Starting phenix.real_space_refine on Fri Mar 6 01:22:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qus_14153/03_2026/7qus_14153.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qus_14153/03_2026/7qus_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qus_14153/03_2026/7qus_14153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qus_14153/03_2026/7qus_14153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qus_14153/03_2026/7qus_14153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qus_14153/03_2026/7qus_14153.map" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 6.44, per 1000 atoms: 0.24 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: 2.58 Conformation dependent library (CDL) restraints added in 1.3 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: 1.38 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: 6.92 Time building geometry restraints manager: 3.39 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: 0.05 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: 3.710 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.050 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- 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 : 5.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG A 190 TYR 0.014 0.001 TYR B1067 PHE 0.014 0.001 PHE A 823 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00352 (27333) covalent geometry : angle 0.60409 (37170) SS BOND : bond 0.00169 ( 42) SS BOND : angle 0.86235 ( 84) hydrogen bonds : bond 0.11773 ( 1102) hydrogen bonds : angle 6.41468 ( 3108) link_BETA1-3 : bond 0.02160 ( 3) link_BETA1-3 : angle 4.11021 ( 9) link_BETA1-4 : bond 0.00408 ( 12) link_BETA1-4 : angle 3.02035 ( 36) link_BETA1-6 : bond 0.00486 ( 3) link_BETA1-6 : angle 1.35917 ( 9) link_NAG-ASN : bond 0.00418 ( 48) link_NAG-ASN : angle 1.76619 ( 144) *********************** 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 : 1.008 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: 0.5992 time to fit residues: 241.1298 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 : 1.000 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 440 ASN A 556 ASN A 613 GLN A 658 ASN A 690 GLN A 872 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 99 ASN B 164 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 164 ASN C 474 GLN C 556 ASN C 613 GLN C 658 ASN C 690 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1101 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103852 restraints weight = 27572.110| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.96 r_work: 0.3169 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27441 Z= 0.207 Angle : 0.650 10.882 37452 Z= 0.333 Chirality : 0.048 0.393 4389 Planarity : 0.005 0.051 4728 Dihedral : 7.497 59.887 4990 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.95 % Rotamer: Outliers : 3.70 % Allowed : 14.92 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3285 helix: 1.62 (0.20), residues: 687 sheet: 0.37 (0.18), residues: 771 loop : -1.07 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 190 TYR 0.026 0.002 TYR A1067 PHE 0.022 0.002 PHE C 817 TRP 0.012 0.002 TRP C 886 HIS 0.007 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00489 (27333) covalent geometry : angle 0.62409 (37170) SS BOND : bond 0.00455 ( 42) SS BOND : angle 1.18545 ( 84) hydrogen bonds : bond 0.05539 ( 1102) hydrogen bonds : angle 5.72022 ( 3108) link_BETA1-3 : bond 0.01607 ( 3) link_BETA1-3 : angle 4.32856 ( 9) link_BETA1-4 : bond 0.00291 ( 12) link_BETA1-4 : angle 3.48576 ( 36) link_BETA1-6 : bond 0.00170 ( 3) link_BETA1-6 : angle 1.37013 ( 9) link_NAG-ASN : bond 0.00316 ( 48) link_NAG-ASN : angle 2.01656 ( 144) *********************** 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 364 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 258 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: A 137 ASN cc_start: 0.8102 (t0) cc_final: 0.7547 (t0) REVERT: A 143 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7706 (t) REVERT: A 177 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6227 (tmt) REVERT: A 613 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: A 827 THR cc_start: 0.8557 (p) cc_final: 0.8300 (t) REVERT: A 990 GLU cc_start: 0.7879 (tt0) cc_final: 0.7580 (tt0) REVERT: A 1045 LYS cc_start: 0.8747 (tmmt) cc_final: 0.8470 (tmtt) REVERT: A 1081 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 1091 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6876 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: B 52 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: B 177 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.4868 (tmt) REVERT: B 321 GLN cc_start: 0.8439 (mm110) cc_final: 0.8202 (mp-120) REVERT: B 346 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6681 (ttp80) REVERT: B 357 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7431 (tpm170) REVERT: B 571 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8118 (t0) REVERT: B 613 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: B 964 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8227 (mtpt) REVERT: C 143 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8021 (t) REVERT: C 177 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6842 (tmt) REVERT: C 370 ASN cc_start: 0.8629 (t0) cc_final: 0.8058 (m110) REVERT: C 571 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8020 (t70) REVERT: C 613 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: C 795 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5431 (tttm) REVERT: C 964 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8111 (mtpt) REVERT: C 1029 MET cc_start: 0.9031 (tpp) cc_final: 0.8773 (tpp) outliers start: 106 outliers final: 37 residues processed: 332 average time/residue: 0.6364 time to fit residues: 246.3989 Evaluate side-chains 286 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 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 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 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 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 827 THR 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 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE 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 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 964 LYS 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 180 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 306 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 304 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 321 GLN A 658 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 804 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.145985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107659 restraints weight = 27590.887| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.12 r_work: 0.3196 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27441 Z= 0.112 Angle : 0.543 9.191 37452 Z= 0.278 Chirality : 0.044 0.311 4389 Planarity : 0.004 0.047 4728 Dihedral : 6.757 59.796 4976 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.01 % Favored : 96.71 % Rotamer: Outliers : 3.28 % Allowed : 15.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3285 helix: 1.87 (0.20), residues: 687 sheet: 0.34 (0.18), residues: 774 loop : -1.05 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 847 TYR 0.016 0.001 TYR C1067 PHE 0.015 0.001 PHE C 817 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00248 (27333) covalent geometry : angle 0.51513 (37170) SS BOND : bond 0.00287 ( 42) SS BOND : angle 1.49640 ( 84) hydrogen bonds : bond 0.04281 ( 1102) hydrogen bonds : angle 5.36850 ( 3108) link_BETA1-3 : bond 0.01868 ( 3) link_BETA1-3 : angle 3.94739 ( 9) link_BETA1-4 : bond 0.00314 ( 12) link_BETA1-4 : angle 3.15847 ( 36) link_BETA1-6 : bond 0.00311 ( 3) link_BETA1-6 : angle 1.31659 ( 9) link_NAG-ASN : bond 0.00218 ( 48) link_NAG-ASN : angle 1.84222 ( 144) *********************** 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 347 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 253 time to evaluate : 1.051 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 137 ASN cc_start: 0.8171 (t0) cc_final: 0.7625 (t0) REVERT: A 143 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7679 (t) REVERT: A 177 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.5641 (tmt) REVERT: A 554 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: A 613 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: A 827 THR cc_start: 0.8451 (p) cc_final: 0.8218 (t) REVERT: A 933 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8153 (mtpt) REVERT: A 983 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7570 (mtp180) REVERT: A 990 GLU cc_start: 0.7932 (tt0) cc_final: 0.7641 (tt0) REVERT: A 1091 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6812 (ptp-170) REVERT: B 52 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8607 (tp40) REVERT: B 143 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7715 (t) REVERT: B 244 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5697 (pp) REVERT: B 357 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: B 571 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8019 (t70) REVERT: B 613 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: B 964 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8268 (mtpt) REVERT: C 177 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6803 (tmt) REVERT: C 370 ASN cc_start: 0.8616 (t0) cc_final: 0.8062 (m110) REVERT: C 571 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8047 (t70) REVERT: C 613 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7743 (mt0) outliers start: 94 outliers final: 30 residues processed: 317 average time/residue: 0.6312 time to fit residues: 234.7625 Evaluate side-chains 284 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 228 ASP Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 323 THR 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 878 LEU Chi-restraints excluded: chain A residue 933 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 143 VAL Chi-restraints excluded: chain B residue 169 GLU 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 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 645 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 964 LYS Chi-restraints excluded: chain B residue 1010 GLN 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 210 ILE Chi-restraints excluded: chain C residue 228 ASP 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 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 236 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 322 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 223 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 804 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106564 restraints weight = 27043.348| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.97 r_work: 0.3092 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27441 Z= 0.109 Angle : 0.541 9.020 37452 Z= 0.275 Chirality : 0.043 0.302 4389 Planarity : 0.004 0.047 4728 Dihedral : 6.335 57.386 4975 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.26 % Favored : 96.47 % Rotamer: Outliers : 2.86 % Allowed : 15.55 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3285 helix: 2.02 (0.20), residues: 687 sheet: 0.40 (0.18), residues: 765 loop : -1.02 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 190 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE C 817 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00241 (27333) covalent geometry : angle 0.51117 (37170) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.87870 ( 84) hydrogen bonds : bond 0.04061 ( 1102) hydrogen bonds : angle 5.22976 ( 3108) link_BETA1-3 : bond 0.01769 ( 3) link_BETA1-3 : angle 3.78559 ( 9) link_BETA1-4 : bond 0.00338 ( 12) link_BETA1-4 : angle 3.01258 ( 36) link_BETA1-6 : bond 0.00455 ( 3) link_BETA1-6 : angle 1.19554 ( 9) link_NAG-ASN : bond 0.00237 ( 48) link_NAG-ASN : angle 1.80256 ( 144) *********************** 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 326 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 244 time to evaluate : 1.080 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 34 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7682 (mtp85) REVERT: A 137 ASN cc_start: 0.8208 (t0) cc_final: 0.7670 (t0) REVERT: A 143 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7705 (t) REVERT: A 241 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8130 (mt) REVERT: A 554 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: A 613 GLN cc_start: 0.8460 (mp10) cc_final: 0.7739 (mt0) REVERT: A 827 THR cc_start: 0.8435 (p) cc_final: 0.8225 (t) REVERT: A 933 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8184 (mtpt) REVERT: A 964 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8261 (mtpt) REVERT: A 1010 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: B 52 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8604 (tp40) REVERT: B 143 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7807 (t) REVERT: B 177 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.4232 (tmt) REVERT: B 244 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5800 (pp) REVERT: B 357 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7246 (ttm170) REVERT: B 571 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8079 (t70) REVERT: B 613 GLN cc_start: 0.8557 (mp10) cc_final: 0.7816 (mt0) REVERT: C 34 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7701 (mtp85) REVERT: C 177 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6833 (tmt) REVERT: C 370 ASN cc_start: 0.8596 (t0) cc_final: 0.8079 (m110) REVERT: C 571 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (t70) REVERT: C 613 GLN cc_start: 0.8422 (mp10) cc_final: 0.7679 (mt0) REVERT: C 1010 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7936 (mp10) outliers start: 82 outliers final: 27 residues processed: 300 average time/residue: 0.6608 time to fit residues: 231.6615 Evaluate side-chains 282 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG 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 241 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU 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 60 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 169 GLU 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 244 LEU Chi-restraints excluded: chain B residue 323 THR 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 638 THR Chi-restraints excluded: chain B residue 645 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 1010 GLN Chi-restraints excluded: chain C residue 34 ARG 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 661 GLU Chi-restraints excluded: chain C residue 719 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 275 optimal weight: 0.0030 chunk 23 optimal weight: 8.9990 chunk 286 optimal weight: 0.2980 chunk 135 optimal weight: 7.9990 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 804 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103055 restraints weight = 27008.226| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.95 r_work: 0.3029 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27441 Z= 0.161 Angle : 0.590 9.876 37452 Z= 0.300 Chirality : 0.045 0.357 4389 Planarity : 0.004 0.050 4728 Dihedral : 6.333 59.383 4975 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.44 % Favored : 96.29 % Rotamer: Outliers : 3.10 % Allowed : 15.17 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3285 helix: 1.84 (0.20), residues: 687 sheet: 0.31 (0.18), residues: 807 loop : -1.01 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 190 TYR 0.022 0.002 TYR C1067 PHE 0.013 0.002 PHE B 759 TRP 0.011 0.002 TRP C 886 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00377 (27333) covalent geometry : angle 0.56033 (37170) SS BOND : bond 0.00453 ( 42) SS BOND : angle 1.64324 ( 84) hydrogen bonds : bond 0.04805 ( 1102) hydrogen bonds : angle 5.42380 ( 3108) link_BETA1-3 : bond 0.01663 ( 3) link_BETA1-3 : angle 3.84201 ( 9) link_BETA1-4 : bond 0.00290 ( 12) link_BETA1-4 : angle 3.37968 ( 36) link_BETA1-6 : bond 0.00393 ( 3) link_BETA1-6 : angle 1.27499 ( 9) link_NAG-ASN : bond 0.00202 ( 48) link_NAG-ASN : angle 2.02078 ( 144) *********************** 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 336 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 247 time to evaluate : 0.880 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: symmetry clash REVERT: A 177 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.5099 (tmt) REVERT: A 554 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: A 613 GLN cc_start: 0.8576 (mp10) cc_final: 0.7768 (mt0) REVERT: A 827 THR cc_start: 0.8488 (p) cc_final: 0.8249 (t) REVERT: A 933 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8114 (mtpt) REVERT: A 964 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8291 (mtpt) REVERT: A 1010 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: A 1113 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8100 (mm-40) REVERT: B 52 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8633 (tp40) REVERT: B 60 SER cc_start: 0.7921 (OUTLIER) cc_final: 0.7617 (m) REVERT: B 143 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7771 (t) REVERT: B 357 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7170 (ttm170) REVERT: B 370 ASN cc_start: 0.8490 (t0) cc_final: 0.8106 (m-40) REVERT: B 571 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8130 (t70) REVERT: B 613 GLN cc_start: 0.8650 (mp10) cc_final: 0.7917 (mt0) REVERT: B 933 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (mtmm) REVERT: B 964 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8325 (mtpt) REVERT: B 1045 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8528 (tmtt) REVERT: C 177 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6796 (tmt) REVERT: C 571 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8112 (t70) REVERT: C 606 ASN cc_start: 0.8718 (m110) cc_final: 0.8514 (m-40) REVERT: C 613 GLN cc_start: 0.8582 (mp10) cc_final: 0.7845 (mt0) REVERT: C 1010 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: C 1029 MET cc_start: 0.9088 (tpp) cc_final: 0.8836 (tpp) outliers start: 89 outliers final: 37 residues processed: 309 average time/residue: 0.6223 time to fit residues: 225.6717 Evaluate side-chains 287 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 719 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 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 A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 60 SER 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 323 THR 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 638 THR 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 933 LYS 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 255 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 236 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 207 HIS B 334 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 804 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103140 restraints weight = 27109.721| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.96 r_work: 0.3021 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27441 Z= 0.150 Angle : 0.590 12.214 37452 Z= 0.300 Chirality : 0.045 0.347 4389 Planarity : 0.004 0.050 4728 Dihedral : 6.173 58.527 4975 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.03 % Allowed : 15.45 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3285 helix: 1.89 (0.20), residues: 687 sheet: 0.34 (0.18), residues: 804 loop : -1.07 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 847 TYR 0.020 0.001 TYR C1067 PHE 0.014 0.001 PHE B1121 TRP 0.010 0.001 TRP B 886 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00347 (27333) covalent geometry : angle 0.55755 (37170) SS BOND : bond 0.00494 ( 42) SS BOND : angle 2.11970 ( 84) hydrogen bonds : bond 0.04611 ( 1102) hydrogen bonds : angle 5.37198 ( 3108) link_BETA1-3 : bond 0.01651 ( 3) link_BETA1-3 : angle 3.67441 ( 9) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 3.30674 ( 36) link_BETA1-6 : bond 0.00491 ( 3) link_BETA1-6 : angle 1.17225 ( 9) link_NAG-ASN : bond 0.00256 ( 48) link_NAG-ASN : angle 2.01913 ( 144) *********************** 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 322 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 235 time to evaluate : 1.224 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 554 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: A 613 GLN cc_start: 0.8612 (mp10) cc_final: 0.7809 (mt0) REVERT: A 827 THR cc_start: 0.8424 (p) cc_final: 0.8187 (t) REVERT: A 933 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (mtpt) REVERT: A 964 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8289 (mtpt) REVERT: A 1010 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: B 52 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8631 (tp40) REVERT: B 60 SER cc_start: 0.7938 (OUTLIER) cc_final: 0.7650 (m) REVERT: B 143 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7771 (t) REVERT: B 244 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6010 (pp) REVERT: B 321 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7573 (mp-120) REVERT: B 357 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7195 (ttm170) REVERT: B 370 ASN cc_start: 0.8482 (t0) cc_final: 0.8088 (m-40) REVERT: B 571 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8163 (t70) REVERT: B 613 GLN cc_start: 0.8630 (mp10) cc_final: 0.7903 (mt0) REVERT: B 795 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5626 (mtpt) REVERT: B 933 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8223 (mtmm) REVERT: B 964 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8315 (mtpt) REVERT: B 1045 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8528 (tmtt) REVERT: C 161 SER cc_start: 0.8281 (t) cc_final: 0.8066 (m) REVERT: C 177 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6795 (tmt) REVERT: C 571 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8099 (t70) REVERT: C 606 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8525 (m-40) REVERT: C 613 GLN cc_start: 0.8615 (mp10) cc_final: 0.7916 (mt0) REVERT: C 1010 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: C 1091 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6397 (ptp-170) outliers start: 87 outliers final: 41 residues processed: 295 average time/residue: 0.6573 time to fit residues: 227.3467 Evaluate side-chains 296 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 554 GLU Chi-restraints excluded: chain A residue 572 THR 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 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 60 SER 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 321 GLN 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 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 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 933 LYS 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 60 SER 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 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 606 ASN 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 1018 ILE Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 27 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 325 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 99 ASN B 207 HIS B 334 ASN B 804 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS C 99 ASN C 804 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102796 restraints weight = 26917.245| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.95 r_work: 0.3025 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2873 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= 0.152 Angle : 0.596 15.555 37452 Z= 0.302 Chirality : 0.045 0.354 4389 Planarity : 0.004 0.050 4728 Dihedral : 6.088 58.599 4975 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.35 % Favored : 96.38 % Rotamer: Outliers : 3.21 % Allowed : 15.20 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3285 helix: 1.89 (0.20), residues: 687 sheet: 0.32 (0.18), residues: 807 loop : -1.09 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 847 TYR 0.020 0.001 TYR C1067 PHE 0.014 0.001 PHE B1121 TRP 0.011 0.001 TRP B 886 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00351 (27333) covalent geometry : angle 0.56342 (37170) SS BOND : bond 0.00490 ( 42) SS BOND : angle 2.11377 ( 84) hydrogen bonds : bond 0.04641 ( 1102) hydrogen bonds : angle 5.37464 ( 3108) link_BETA1-3 : bond 0.01643 ( 3) link_BETA1-3 : angle 3.63404 ( 9) link_BETA1-4 : bond 0.00304 ( 12) link_BETA1-4 : angle 3.34135 ( 36) link_BETA1-6 : bond 0.00459 ( 3) link_BETA1-6 : angle 1.19820 ( 9) link_NAG-ASN : bond 0.00267 ( 48) link_NAG-ASN : angle 2.03406 ( 144) *********************** 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 327 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 235 time to evaluate : 1.039 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 101 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7998 (mp) REVERT: A 242 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 281 GLU cc_start: 0.8379 (pm20) cc_final: 0.8108 (pm20) REVERT: A 554 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: A 613 GLN cc_start: 0.8669 (mp10) cc_final: 0.7895 (mt0) REVERT: A 827 THR cc_start: 0.8420 (p) cc_final: 0.8159 (t) REVERT: A 933 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8091 (mtpt) REVERT: A 964 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8274 (mtpt) REVERT: A 1010 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: B 52 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8630 (tp40) REVERT: B 60 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7671 (m) REVERT: B 143 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7805 (t) REVERT: B 244 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.5981 (pp) REVERT: B 321 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7568 (mp-120) REVERT: B 357 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7165 (ttm170) REVERT: B 370 ASN cc_start: 0.8485 (t0) cc_final: 0.8078 (m-40) REVERT: B 571 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8220 (t70) REVERT: B 613 GLN cc_start: 0.8636 (mp10) cc_final: 0.7870 (mt0) REVERT: B 795 LYS cc_start: 0.5953 (OUTLIER) cc_final: 0.5616 (mtpt) REVERT: B 827 THR cc_start: 0.8453 (p) cc_final: 0.8125 (t) REVERT: B 933 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8218 (mtmm) REVERT: B 964 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8313 (mtpt) REVERT: B 1010 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: B 1045 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8525 (tmtt) REVERT: C 177 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6797 (tmt) REVERT: C 571 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8106 (t70) REVERT: C 606 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8522 (m-40) REVERT: C 613 GLN cc_start: 0.8619 (mp10) cc_final: 0.7920 (mt0) REVERT: C 1010 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: C 1091 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.6440 (ptp-170) outliers start: 92 outliers final: 42 residues processed: 302 average time/residue: 0.6656 time to fit residues: 235.4049 Evaluate side-chains 297 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain A residue 101 ILE 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 554 GLU Chi-restraints excluded: chain A residue 572 THR 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 60 SER 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 321 GLN 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 645 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 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 933 LYS 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 60 SER 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 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 606 ASN 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 934 ILE 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 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 297 optimal weight: 0.0670 chunk 194 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 321 GLN A 556 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN 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 ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102091 restraints weight = 27044.726| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.00 r_work: 0.3013 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2941 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= 0.160 Angle : 0.611 15.394 37452 Z= 0.310 Chirality : 0.045 0.359 4389 Planarity : 0.004 0.054 4728 Dihedral : 6.064 58.908 4974 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.29 % Favored : 96.44 % Rotamer: Outliers : 3.03 % Allowed : 15.41 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3285 helix: 1.89 (0.20), residues: 687 sheet: 0.27 (0.18), residues: 834 loop : -1.12 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 847 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE A 140 TRP 0.012 0.001 TRP B 886 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00370 (27333) covalent geometry : angle 0.57702 (37170) SS BOND : bond 0.00481 ( 42) SS BOND : angle 2.32717 ( 84) hydrogen bonds : bond 0.04726 ( 1102) hydrogen bonds : angle 5.38913 ( 3108) link_BETA1-3 : bond 0.01636 ( 3) link_BETA1-3 : angle 3.57765 ( 9) link_BETA1-4 : bond 0.00273 ( 12) link_BETA1-4 : angle 3.37521 ( 36) link_BETA1-6 : bond 0.00469 ( 3) link_BETA1-6 : angle 1.23903 ( 9) link_NAG-ASN : bond 0.00319 ( 48) link_NAG-ASN : angle 2.09044 ( 144) *********************** 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 328 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 241 time to evaluate : 1.029 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: 0.8967 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: A 101 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 177 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.4671 (tmt) REVERT: A 242 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7921 (mt) REVERT: A 370 ASN cc_start: 0.8613 (t0) cc_final: 0.8154 (m-40) REVERT: A 554 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: A 613 GLN cc_start: 0.8679 (mp10) cc_final: 0.7907 (mt0) REVERT: A 827 THR cc_start: 0.8420 (p) cc_final: 0.8152 (t) REVERT: A 933 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8124 (mtpt) REVERT: A 964 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8295 (mtpt) REVERT: A 1010 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: A 1113 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: B 52 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8643 (tp40) REVERT: B 60 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7704 (m) REVERT: B 143 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 153 MET cc_start: 0.6963 (ptt) cc_final: 0.6707 (mtt) REVERT: B 244 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6054 (pp) REVERT: B 321 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7582 (mp-120) REVERT: B 357 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.7212 (ttm170) REVERT: B 370 ASN cc_start: 0.8498 (t0) cc_final: 0.8086 (m-40) REVERT: B 571 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8244 (t70) REVERT: B 613 GLN cc_start: 0.8654 (mp10) cc_final: 0.7949 (mt0) REVERT: B 675 GLN cc_start: 0.7568 (mm110) cc_final: 0.7354 (mm110) REVERT: B 795 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.5644 (mtpt) REVERT: B 827 THR cc_start: 0.8469 (p) cc_final: 0.8152 (t) REVERT: B 964 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8328 (mtpt) REVERT: B 1010 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: B 1045 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8543 (tmtt) REVERT: C 177 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6762 (tmt) REVERT: C 571 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8141 (t70) REVERT: C 606 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: C 613 GLN cc_start: 0.8633 (mp10) cc_final: 0.7975 (mt0) REVERT: C 1010 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: C 1091 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6467 (ptp-170) outliers start: 87 outliers final: 45 residues processed: 302 average time/residue: 0.6533 time to fit residues: 230.7794 Evaluate side-chains 303 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 101 ILE 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 242 LEU 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 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 A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 321 GLN 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 645 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 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 60 SER 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 606 ASN 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 934 ILE 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 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 78 optimal weight: 4.9990 chunk 125 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 250 optimal weight: 0.2980 chunk 185 optimal weight: 0.7980 chunk 264 optimal weight: 0.8980 chunk 228 optimal weight: 8.9990 chunk 270 optimal weight: 0.0970 chunk 251 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 99 ASN B 334 ASN B 474 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 804 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106791 restraints weight = 27145.411| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.05 r_work: 0.3116 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27441 Z= 0.099 Angle : 0.541 11.595 37452 Z= 0.274 Chirality : 0.043 0.304 4389 Planarity : 0.004 0.050 4728 Dihedral : 5.494 58.470 4974 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.04 % Favored : 96.68 % Rotamer: Outliers : 1.99 % Allowed : 16.49 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3285 helix: 2.25 (0.20), residues: 669 sheet: 0.28 (0.18), residues: 789 loop : -1.01 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 847 TYR 0.015 0.001 TYR A1067 PHE 0.015 0.001 PHE C1121 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00216 (27333) covalent geometry : angle 0.51190 (37170) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.89742 ( 84) hydrogen bonds : bond 0.03727 ( 1102) hydrogen bonds : angle 5.08242 ( 3108) link_BETA1-3 : bond 0.01902 ( 3) link_BETA1-3 : angle 3.56363 ( 9) link_BETA1-4 : bond 0.00285 ( 12) link_BETA1-4 : angle 2.94894 ( 36) link_BETA1-6 : bond 0.00398 ( 3) link_BETA1-6 : angle 1.26522 ( 9) link_NAG-ASN : bond 0.00261 ( 48) link_NAG-ASN : angle 1.80991 ( 144) *********************** 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 309 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 1.059 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 101 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7923 (mp) REVERT: A 281 GLU cc_start: 0.8383 (pm20) cc_final: 0.8143 (pm20) REVERT: A 554 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 613 GLN cc_start: 0.8582 (mp10) cc_final: 0.7731 (mt0) REVERT: A 827 THR cc_start: 0.8338 (p) cc_final: 0.8076 (t) REVERT: A 1010 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: B 143 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7805 (t) REVERT: B 370 ASN cc_start: 0.8465 (t0) cc_final: 0.8078 (m-40) REVERT: B 571 ASP cc_start: 0.8440 (m-30) cc_final: 0.8142 (t70) REVERT: B 613 GLN cc_start: 0.8602 (mp10) cc_final: 0.7837 (mt0) REVERT: B 795 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5649 (mtpt) REVERT: B 827 THR cc_start: 0.8460 (p) cc_final: 0.8132 (t) REVERT: B 1010 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: B 1091 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7449 (ptp-170) REVERT: C 529 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8076 (tttm) REVERT: C 571 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7999 (t70) REVERT: C 613 GLN cc_start: 0.8566 (mp10) cc_final: 0.7818 (mt0) REVERT: C 1010 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: C 1091 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6162 (ptp-170) outliers start: 57 outliers final: 29 residues processed: 291 average time/residue: 0.6447 time to fit residues: 220.4394 Evaluate side-chains 273 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain A residue 101 ILE 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 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1091 ARG 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 489 TYR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE 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 60 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 180 optimal weight: 0.1980 chunk 241 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 926 GLN A1135 ASN B 99 ASN B 334 ASN B 474 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 245 HIS C 556 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105270 restraints weight = 26974.949| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.96 r_work: 0.3058 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27441 Z= 0.119 Angle : 0.555 10.587 37452 Z= 0.281 Chirality : 0.044 0.330 4389 Planarity : 0.004 0.053 4728 Dihedral : 5.553 59.169 4974 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.26 % Favored : 96.47 % Rotamer: Outliers : 1.43 % Allowed : 17.36 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3285 helix: 2.13 (0.20), residues: 687 sheet: 0.29 (0.18), residues: 789 loop : -1.04 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 847 TYR 0.018 0.001 TYR C1067 PHE 0.013 0.001 PHE B1121 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00268 (27333) covalent geometry : angle 0.52625 (37170) SS BOND : bond 0.00359 ( 42) SS BOND : angle 1.78650 ( 84) hydrogen bonds : bond 0.04090 ( 1102) hydrogen bonds : angle 5.14883 ( 3108) link_BETA1-3 : bond 0.01765 ( 3) link_BETA1-3 : angle 3.60477 ( 9) link_BETA1-4 : bond 0.00293 ( 12) link_BETA1-4 : angle 3.09081 ( 36) link_BETA1-6 : bond 0.00405 ( 3) link_BETA1-6 : angle 1.26052 ( 9) link_NAG-ASN : bond 0.00249 ( 48) link_NAG-ASN : angle 1.89921 ( 144) ********************** 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 278 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 1.055 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 101 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 281 GLU cc_start: 0.8380 (pm20) cc_final: 0.8104 (pm20) REVERT: A 554 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: A 613 GLN cc_start: 0.8580 (mp10) cc_final: 0.7765 (mt0) REVERT: A 827 THR cc_start: 0.8339 (p) cc_final: 0.8070 (t) REVERT: A 1010 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: B 60 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7669 (m) REVERT: B 370 ASN cc_start: 0.8495 (t0) cc_final: 0.8075 (m-40) REVERT: B 571 ASP cc_start: 0.8485 (m-30) cc_final: 0.8163 (t70) REVERT: B 613 GLN cc_start: 0.8600 (mp10) cc_final: 0.7842 (mt0) REVERT: B 795 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5597 (mtpt) REVERT: B 827 THR cc_start: 0.8426 (p) cc_final: 0.8112 (t) REVERT: B 1010 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: B 1091 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7491 (ptp-170) REVERT: C 529 LYS cc_start: 0.8670 (mmtm) cc_final: 0.8029 (tttm) REVERT: C 571 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8062 (t70) REVERT: C 613 GLN cc_start: 0.8613 (mp10) cc_final: 0.7884 (mt0) REVERT: C 1010 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7886 (mp10) outliers start: 41 outliers final: 27 residues processed: 267 average time/residue: 0.6319 time to fit residues: 198.4167 Evaluate side-chains 271 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain A residue 101 ILE 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 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1091 ARG 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 571 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 134 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 172 optimal weight: 0.3980 chunk 325 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN B 207 HIS B 334 ASN B 474 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101676 restraints weight = 26990.696| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.04 r_work: 0.3016 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3044 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= 0.173 Angle : 0.618 12.554 37452 Z= 0.313 Chirality : 0.046 0.371 4389 Planarity : 0.004 0.050 4728 Dihedral : 5.912 59.365 4974 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.44 % Favored : 96.29 % Rotamer: Outliers : 1.74 % Allowed : 16.98 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3285 helix: 1.91 (0.20), residues: 687 sheet: 0.27 (0.18), residues: 834 loop : -1.11 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 847 TYR 0.021 0.002 TYR C1067 PHE 0.018 0.002 PHE B 168 TRP 0.012 0.002 TRP B 886 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00408 (27333) covalent geometry : angle 0.58489 (37170) SS BOND : bond 0.00564 ( 42) SS BOND : angle 2.17796 ( 84) hydrogen bonds : bond 0.04854 ( 1102) hydrogen bonds : angle 5.37724 ( 3108) link_BETA1-3 : bond 0.01583 ( 3) link_BETA1-3 : angle 3.60395 ( 9) link_BETA1-4 : bond 0.00280 ( 12) link_BETA1-4 : angle 3.42030 ( 36) link_BETA1-6 : bond 0.00461 ( 3) link_BETA1-6 : angle 1.21495 ( 9) link_NAG-ASN : bond 0.00280 ( 48) link_NAG-ASN : angle 2.07802 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12043.33 seconds wall clock time: 205 minutes 17.67 seconds (12317.67 seconds total)