVERT: A 892 MET cc_start: 0.7132 (mtt) cc_final: 0.6529 (mtt) REVERT: A 1002 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: A 1064 GLU cc_start: 0.7755 (mp0) cc_final: 0.7521 (mp0) REVERT: B 550 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6474 (tm-30) REVERT: B 582 ASP cc_start: 0.7877 (p0) cc_final: 0.7555 (p0) REVERT: B 731 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8431 (p) REVERT: B 765 GLU cc_start: 0.7585 (tp30) cc_final: 0.7353 (tp30) REVERT: B 768 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7979 (ttpt) REVERT: B 878 TRP cc_start: 0.7839 (p90) cc_final: 0.6600 (p90) REVERT: B 1042 MET cc_start: 0.7848 (ptm) cc_final: 0.7491 (ptp) REVERT: C 115 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: C 204 SER cc_start: 0.8566 (p) cc_final: 0.8251 (p) REVERT: C 244 HIS cc_start: 0.6060 (t-90) cc_final: 0.5717 (t70) REVERT: C 331 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6918 (mm) REVERT: C 737 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: C 751 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.6314 (m-80) REVERT: C 768 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7830 (tttt) REVERT: C 772 GLU cc_start: 0.7438 (pt0) cc_final: 0.7119 (pt0) REVERT: C 1002 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7245 (mp10) outliers start: 71 outliers final: 33 residues processed: 324 average time/residue: 1.1085 time to fit residues: 433.6985 Evaluate side-chains 301 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 3.388 ------------------------------------------------------------------------------- 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 331 LEU Chi-restraints excluded: chain A residue 513 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 1002 GLN 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 331 LEU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 550 GLU 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 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 69 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 115 GLN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 263 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 319 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 170 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** 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 = 0.4066 r_free = 0.4066 target = 0.175259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148968 restraints weight = 36321.728| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.13 r_work: 0.3659 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27719 Z= 0.143 Angle : 0.664 20.378 37885 Z= 0.328 Chirality : 0.048 0.658 4452 Planarity : 0.004 0.054 4782 Dihedral : 6.909 77.159 5067 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.66 % Allowed : 14.89 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3339 helix: 0.52 (0.19), residues: 759 sheet: -0.29 (0.21), residues: 660 loop : -1.65 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1094 HIS 0.004 0.001 HIS B1080 PHE 0.033 0.001 PHE B 809 TYR 0.019 0.001 TYR A1059 ARG 0.006 0.000 ARG C1083 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 54) link_NAG-ASN : angle 4.10752 ( 162) link_BETA1-4 : bond 0.00328 ( 15) link_BETA1-4 : angle 1.79061 ( 45) hydrogen bonds : bond 0.03750 ( 1011) hydrogen bonds : angle 5.88221 ( 2805) SS BOND : bond 0.00545 ( 44) SS BOND : angle 1.87972 ( 88) covalent geometry : bond 0.00320 (27606) covalent geometry : angle 0.59947 (37590) *********************** 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 346 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 269 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0911 (mmp) cc_final: -0.0568 (mpp) REVERT: A 257 PHE cc_start: 0.6978 (m-80) cc_final: 0.6370 (m-80) REVERT: A 402 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 740 GLU cc_start: 0.7195 (pm20) cc_final: 0.6947 (pm20) REVERT: A 765 GLU cc_start: 0.7844 (tp30) cc_final: 0.7504 (tp30) REVERT: A 980 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: A 1002 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: A 1064 GLU cc_start: 0.7645 (mp0) cc_final: 0.7416 (mp0) REVERT: B 204 SER cc_start: 0.8643 (p) cc_final: 0.8361 (p) REVERT: B 353 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7898 (ttm110) REVERT: B 402 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7794 (mt-10) REVERT: B 550 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: B 731 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8460 (p) REVERT: B 765 GLU cc_start: 0.7549 (tp30) cc_final: 0.7331 (tp30) REVERT: B 768 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8007 (ttpt) REVERT: B 878 TRP cc_start: 0.7867 (p90) cc_final: 0.6626 (p90) REVERT: B 1042 MET cc_start: 0.7878 (ptm) cc_final: 0.7527 (ptp) REVERT: C 85 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: C 331 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6889 (mm) REVERT: C 737 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: C 751 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: C 768 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8399 (tmmt) REVERT: C 1122 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.6294 (pp) outliers start: 77 outliers final: 41 residues processed: 317 average time/residue: 1.1393 time to fit residues: 435.3183 Evaluate side-chains 312 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 628 THR 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 1100 ASN Chi-restraints excluded: chain A residue 1113 PHE Chi-restraints excluded: chain A residue 1125 VAL 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 550 GLU 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 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 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 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 740 GLU 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 1122 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 300 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 274 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1075 HIS C 754 GLN C 949 GLN C1075 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.150315 restraints weight = 36247.117| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.04 r_work: 0.3666 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27719 Z= 0.146 Angle : 0.663 20.279 37885 Z= 0.329 Chirality : 0.048 0.656 4452 Planarity : 0.004 0.052 4782 Dihedral : 6.823 77.011 5067 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.42 % Allowed : 15.58 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3339 helix: 0.55 (0.19), residues: 759 sheet: -0.14 (0.21), residues: 642 loop : -1.68 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1094 HIS 0.003 0.001 HIS A1040 PHE 0.026 0.001 PHE B 809 TYR 0.017 0.001 TYR A 699 ARG 0.006 0.000 ARG C1083 Details of bonding type rmsd link_NAG-ASN : bond 0.00791 ( 54) link_NAG-ASN : angle 4.07701 ( 162) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.78080 ( 45) hydrogen bonds : bond 0.03722 ( 1011) hydrogen bonds : angle 5.85902 ( 2805) SS BOND : bond 0.00503 ( 44) SS BOND : angle 1.80223 ( 88) covalent geometry : bond 0.00327 (27606) covalent geometry : angle 0.60033 (37590) *********************** 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 337 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 267 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0802 (mmp) cc_final: -0.0443 (mpp) REVERT: A 257 PHE cc_start: 0.6996 (m-80) cc_final: 0.6381 (m-80) REVERT: A 740 GLU cc_start: 0.7195 (pm20) cc_final: 0.6966 (pm20) REVERT: A 765 GLU cc_start: 0.7862 (tp30) cc_final: 0.7498 (tp30) REVERT: A 1002 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: A 1064 GLU cc_start: 0.7677 (mp0) cc_final: 0.7462 (mp0) REVERT: B 204 SER cc_start: 0.8636 (p) cc_final: 0.8353 (p) REVERT: B 353 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7900 (ttm110) REVERT: B 550 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: B 751 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: B 765 GLU cc_start: 0.7537 (tp30) cc_final: 0.7317 (tp30) REVERT: B 768 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: B 878 TRP cc_start: 0.7854 (p90) cc_final: 0.6597 (p90) REVERT: B 1042 MET cc_start: 0.7875 (ptm) cc_final: 0.7502 (ptp) REVERT: C 115 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: C 204 SER cc_start: 0.8545 (p) cc_final: 0.8225 (p) REVERT: C 244 HIS cc_start: 0.6060 (t-90) cc_final: 0.5701 (t70) REVERT: C 331 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6888 (mm) REVERT: C 737 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: C 751 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: C 768 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8389 (tmmt) REVERT: C 892 MET cc_start: 0.6391 (ptm) cc_final: 0.6177 (ptm) REVERT: C 1002 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: C 1122 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.6153 (pp) outliers start: 70 outliers final: 37 residues processed: 309 average time/residue: 1.1064 time to fit residues: 410.7712 Evaluate side-chains 301 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 2.770 ------------------------------------------------------------------------------- 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 331 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU 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 1002 GLN 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 331 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 550 GLU 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 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 513 LEU 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 1122 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 226 optimal weight: 0.7980 chunk 323 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** ** A1075 HIS ** 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 = 0.4048 r_free = 0.4048 target = 0.173543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148216 restraints weight = 36434.323| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.01 r_work: 0.3629 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27719 Z= 0.201 Angle : 0.805 55.796 37885 Z= 0.418 Chirality : 0.050 0.645 4452 Planarity : 0.005 0.059 4782 Dihedral : 7.228 76.556 5067 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.21 % Allowed : 15.96 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3339 helix: 0.44 (0.19), residues: 759 sheet: -0.29 (0.20), residues: 690 loop : -1.70 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1094 HIS 0.005 0.001 HIS A 34 PHE 0.027 0.002 PHE B 809 TYR 0.017 0.002 TYR C 419 ARG 0.006 0.001 ARG C1083 Details of bonding type rmsd link_NAG-ASN : bond 0.00919 ( 54) link_NAG-ASN : angle 4.21595 ( 162) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 1.76922 ( 45) hydrogen bonds : bond 0.03966 ( 1011) hydrogen bonds : angle 5.95535 ( 2805) SS BOND : bond 0.00611 ( 44) SS BOND : angle 1.89107 ( 88) covalent geometry : bond 0.00463 (27606) covalent geometry : angle 0.75081 (37590) *********************** 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 319 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0771 (mmp) cc_final: -0.0486 (mpp) REVERT: A 257 PHE cc_start: 0.7008 (m-80) cc_final: 0.6373 (m-80) REVERT: A 765 GLU cc_start: 0.7927 (tp30) cc_final: 0.7571 (tp30) REVERT: A 1002 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: A 1064 GLU cc_start: 0.7761 (mp0) cc_final: 0.7557 (mp0) REVERT: B 204 SER cc_start: 0.8671 (p) cc_final: 0.8403 (p) REVERT: B 353 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7906 (ttm110) REVERT: B 550 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: B 582 ASP cc_start: 0.8021 (p0) cc_final: 0.7754 (p0) REVERT: B 751 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: B 765 GLU cc_start: 0.7615 (tp30) cc_final: 0.7389 (tp30) REVERT: B 768 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: B 878 TRP cc_start: 0.7876 (p90) cc_final: 0.6637 (p90) REVERT: B 1042 MET cc_start: 0.7997 (ptm) cc_final: 0.7676 (ptp) REVERT: C 85 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: C 115 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: C 204 SER cc_start: 0.8571 (p) cc_final: 0.8257 (p) REVERT: C 244 HIS cc_start: 0.6134 (t-90) cc_final: 0.5926 (t-90) REVERT: C 331 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6940 (mm) REVERT: C 737 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: C 751 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: C 768 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8421 (tmmt) REVERT: C 1002 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: C 1122 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6292 (pp) outliers start: 64 outliers final: 39 residues processed: 295 average time/residue: 1.1565 time to fit residues: 413.3376 Evaluate side-chains 303 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 479 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU 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 1002 GLN 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 353 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 550 GLU 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 513 LEU 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 Chi-restraints excluded: chain C residue 1122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 79 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 323 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** 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 = 0.4058 r_free = 0.4058 target = 0.174503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149671 restraints weight = 36246.093| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.05 r_work: 0.3646 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27719 Z= 0.153 Angle : 0.781 53.271 37885 Z= 0.408 Chirality : 0.049 0.639 4452 Planarity : 0.004 0.060 4782 Dihedral : 7.132 77.052 5067 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.87 % Allowed : 16.37 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3339 helix: 0.49 (0.19), residues: 759 sheet: -0.29 (0.20), residues: 690 loop : -1.68 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1094 HIS 0.004 0.001 HIS A1075 PHE 0.025 0.001 PHE B 809 TYR 0.014 0.001 TYR A 699 ARG 0.007 0.000 ARG C1083 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 54) link_NAG-ASN : angle 4.15825 ( 162) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 1.78521 ( 45) hydrogen bonds : bond 0.03845 ( 1011) hydrogen bonds : angle 5.92502 ( 2805) SS BOND : bond 0.00505 ( 44) SS BOND : angle 1.83604 ( 88) covalent geometry : bond 0.00346 (27606) covalent geometry : angle 0.72685 (37590) ********************** 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 311 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 257 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.0730 (mmp) cc_final: -0.0532 (mpp) REVERT: A 257 PHE cc_start: 0.6981 (m-80) cc_final: 0.6361 (m-80) REVERT: A 765 GLU cc_start: 0.7869 (tp30) cc_final: 0.7527 (tp30) REVERT: A 1002 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: A 1064 GLU cc_start: 0.7724 (mp0) cc_final: 0.7523 (mp0) REVERT: B 204 SER cc_start: 0.8663 (p) cc_final: 0.8395 (p) REVERT: B 353 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7903 (ttm110) REVERT: B 550 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: B 582 ASP cc_start: 0.7956 (p0) cc_final: 0.7681 (p0) REVERT: B 751 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: B 765 GLU cc_start: 0.7572 (tp30) cc_final: 0.7348 (tp30) REVERT: B 768 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7993 (ttpt) REVERT: B 878 TRP cc_start: 0.7874 (p90) cc_final: 0.6634 (p90) REVERT: B 1042 MET cc_start: 0.7946 (ptm) cc_final: 0.7632 (ptp) REVERT: C 115 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7457 (mt0) REVERT: C 204 SER cc_start: 0.8521 (p) cc_final: 0.8220 (p) REVERT: C 244 HIS cc_start: 0.6177 (t-90) cc_final: 0.5945 (t-90) REVERT: C 331 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6919 (mm) REVERT: C 737 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: C 751 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: C 768 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8422 (tmmt) REVERT: C 1002 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: C 1122 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6262 (pp) outliers start: 54 outliers final: 39 residues processed: 290 average time/residue: 1.1544 time to fit residues: 401.4102 Evaluate side-chains 304 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 253 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 479 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 550 GLU 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 1002 GLN 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 353 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 550 GLU 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 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 513 LEU 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 Chi-restraints excluded: chain C residue 1122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 146 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 290 optimal weight: 10.0000 chunk 180 optimal weight: 0.0070 chunk 235 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 609 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 = 0.4049 r_free = 0.4049 target = 0.173671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147566 restraints weight = 36309.269| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.12 r_work: 0.3637 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27719 Z= 0.188 Angle : 0.786 49.883 37885 Z= 0.411 Chirality : 0.049 0.629 4452 Planarity : 0.004 0.060 4782 Dihedral : 7.238 77.308 5067 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.93 % Allowed : 16.58 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3339 helix: 0.45 (0.19), residues: 759 sheet: -0.29 (0.20), residues: 690 loop : -1.69 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1094 HIS 0.004 0.001 HIS A1040 PHE 0.027 0.002 PHE B 809 TYR 0.016 0.002 TYR C 419 ARG 0.006 0.000 ARG C1083 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 54) link_NAG-ASN : angle 4.11818 ( 162) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.77752 ( 45) hydrogen bonds : bond 0.03929 ( 1011) hydrogen bonds : angle 5.94246 ( 2805) SS BOND : bond 0.00603 ( 44) SS BOND : angle 1.83761 ( 88) covalent geometry : bond 0.00432 (27606) covalent geometry : angle 0.73374 (37590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19350.36 seconds wall clock time: 334 minutes 39.28 seconds (20079.28 seconds total)