Starting phenix.real_space_refine on Mon Jun 23 07:45:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qus_14153/06_2025/7qus_14153.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qus_14153/06_2025/7qus_14153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qus_14153/06_2025/7qus_14153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qus_14153/06_2025/7qus_14153.map" model { file = "/net/cci-nas-00/data/ceres_data/7qus_14153/06_2025/7qus_14153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qus_14153/06_2025/7qus_14153.cif" } resolution = 2.39 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= 0.005 sd= 0.161 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 120 5.16 5 C 16998 2.51 5 N 4377 2.21 5 O 5247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 1.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26742 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Chain: "B" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Chain: "C" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 16.35, per 1000 atoms: 0.61 Number of scatterers: 26742 At special positions: 0 Unit cell: (151.7, 154.16, 165.64, 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 120 16.00 O 5247 8.00 N 4377 7.00 C 16998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 2 " " NAG O 1 " - " FUC O 2 " 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 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 149 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 149 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 165 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 165 " Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 3.1 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 51 sheets defined 25.0% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.759A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.451A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.601A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 837 through 842 removed outlier: 6.399A pdb=" N GLY A 842 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.884A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.563A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.125A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.759A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.452A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.601A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 837 through 842 removed outlier: 6.401A pdb=" N GLY B 842 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.884A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.563A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.125A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.759A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.452A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.601A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 837 through 842 removed outlier: 6.400A pdb=" N GLY C 842 " --> pdb=" O ASP C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 848 Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.884A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.564A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.124A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.029A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.029A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.070A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.251A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 167 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.680A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.027A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.191A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.519A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.423A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.664A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.971A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.245A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.557A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1121 through 1125 removed outlier: 4.386A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.028A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.028A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.070A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.251A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 167 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.680A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.027A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.190A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.519A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.423A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.664A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.971A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.246A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1125 removed outlier: 4.386A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.029A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.029A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.070A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.251A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 167 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.680A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.335A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.027A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.191A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.518A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.423A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.664A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.971A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.245A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1121 through 1125 removed outlier: 4.387A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1171 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.62 Time building geometry restraints manager: 7.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8502 1.35 - 1.47: 7013 1.47 - 1.59: 11668 1.59 - 1.72: 0 1.72 - 1.84: 150 Bond restraints: 27333 Sorted by residual: bond pdb=" C13 EIC C1301 " pdb=" C14 EIC C1301 " ideal model delta sigma weight residual 1.496 1.553 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C13 EIC A1313 " pdb=" C14 EIC A1313 " ideal model delta sigma weight residual 1.496 1.553 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" C13 EIC B1313 " pdb=" C14 EIC B1313 " ideal model delta sigma weight residual 1.496 1.553 -0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" C1 FUC O 2 " pdb=" O5 FUC O 2 " ideal model delta sigma weight residual 1.400 1.455 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 FUC K 2 " pdb=" O5 FUC K 2 " ideal model delta sigma weight residual 1.400 1.455 -0.055 2.00e-02 2.50e+03 7.52e+00 ... (remaining 27328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 37131 5.00 - 10.00: 33 10.00 - 15.00: 0 15.00 - 20.01: 3 20.01 - 25.01: 3 Bond angle restraints: 37170 Sorted by residual: angle pdb=" C11 EIC C1301 " pdb=" C10 EIC C1301 " pdb=" C9 EIC C1301 " ideal model delta sigma weight residual 127.32 152.33 -25.01 3.00e+00 1.11e-01 6.95e+01 angle pdb=" C11 EIC B1313 " pdb=" C10 EIC B1313 " pdb=" C9 EIC B1313 " ideal model delta sigma weight residual 127.32 152.32 -25.00 3.00e+00 1.11e-01 6.94e+01 angle pdb=" C11 EIC A1313 " pdb=" C10 EIC A1313 " pdb=" C9 EIC A1313 " ideal model delta sigma weight residual 127.32 152.30 -24.98 3.00e+00 1.11e-01 6.93e+01 angle pdb=" C10 EIC A1313 " pdb=" C9 EIC A1313 " pdb=" C8 EIC A1313 " ideal model delta sigma weight residual 127.75 111.86 15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C10 EIC B1313 " pdb=" C9 EIC B1313 " pdb=" C8 EIC B1313 " ideal model delta sigma weight residual 127.75 111.87 15.88 3.00e+00 1.11e-01 2.80e+01 ... (remaining 37165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15023 17.95 - 35.89: 1540 35.89 - 53.84: 401 53.84 - 71.78: 106 71.78 - 89.73: 30 Dihedral angle restraints: 17100 sinusoidal: 7497 harmonic: 9603 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -49.16 -36.84 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -49.20 -36.80 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -49.22 -36.78 1 1.00e+01 1.00e-02 1.91e+01 ... (remaining 17097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3519 0.050 - 0.100: 661 0.100 - 0.149: 203 0.149 - 0.199: 3 0.199 - 0.249: 3 Chirality restraints: 4389 Sorted by residual: chirality pdb=" C4 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" C5 NAG K 1 " pdb=" O4 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C4 NAG O 1 " pdb=" C3 NAG O 1 " pdb=" C5 NAG O 1 " pdb=" O4 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4386 not shown) Planarity restraints: 4776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 478 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO C 479 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 479 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 478 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO B 479 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.026 5.00e-02 4.00e+02 ... (remaining 4773 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2277 2.75 - 3.29: 25138 3.29 - 3.82: 46138 3.82 - 4.36: 56567 4.36 - 4.90: 95462 Nonbonded interactions: 225582 Sorted by model distance: nonbonded pdb=" OG1 THR A 547 " pdb=" OG SER B 982 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O ARG C 646 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O ARG A 646 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR B 645 " pdb=" O ARG B 646 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN A 360 " pdb=" OG1 THR A 523 " model vdw 2.266 3.040 ... (remaining 225577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1139 or resid 1302 through 1312)) selection = (chain 'B' and (resid 14 through 1139 or resid 1302 through 1312)) selection = (chain 'C' and (resid 14 through 1139 or resid 1302 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } 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: 3.570 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: 1.110 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 64.970 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.180 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27441 Z= 0.175 Angle : 0.624 25.007 37452 Z= 0.284 Chirality : 0.043 0.249 4389 Planarity : 0.004 0.046 4728 Dihedral : 15.760 89.727 10812 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Rotamer: Outliers : 1.46 % Allowed : 17.50 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3285 helix: 1.80 (0.20), residues: 702 sheet: 0.54 (0.19), residues: 723 loop : -0.92 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A1101 PHE 0.014 0.001 PHE A 823 TYR 0.014 0.001 TYR B1067 ARG 0.006 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 48) link_NAG-ASN : angle 1.76619 ( 144) link_BETA1-4 : bond 0.00408 ( 12) link_BETA1-4 : angle 3.02035 ( 36) hydrogen bonds : bond 0.11773 ( 1102) hydrogen bonds : angle 6.41468 ( 3108) link_BETA1-6 : bond 0.00486 ( 3) link_BETA1-6 : angle 1.35917 ( 9) SS BOND : bond 0.00169 ( 42) SS BOND : angle 0.86235 ( 84) link_BETA1-3 : bond 0.02160 ( 3) link_BETA1-3 : angle 4.11021 ( 9) covalent geometry : bond 0.00352 (27333) covalent geometry : angle 0.60409 (37170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8089 (t0) cc_final: 0.7604 (t0) REVERT: A 613 GLN cc_start: 0.8391 (mt0) cc_final: 0.7901 (mt0) REVERT: A 827 THR cc_start: 0.8576 (p) cc_final: 0.8321 (t) REVERT: B 529 LYS cc_start: 0.7948 (tttm) cc_final: 0.7666 (tppt) REVERT: C 29 THR cc_start: 0.8454 (t) cc_final: 0.8252 (m) REVERT: C 370 ASN cc_start: 0.8259 (t0) cc_final: 0.7823 (m-40) REVERT: C 571 ASP cc_start: 0.8027 (m-30) cc_final: 0.7809 (t70) REVERT: C 613 GLN cc_start: 0.8168 (mt0) cc_final: 0.7684 (mt0) REVERT: C 675 GLN cc_start: 0.7301 (mm110) cc_final: 0.7063 (mm110) REVERT: C 869 MET cc_start: 0.9189 (mtt) cc_final: 0.8912 (mtt) REVERT: C 986 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7686 (ttpt) REVERT: C 990 GLU cc_start: 0.7360 (tt0) cc_final: 0.6969 (tt0) outliers start: 42 outliers final: 19 residues processed: 339 average time/residue: 1.1461 time to fit residues: 464.4413 Evaluate side-chains 250 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 85 optimal weight: 0.3980 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 258 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 440 ASN A 556 ASN A 613 GLN A 658 ASN A 690 GLN A 872 GLN A 926 GLN A1101 HIS B 99 ASN B 334 ASN B 613 GLN B 658 ASN B 690 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1101 HIS C 52 GLN C 99 ASN C 474 GLN C 556 ASN C 613 GLN C 658 ASN C 690 GLN C 926 GLN C1058 HIS C1101 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106601 restraints weight = 27438.542| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.14 r_work: 0.3210 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27441 Z= 0.165 Angle : 0.611 9.721 37452 Z= 0.313 Chirality : 0.046 0.362 4389 Planarity : 0.004 0.050 4728 Dihedral : 7.287 59.935 4990 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.10 % Rotamer: Outliers : 3.63 % Allowed : 14.92 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3285 helix: 1.88 (0.20), residues: 669 sheet: 0.40 (0.19), residues: 738 loop : -1.05 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS C 245 PHE 0.024 0.002 PHE C 817 TYR 0.025 0.002 TYR A1067 ARG 0.010 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 48) link_NAG-ASN : angle 1.82163 ( 144) link_BETA1-4 : bond 0.00306 ( 12) link_BETA1-4 : angle 3.13544 ( 36) hydrogen bonds : bond 0.04881 ( 1102) hydrogen bonds : angle 5.50651 ( 3108) link_BETA1-6 : bond 0.00169 ( 3) link_BETA1-6 : angle 1.54089 ( 9) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.05582 ( 84) link_BETA1-3 : bond 0.01672 ( 3) link_BETA1-3 : angle 4.48458 ( 9) covalent geometry : bond 0.00378 (27333) covalent geometry : angle 0.58774 (37170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 266 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8645 (tt0) REVERT: A 137 ASN cc_start: 0.8090 (t0) cc_final: 0.7563 (t0) REVERT: A 143 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7735 (t) REVERT: A 177 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6172 (tmt) REVERT: A 613 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: A 795 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5751 (mmmt) REVERT: A 827 THR cc_start: 0.8491 (p) cc_final: 0.8251 (t) REVERT: A 1045 LYS cc_start: 0.8736 (tmmt) cc_final: 0.8454 (tmtt) REVERT: A 1081 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8608 (mm) REVERT: A 1091 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6863 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: B 52 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: B 177 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.4820 (tmt) REVERT: B 321 GLN cc_start: 0.8457 (mm110) cc_final: 0.8203 (mp-120) REVERT: B 346 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6713 (ttp80) REVERT: B 357 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7196 (ttm170) REVERT: B 571 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8137 (t0) REVERT: B 613 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7934 (mt0) REVERT: B 964 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8242 (mtpt) REVERT: C 143 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8040 (t) REVERT: C 177 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6805 (tmt) REVERT: C 370 ASN cc_start: 0.8611 (t0) cc_final: 0.8091 (m110) REVERT: C 571 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8023 (t70) REVERT: C 613 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: C 675 GLN cc_start: 0.7437 (mm110) cc_final: 0.7220 (mm110) outliers start: 104 outliers final: 35 residues processed: 341 average time/residue: 1.3265 time to fit residues: 531.4979 Evaluate side-chains 288 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 50 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 279 optimal weight: 7.9990 chunk 312 optimal weight: 4.9990 chunk 323 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 0.0050 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 239 GLN A 658 ASN A 872 GLN B 99 ASN B 164 ASN B 334 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 804 GLN C1101 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104820 restraints weight = 27370.146| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.13 r_work: 0.3155 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27441 Z= 0.172 Angle : 0.599 10.166 37452 Z= 0.306 Chirality : 0.046 0.349 4389 Planarity : 0.004 0.050 4728 Dihedral : 6.882 59.295 4977 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.20 % Favored : 96.53 % Rotamer: Outliers : 3.42 % Allowed : 14.89 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3285 helix: 1.74 (0.20), residues: 687 sheet: 0.33 (0.18), residues: 804 loop : -1.01 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 886 HIS 0.003 0.001 HIS B 245 PHE 0.014 0.002 PHE B1121 TYR 0.022 0.002 TYR B 612 ARG 0.009 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 48) link_NAG-ASN : angle 1.99297 ( 144) link_BETA1-4 : bond 0.00344 ( 12) link_BETA1-4 : angle 3.43359 ( 36) hydrogen bonds : bond 0.04993 ( 1102) hydrogen bonds : angle 5.51017 ( 3108) link_BETA1-6 : bond 0.00412 ( 3) link_BETA1-6 : angle 1.21026 ( 9) SS BOND : bond 0.00513 ( 42) SS BOND : angle 1.66781 ( 84) link_BETA1-3 : bond 0.01718 ( 3) link_BETA1-3 : angle 3.84842 ( 9) covalent geometry : bond 0.00401 (27333) covalent geometry : angle 0.56963 (37170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 250 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: A 137 ASN cc_start: 0.8157 (t0) cc_final: 0.7607 (t0) REVERT: A 143 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7692 (t) REVERT: A 177 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.5956 (tmt) REVERT: A 554 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 613 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: A 827 THR cc_start: 0.8530 (p) cc_final: 0.8302 (t) REVERT: A 933 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8192 (mtpt) REVERT: A 964 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8291 (mtpt) REVERT: A 983 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7484 (mtp180) REVERT: A 990 GLU cc_start: 0.7996 (tt0) cc_final: 0.7708 (tt0) REVERT: A 1081 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8669 (mm) REVERT: A 1091 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6816 (ptp-170) REVERT: B 52 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8639 (tp40) REVERT: B 143 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7774 (t) REVERT: B 244 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5867 (pp) REVERT: B 357 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7205 (ttm170) REVERT: B 571 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8179 (t0) REVERT: B 613 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: B 804 GLN cc_start: 0.8586 (mt0) cc_final: 0.8342 (mt0) REVERT: B 964 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8305 (mtpt) REVERT: B 1045 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (tmtt) REVERT: C 177 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6841 (tmt) REVERT: C 370 ASN cc_start: 0.8628 (t0) cc_final: 0.8093 (m110) REVERT: C 571 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (t70) REVERT: C 613 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7951 (mt0) REVERT: C 795 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5599 (tttm) outliers start: 98 outliers final: 36 residues processed: 316 average time/residue: 1.3580 time to fit residues: 511.6205 Evaluate side-chains 290 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 36 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 164 ASN A 314 GLN A 613 GLN A 913 GLN A1058 HIS B 99 ASN B 207 HIS B 314 GLN B 613 GLN B 690 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 164 ASN C 314 GLN C 613 GLN C 804 GLN C1101 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098957 restraints weight = 27182.604| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.98 r_work: 0.2957 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 27441 Z= 0.299 Angle : 0.733 14.623 37452 Z= 0.372 Chirality : 0.052 0.421 4389 Planarity : 0.005 0.056 4728 Dihedral : 7.151 59.765 4975 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.96 % Favored : 95.77 % Rotamer: Outliers : 3.87 % Allowed : 14.40 % Favored : 81.73 % 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: -0.27 (0.14), residues: 3285 helix: 1.46 (0.20), residues: 684 sheet: 0.34 (0.18), residues: 792 loop : -1.10 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 886 HIS 0.007 0.001 HIS A 245 PHE 0.019 0.002 PHE C 59 TYR 0.026 0.002 TYR A1067 ARG 0.009 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 48) link_NAG-ASN : angle 2.41503 ( 144) link_BETA1-4 : bond 0.00411 ( 12) link_BETA1-4 : angle 4.07552 ( 36) hydrogen bonds : bond 0.06084 ( 1102) hydrogen bonds : angle 5.80674 ( 3108) link_BETA1-6 : bond 0.00573 ( 3) link_BETA1-6 : angle 1.16363 ( 9) SS BOND : bond 0.00884 ( 42) SS BOND : angle 2.48073 ( 84) link_BETA1-3 : bond 0.01352 ( 3) link_BETA1-3 : angle 3.88778 ( 9) covalent geometry : bond 0.00724 (27333) covalent geometry : angle 0.69608 (37170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 241 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: A 143 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7891 (t) REVERT: A 177 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6157 (tmt) REVERT: A 554 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: A 613 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: A 827 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8328 (t) REVERT: A 907 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8578 (m-40) REVERT: A 933 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8179 (mtpt) REVERT: A 964 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: A 983 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7401 (mtp180) REVERT: A 1113 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8232 (mm-40) REVERT: B 52 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: B 143 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.7931 (t) REVERT: B 177 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.4555 (tmt) REVERT: B 197 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 357 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.7587 (tpm170) REVERT: B 571 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8219 (t70) REVERT: B 613 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: B 795 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5742 (mtpt) REVERT: B 804 GLN cc_start: 0.8647 (mt0) cc_final: 0.8445 (mt0) REVERT: B 964 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8381 (mtpt) REVERT: B 1091 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7636 (ptp-170) REVERT: C 143 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8094 (t) REVERT: C 177 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6784 (tmt) REVERT: C 571 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8142 (t70) REVERT: C 613 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: C 1113 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8268 (mm110) outliers start: 111 outliers final: 43 residues processed: 313 average time/residue: 1.3014 time to fit residues: 478.5753 Evaluate side-chains 293 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 308 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 556 ASN A1135 ASN B 99 ASN B 207 HIS ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 804 GLN C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101512 restraints weight = 27022.727| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.94 r_work: 0.2992 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27441 Z= 0.156 Angle : 0.610 15.262 37452 Z= 0.310 Chirality : 0.046 0.383 4389 Planarity : 0.004 0.052 4728 Dihedral : 6.651 59.984 4975 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.32 % Favored : 96.41 % Rotamer: Outliers : 3.38 % Allowed : 15.27 % Favored : 81.35 % 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: -0.25 (0.14), residues: 3285 helix: 1.67 (0.20), residues: 687 sheet: 0.28 (0.18), residues: 834 loop : -1.17 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.003 0.001 HIS C 245 PHE 0.016 0.001 PHE A 140 TYR 0.020 0.002 TYR A1067 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 48) link_NAG-ASN : angle 2.16997 ( 144) link_BETA1-4 : bond 0.00279 ( 12) link_BETA1-4 : angle 3.63232 ( 36) hydrogen bonds : bond 0.04824 ( 1102) hydrogen bonds : angle 5.52410 ( 3108) link_BETA1-6 : bond 0.00408 ( 3) link_BETA1-6 : angle 1.25885 ( 9) SS BOND : bond 0.00663 ( 42) SS BOND : angle 2.01801 ( 84) link_BETA1-3 : bond 0.01556 ( 3) link_BETA1-3 : angle 3.75756 ( 9) covalent geometry : bond 0.00359 (27333) covalent geometry : angle 0.57500 (37170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 243 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: A 143 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7817 (t) REVERT: A 370 ASN cc_start: 0.8606 (t0) cc_final: 0.8135 (m-40) REVERT: A 554 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 613 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: A 827 THR cc_start: 0.8490 (p) cc_final: 0.8227 (t) REVERT: A 983 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7438 (mtp180) REVERT: B 52 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: B 143 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.7889 (t) REVERT: B 244 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6158 (pp) REVERT: B 357 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7543 (tpm170) REVERT: B 370 ASN cc_start: 0.8509 (t0) cc_final: 0.8089 (m-40) REVERT: B 571 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8208 (t70) REVERT: B 613 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: B 804 GLN cc_start: 0.8638 (mt0) cc_final: 0.8410 (mt0) REVERT: B 827 THR cc_start: 0.8542 (p) cc_final: 0.8222 (t) REVERT: B 964 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8331 (mtpt) REVERT: C 143 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8005 (t) REVERT: C 177 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6808 (tmt) REVERT: C 571 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8114 (t70) REVERT: C 613 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: C 1091 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.6437 (ptp-170) outliers start: 97 outliers final: 39 residues processed: 311 average time/residue: 1.2570 time to fit residues: 461.1411 Evaluate side-chains 286 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1091 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 263 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 556 ASN A 613 GLN B 99 ASN B 207 HIS B 334 ASN B 613 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 613 GLN C 804 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100710 restraints weight = 27030.647| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.04 r_work: 0.2997 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27441 Z= 0.185 Angle : 0.652 18.849 37452 Z= 0.330 Chirality : 0.047 0.369 4389 Planarity : 0.004 0.053 4728 Dihedral : 6.586 59.789 4974 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.56 % Favored : 96.16 % Rotamer: Outliers : 3.14 % Allowed : 15.20 % Favored : 81.66 % Cbeta Deviations : 0.03 % 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: -0.22 (0.14), residues: 3285 helix: 1.68 (0.20), residues: 687 sheet: 0.28 (0.18), residues: 816 loop : -1.13 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 886 HIS 0.004 0.001 HIS C 245 PHE 0.014 0.002 PHE B1121 TYR 0.022 0.002 TYR A1067 ARG 0.010 0.001 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 48) link_NAG-ASN : angle 2.20921 ( 144) link_BETA1-4 : bond 0.00321 ( 12) link_BETA1-4 : angle 3.64455 ( 36) hydrogen bonds : bond 0.05064 ( 1102) hydrogen bonds : angle 5.53915 ( 3108) link_BETA1-6 : bond 0.00537 ( 3) link_BETA1-6 : angle 1.17983 ( 9) SS BOND : bond 0.00640 ( 42) SS BOND : angle 2.57621 ( 84) link_BETA1-3 : bond 0.01536 ( 3) link_BETA1-3 : angle 3.61668 ( 9) covalent geometry : bond 0.00433 (27333) covalent geometry : angle 0.61480 (37170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 235 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: A 143 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7836 (t) REVERT: A 242 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7938 (mt) REVERT: A 370 ASN cc_start: 0.8611 (t0) cc_final: 0.8152 (m-40) REVERT: A 554 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 613 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: A 827 THR cc_start: 0.8478 (p) cc_final: 0.8208 (t) REVERT: A 933 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (mtpt) REVERT: A 964 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8312 (mtpt) REVERT: A 983 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7404 (mtp180) REVERT: B 52 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: B 143 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.7911 (t) REVERT: B 153 MET cc_start: 0.7011 (ptt) cc_final: 0.6797 (mtt) REVERT: B 244 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6178 (pp) REVERT: B 357 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7531 (tpm170) REVERT: B 370 ASN cc_start: 0.8511 (t0) cc_final: 0.8097 (m-40) REVERT: B 571 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8236 (t70) REVERT: B 613 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: B 804 GLN cc_start: 0.8590 (mt0) cc_final: 0.8373 (mt0) REVERT: B 964 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8322 (mtpt) REVERT: C 177 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6895 (tmt) REVERT: C 571 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8151 (t70) REVERT: C 613 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: C 1091 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.6510 (ptp-170) outliers start: 90 outliers final: 48 residues processed: 297 average time/residue: 1.2787 time to fit residues: 448.9447 Evaluate side-chains 294 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 47 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 268 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 556 ASN A 954 GLN B 99 ASN B 207 HIS B 334 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 804 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.100208 restraints weight = 26989.318| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.98 r_work: 0.2989 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27441 Z= 0.197 Angle : 0.647 17.018 37452 Z= 0.329 Chirality : 0.047 0.387 4389 Planarity : 0.004 0.052 4728 Dihedral : 6.546 59.746 4974 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.59 % Favored : 96.13 % Rotamer: Outliers : 3.24 % Allowed : 15.27 % Favored : 81.49 % 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: -0.26 (0.14), residues: 3285 helix: 1.66 (0.20), residues: 687 sheet: 0.24 (0.18), residues: 846 loop : -1.16 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 886 HIS 0.004 0.001 HIS C 245 PHE 0.014 0.002 PHE B1121 TYR 0.023 0.002 TYR A1067 ARG 0.009 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 48) link_NAG-ASN : angle 2.21434 ( 144) link_BETA1-4 : bond 0.00283 ( 12) link_BETA1-4 : angle 3.78306 ( 36) hydrogen bonds : bond 0.05153 ( 1102) hydrogen bonds : angle 5.56804 ( 3108) link_BETA1-6 : bond 0.00431 ( 3) link_BETA1-6 : angle 1.24043 ( 9) SS BOND : bond 0.00592 ( 42) SS BOND : angle 2.20298 ( 84) link_BETA1-3 : bond 0.01521 ( 3) link_BETA1-3 : angle 3.67690 ( 9) covalent geometry : bond 0.00465 (27333) covalent geometry : angle 0.61137 (37170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 241 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: A 143 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 242 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7921 (mt) REVERT: A 370 ASN cc_start: 0.8616 (t0) cc_final: 0.8158 (m-40) REVERT: A 554 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 613 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: A 827 THR cc_start: 0.8477 (p) cc_final: 0.8196 (t) REVERT: A 933 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8148 (mtpt) REVERT: A 964 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8312 (mtpt) REVERT: A 983 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7417 (mtp180) REVERT: B 52 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: B 143 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.7906 (t) REVERT: B 357 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7546 (tpm170) REVERT: B 370 ASN cc_start: 0.8509 (t0) cc_final: 0.8092 (m-40) REVERT: B 571 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8242 (t70) REVERT: B 613 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: B 795 LYS cc_start: 0.6042 (OUTLIER) cc_final: 0.5721 (mtpt) REVERT: B 804 GLN cc_start: 0.8588 (mt0) cc_final: 0.8352 (mt0) REVERT: B 964 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8335 (mtpt) REVERT: B 1086 LYS cc_start: 0.8583 (pttp) cc_final: 0.8304 (pttm) REVERT: C 177 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6883 (tmt) REVERT: C 554 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: C 571 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8141 (t70) REVERT: C 613 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: C 1091 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6594 (ptp-170) REVERT: C 1113 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8245 (mm110) outliers start: 93 outliers final: 49 residues processed: 305 average time/residue: 1.4565 time to fit residues: 524.9332 Evaluate side-chains 301 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 231 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 272 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 237 optimal weight: 0.8980 chunk 218 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 556 ASN A 613 GLN A 954 GLN B 99 ASN B 207 HIS B 334 ASN B 474 GLN B 613 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS C 99 ASN C 556 ASN C 613 GLN C 804 GLN C1010 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103860 restraints weight = 26965.154| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.90 r_work: 0.3043 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27441 Z= 0.118 Angle : 0.569 12.846 37452 Z= 0.289 Chirality : 0.044 0.344 4389 Planarity : 0.004 0.050 4728 Dihedral : 6.037 59.389 4974 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.26 % Favored : 96.47 % Rotamer: Outliers : 2.55 % Allowed : 15.79 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3285 helix: 1.91 (0.20), residues: 687 sheet: 0.29 (0.18), residues: 834 loop : -1.16 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS A 66 PHE 0.020 0.001 PHE A 140 TYR 0.018 0.001 TYR A1067 ARG 0.008 0.000 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 48) link_NAG-ASN : angle 2.00428 ( 144) link_BETA1-4 : bond 0.00288 ( 12) link_BETA1-4 : angle 3.41781 ( 36) hydrogen bonds : bond 0.04236 ( 1102) hydrogen bonds : angle 5.31057 ( 3108) link_BETA1-6 : bond 0.00429 ( 3) link_BETA1-6 : angle 1.25095 ( 9) SS BOND : bond 0.00486 ( 42) SS BOND : angle 1.79658 ( 84) link_BETA1-3 : bond 0.01772 ( 3) link_BETA1-3 : angle 3.60002 ( 9) covalent geometry : bond 0.00264 (27333) covalent geometry : angle 0.53723 (37170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 249 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7734 (mtp85) REVERT: A 281 GLU cc_start: 0.8360 (pm20) cc_final: 0.8083 (pm20) REVERT: A 370 ASN cc_start: 0.8555 (t0) cc_final: 0.8121 (m-40) REVERT: A 554 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 613 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: A 827 THR cc_start: 0.8373 (p) cc_final: 0.8094 (t) REVERT: A 964 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8241 (mtpt) REVERT: A 1081 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8639 (mm) REVERT: B 52 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8602 (tp40) REVERT: B 143 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7817 (t) REVERT: B 357 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7218 (ttm170) REVERT: B 370 ASN cc_start: 0.8503 (t0) cc_final: 0.8107 (m-40) REVERT: B 571 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8109 (t70) REVERT: B 613 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: B 804 GLN cc_start: 0.8542 (mt0) cc_final: 0.8310 (mt0) REVERT: B 827 THR cc_start: 0.8468 (p) cc_final: 0.8153 (t) REVERT: B 964 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8291 (mtpt) REVERT: B 1010 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: B 1045 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8574 (tmtt) REVERT: C 554 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: C 571 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8073 (t70) REVERT: C 613 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: C 1010 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: C 1091 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6416 (ptp-170) outliers start: 73 outliers final: 33 residues processed: 294 average time/residue: 1.8145 time to fit residues: 629.0141 Evaluate side-chains 288 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 6.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1091 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 246 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 245 HIS A 556 ASN A 935 GLN A 954 GLN B 99 ASN B 207 HIS B 334 ASN B 474 GLN B 926 GLN C 99 ASN C 556 ASN C 804 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099505 restraints weight = 27137.537| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.94 r_work: 0.2984 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 27441 Z= 0.258 Angle : 0.712 20.063 37452 Z= 0.360 Chirality : 0.050 0.417 4389 Planarity : 0.005 0.053 4728 Dihedral : 6.542 59.653 4974 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.93 % Favored : 95.86 % Rotamer: Outliers : 2.55 % Allowed : 15.79 % Favored : 81.66 % Cbeta Deviations : 0.03 % 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: -0.25 (0.14), residues: 3285 helix: 1.62 (0.20), residues: 687 sheet: 0.24 (0.18), residues: 840 loop : -1.12 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.005 0.001 HIS C 245 PHE 0.017 0.002 PHE B 759 TYR 0.025 0.002 TYR A1067 ARG 0.013 0.001 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 48) link_NAG-ASN : angle 2.30853 ( 144) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 3.95893 ( 36) hydrogen bonds : bond 0.05693 ( 1102) hydrogen bonds : angle 5.66140 ( 3108) link_BETA1-6 : bond 0.00485 ( 3) link_BETA1-6 : angle 1.21245 ( 9) SS BOND : bond 0.00845 ( 42) SS BOND : angle 2.63948 ( 84) link_BETA1-3 : bond 0.01439 ( 3) link_BETA1-3 : angle 3.68545 ( 9) covalent geometry : bond 0.00609 (27333) covalent geometry : angle 0.67486 (37170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 234 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: A 370 ASN cc_start: 0.8627 (t0) cc_final: 0.8145 (m-40) REVERT: A 554 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: A 613 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: A 827 THR cc_start: 0.8503 (p) cc_final: 0.8211 (t) REVERT: A 933 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8162 (mtpt) REVERT: A 964 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8344 (mtpt) REVERT: B 52 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: B 143 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7907 (t) REVERT: B 357 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7558 (tpm170) REVERT: B 370 ASN cc_start: 0.8511 (t0) cc_final: 0.8091 (m-40) REVERT: B 571 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8202 (t70) REVERT: B 613 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: B 795 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5732 (mtpt) REVERT: B 804 GLN cc_start: 0.8601 (mt0) cc_final: 0.8381 (mt0) REVERT: B 964 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8345 (mtpt) REVERT: B 1010 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: C 554 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: C 571 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8171 (t70) REVERT: C 613 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: C 1010 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: C 1091 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6619 (ptp-170) REVERT: C 1113 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8258 (mm110) outliers start: 73 outliers final: 37 residues processed: 283 average time/residue: 1.2762 time to fit residues: 425.3996 Evaluate side-chains 282 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 48 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 47 optimal weight: 0.0060 chunk 298 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 198 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.7176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 556 ASN A 613 GLN A 954 GLN A1010 GLN B 99 ASN B 207 HIS B 334 ASN B 474 GLN B 613 GLN B1101 HIS C 99 ASN C 556 ASN C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103986 restraints weight = 26971.741| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.90 r_work: 0.3051 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27441 Z= 0.118 Angle : 0.593 15.724 37452 Z= 0.300 Chirality : 0.044 0.330 4389 Planarity : 0.004 0.050 4728 Dihedral : 5.985 59.007 4974 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.23 % Favored : 96.53 % Rotamer: Outliers : 1.78 % Allowed : 16.60 % Favored : 81.62 % 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: -0.17 (0.14), residues: 3285 helix: 1.89 (0.20), residues: 687 sheet: 0.22 (0.18), residues: 846 loop : -1.13 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A 66 PHE 0.015 0.001 PHE C1121 TYR 0.018 0.001 TYR A1067 ARG 0.014 0.001 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 48) link_NAG-ASN : angle 2.06121 ( 144) link_BETA1-4 : bond 0.00254 ( 12) link_BETA1-4 : angle 3.32891 ( 36) hydrogen bonds : bond 0.04245 ( 1102) hydrogen bonds : angle 5.30646 ( 3108) link_BETA1-6 : bond 0.00420 ( 3) link_BETA1-6 : angle 1.35020 ( 9) SS BOND : bond 0.00380 ( 42) SS BOND : angle 2.45650 ( 84) link_BETA1-3 : bond 0.01809 ( 3) link_BETA1-3 : angle 3.49307 ( 9) covalent geometry : bond 0.00263 (27333) covalent geometry : angle 0.55704 (37170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8375 (pm20) cc_final: 0.8144 (pm20) REVERT: A 346 ARG cc_start: 0.8125 (tpt-90) cc_final: 0.7691 (tpt-90) REVERT: A 370 ASN cc_start: 0.8545 (t0) cc_final: 0.8118 (m-40) REVERT: A 554 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 613 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: A 827 THR cc_start: 0.8352 (p) cc_final: 0.8068 (t) REVERT: A 1010 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: B 52 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8598 (tp40) REVERT: B 143 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7815 (t) REVERT: B 357 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7205 (ttm170) REVERT: B 370 ASN cc_start: 0.8473 (t0) cc_final: 0.8067 (m-40) REVERT: B 571 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8104 (t70) REVERT: B 613 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: B 804 GLN cc_start: 0.8536 (mt0) cc_final: 0.8317 (mt0) REVERT: B 827 THR cc_start: 0.8473 (p) cc_final: 0.8162 (t) REVERT: B 964 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8279 (mtpt) REVERT: B 1010 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: B 1045 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8570 (tmtt) REVERT: C 158 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7804 (mmm-85) REVERT: C 370 ASN cc_start: 0.8541 (t0) cc_final: 0.8051 (m110) REVERT: C 554 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: C 571 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8055 (t70) REVERT: C 613 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: C 1010 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: C 1091 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6429 (ptp-170) outliers start: 51 outliers final: 30 residues processed: 271 average time/residue: 1.3480 time to fit residues: 431.3752 Evaluate side-chains 276 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1091 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 182 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 556 ASN A 954 GLN B 99 ASN B 207 HIS B 334 ASN B 474 GLN C 99 ASN C 556 ASN C 787 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099450 restraints weight = 27089.320| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.90 r_work: 0.2968 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 27441 Z= 0.264 Angle : 0.719 19.035 37452 Z= 0.364 Chirality : 0.050 0.423 4389 Planarity : 0.005 0.053 4728 Dihedral : 6.519 59.949 4974 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 2.20 % Allowed : 16.18 % Favored : 81.62 % 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: -0.27 (0.14), residues: 3285 helix: 1.60 (0.20), residues: 687 sheet: 0.24 (0.18), residues: 837 loop : -1.14 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 886 HIS 0.005 0.001 HIS C 245 PHE 0.020 0.002 PHE A 140 TYR 0.025 0.002 TYR A1067 ARG 0.009 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 48) link_NAG-ASN : angle 2.34788 ( 144) link_BETA1-4 : bond 0.00280 ( 12) link_BETA1-4 : angle 4.02499 ( 36) hydrogen bonds : bond 0.05755 ( 1102) hydrogen bonds : angle 5.66262 ( 3108) link_BETA1-6 : bond 0.00493 ( 3) link_BETA1-6 : angle 1.24109 ( 9) SS BOND : bond 0.00727 ( 42) SS BOND : angle 2.67270 ( 84) link_BETA1-3 : bond 0.01496 ( 3) link_BETA1-3 : angle 3.67682 ( 9) covalent geometry : bond 0.00625 (27333) covalent geometry : angle 0.68119 (37170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29437.30 seconds wall clock time: 514 minutes 11.98 seconds (30851.98 seconds total)