Starting phenix.real_space_refine on Fri Feb 6 09:29:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlx_27519/02_2026/8dlx_27519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlx_27519/02_2026/8dlx_27519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dlx_27519/02_2026/8dlx_27519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlx_27519/02_2026/8dlx_27519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlx_27519/02_2026/8dlx_27519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlx_27519/02_2026/8dlx_27519.map" } resolution = 2.45 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= -0.002 sd= 0.042 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 106 5.16 5 C 15445 2.51 5 N 3979 2.21 5 O 4763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24293 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7838 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 53, 'TRANS': 949} Chain breaks: 8 Chain: "B" Number of atoms: 6571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6571 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 45, 'TRANS': 797} Chain breaks: 8 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.26, per 1000 atoms: 0.26 Number of scatterers: 24293 At special positions: 0 Unit cell: (137, 146, 182, 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 106 16.00 O 4763 8.00 N 3979 7.00 C 15445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " 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 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 39 sheets defined 24.9% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.844A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.526A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.436A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.085A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (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 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.633A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.926A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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: 4.050A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.548A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.960A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (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 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.558A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.916A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.737A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.577A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.518A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.113A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.344A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.892A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (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 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.654A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.957A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.548A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.305A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.545A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.512A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.414A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.506A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.014A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.903A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.691A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.163A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.829A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.727A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.850A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.279A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.740A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.117A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 6.836A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.457A 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: 8.764A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.786A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.620A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.959A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.461A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.885A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.323A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC8, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 6.425A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.120A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.044A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.459A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.250A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.674A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.206A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.261A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.944A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7448 1.34 - 1.46: 6228 1.46 - 1.59: 11015 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 24827 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 ... (remaining 24822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 32767 2.23 - 4.46: 937 4.46 - 6.69: 67 6.69 - 8.91: 15 8.91 - 11.14: 5 Bond angle restraints: 33791 Sorted by residual: angle pdb=" CB ARG A 357 " pdb=" CG ARG A 357 " pdb=" CD ARG A 357 " ideal model delta sigma weight residual 111.30 100.16 11.14 2.30e+00 1.89e-01 2.35e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.46 -5.76 1.22e+00 6.72e-01 2.23e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.19 -5.49 1.22e+00 6.72e-01 2.03e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.14 -5.44 1.22e+00 6.72e-01 1.99e+01 angle pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" C PHE A 377 " ideal model delta sigma weight residual 107.37 99.25 8.12 2.07e+00 2.33e-01 1.54e+01 ... (remaining 33786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14349 17.96 - 35.91: 956 35.91 - 53.87: 164 53.87 - 71.83: 66 71.83 - 89.78: 28 Dihedral angle restraints: 15563 sinusoidal: 6832 harmonic: 8731 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 126.41 -33.41 1 1.00e+01 1.00e-02 1.59e+01 dihedral pdb=" CA ASP C 994 " pdb=" CB ASP C 994 " pdb=" CG ASP C 994 " pdb=" OD1 ASP C 994 " ideal model delta sinusoidal sigma weight residual -30.00 -88.35 58.35 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU A1111 " pdb=" CG GLU A1111 " pdb=" CD GLU A1111 " pdb=" OE1 GLU A1111 " ideal model delta sinusoidal sigma weight residual 0.00 -89.78 89.78 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 15560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3349 0.077 - 0.155: 625 0.155 - 0.232: 39 0.232 - 0.309: 5 0.309 - 0.386: 2 Chirality restraints: 4020 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4017 not shown) Planarity restraints: 4335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 486 " -0.042 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE C 486 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE C 486 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 486 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 486 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE C 486 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 486 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 99 " 0.035 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP H 99 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP H 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 99 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 99 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 99 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 99 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 99 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C MET C 902 " 0.042 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.014 2.00e-02 2.50e+03 ... (remaining 4332 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6289 2.80 - 3.33: 20555 3.33 - 3.85: 41617 3.85 - 4.38: 47881 4.38 - 4.90: 82315 Nonbonded interactions: 198657 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASN B 540 " pdb=" OG1 THR B 549 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.298 3.040 ... (remaining 198652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 14 through 455 or resid 493 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.860 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: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.600 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.005 0.102 24924 Z= 0.239 Angle : 0.860 15.060 34044 Z= 0.456 Chirality : 0.056 0.386 4020 Planarity : 0.006 0.060 4294 Dihedral : 13.112 89.782 9825 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % 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: 2951 helix: 1.04 (0.18), residues: 631 sheet: 0.45 (0.18), residues: 718 loop : -0.79 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 995 TYR 0.031 0.002 TYR C1067 PHE 0.057 0.002 PHE C 486 TRP 0.065 0.003 TRP H 99 HIS 0.013 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00503 (24827) covalent geometry : angle 0.83228 (33791) SS BOND : bond 0.00290 ( 38) SS BOND : angle 1.32975 ( 76) hydrogen bonds : bond 0.12787 ( 901) hydrogen bonds : angle 7.27238 ( 2496) link_BETA1-4 : bond 0.00625 ( 18) link_BETA1-4 : angle 1.44673 ( 54) link_NAG-ASN : bond 0.00738 ( 41) link_NAG-ASN : angle 3.52487 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 PRO cc_start: 0.8927 (Cg_exo) cc_final: 0.8419 (Cg_endo) REVERT: B 153 MET cc_start: 0.6723 (mpp) cc_final: 0.6130 (tpt) REVERT: B 198 ASP cc_start: 0.8227 (m-30) cc_final: 0.7701 (p0) REVERT: B 200 TYR cc_start: 0.8560 (m-10) cc_final: 0.7868 (m-80) REVERT: B 238 PHE cc_start: 0.6740 (p90) cc_final: 0.6443 (p90) REVERT: B 240 THR cc_start: 0.7167 (m) cc_final: 0.6891 (t) REVERT: B 990 GLU cc_start: 0.8218 (tt0) cc_final: 0.7880 (tm-30) REVERT: B 1029 MET cc_start: 0.9370 (tpp) cc_final: 0.9105 (tpp) REVERT: C 97 LYS cc_start: 0.8354 (pttt) cc_final: 0.7817 (tptp) REVERT: C 421 TYR cc_start: 0.9025 (m-80) cc_final: 0.8616 (m-10) REVERT: C 434 ILE cc_start: 0.9192 (mt) cc_final: 0.8741 (pp) REVERT: H 34 MET cc_start: 0.7333 (mmm) cc_final: 0.6728 (mmt) REVERT: H 48 ILE cc_start: 0.8035 (mt) cc_final: 0.7609 (mt) REVERT: H 79 TYR cc_start: 0.8198 (m-10) cc_final: 0.7981 (m-80) REVERT: H 82 MET cc_start: 0.6703 (ttt) cc_final: 0.6323 (tmt) REVERT: H 101 TYR cc_start: 0.8567 (m-80) cc_final: 0.8343 (m-80) outliers start: 2 outliers final: 1 residues processed: 182 average time/residue: 0.6620 time to fit residues: 139.8583 Evaluate side-chains 89 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 926 GLN A1002 GLN B 218 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 414 GLN C 580 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.092825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.055862 restraints weight = 75390.837| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.40 r_work: 0.2982 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24924 Z= 0.188 Angle : 0.584 10.988 34044 Z= 0.294 Chirality : 0.045 0.404 4020 Planarity : 0.004 0.059 4294 Dihedral : 6.757 58.975 4454 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.76 % Allowed : 5.67 % Favored : 93.57 % 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: 0.35 (0.15), residues: 2951 helix: 1.83 (0.20), residues: 658 sheet: 0.51 (0.20), residues: 662 loop : -0.54 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 408 TYR 0.026 0.001 TYR H 94 PHE 0.024 0.002 PHE H 29 TRP 0.029 0.002 TRP C 104 HIS 0.007 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00421 (24827) covalent geometry : angle 0.55930 (33791) SS BOND : bond 0.00223 ( 38) SS BOND : angle 0.77879 ( 76) hydrogen bonds : bond 0.04474 ( 901) hydrogen bonds : angle 5.83052 ( 2496) link_BETA1-4 : bond 0.00136 ( 18) link_BETA1-4 : angle 1.22313 ( 54) link_NAG-ASN : bond 0.00559 ( 41) link_NAG-ASN : angle 2.74357 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.116 Fit side-chains REVERT: A 1010 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8521 (mp10) REVERT: B 85 PRO cc_start: 0.8735 (Cg_exo) cc_final: 0.8168 (Cg_endo) REVERT: B 104 TRP cc_start: 0.7924 (m100) cc_final: 0.7706 (m100) REVERT: B 153 MET cc_start: 0.7235 (mpp) cc_final: 0.6554 (tpt) REVERT: B 198 ASP cc_start: 0.8558 (m-30) cc_final: 0.7807 (p0) REVERT: B 200 TYR cc_start: 0.8494 (m-10) cc_final: 0.7854 (m-80) REVERT: B 240 THR cc_start: 0.7172 (m) cc_final: 0.6599 (t) REVERT: B 990 GLU cc_start: 0.8743 (tt0) cc_final: 0.8282 (tm-30) REVERT: C 97 LYS cc_start: 0.8391 (pttt) cc_final: 0.7957 (tptp) REVERT: C 421 TYR cc_start: 0.9028 (m-80) cc_final: 0.8606 (m-10) REVERT: C 434 ILE cc_start: 0.9185 (mt) cc_final: 0.8705 (pp) REVERT: C 993 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9150 (mp) REVERT: H 34 MET cc_start: 0.6579 (mmm) cc_final: 0.6301 (mmp) REVERT: H 48 ILE cc_start: 0.7941 (mt) cc_final: 0.7734 (mp) REVERT: H 52 TYR cc_start: 0.8019 (m-80) cc_final: 0.7762 (m-80) REVERT: H 79 TYR cc_start: 0.8321 (m-10) cc_final: 0.8021 (m-80) REVERT: H 82 MET cc_start: 0.6705 (ttt) cc_final: 0.6480 (tmt) REVERT: H 99 TRP cc_start: 0.7142 (t60) cc_final: 0.6737 (t60) outliers start: 20 outliers final: 5 residues processed: 101 average time/residue: 0.6662 time to fit residues: 78.9664 Evaluate side-chains 85 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 133 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 241 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 196 ASN B 901 GLN B 955 ASN B1002 GLN C 121 ASN C1002 GLN ** H 35 HIS ** 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 = 0.4031 r_free = 0.4031 target = 0.092536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.055770 restraints weight = 75185.939| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.33 r_work: 0.3013 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24924 Z= 0.149 Angle : 0.534 10.505 34044 Z= 0.266 Chirality : 0.045 0.377 4020 Planarity : 0.004 0.051 4294 Dihedral : 5.885 59.602 4452 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.91 % Allowed : 6.77 % Favored : 92.32 % 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: 0.54 (0.15), residues: 2951 helix: 2.36 (0.20), residues: 647 sheet: 0.42 (0.20), residues: 656 loop : -0.47 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 452 TYR 0.026 0.001 TYR H 94 PHE 0.016 0.001 PHE C 238 TRP 0.024 0.002 TRP C 104 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00330 (24827) covalent geometry : angle 0.50974 (33791) SS BOND : bond 0.00126 ( 38) SS BOND : angle 0.60742 ( 76) hydrogen bonds : bond 0.04111 ( 901) hydrogen bonds : angle 5.44585 ( 2496) link_BETA1-4 : bond 0.00373 ( 18) link_BETA1-4 : angle 1.15964 ( 54) link_NAG-ASN : bond 0.00550 ( 41) link_NAG-ASN : angle 2.60900 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9046 (mtm) REVERT: B 153 MET cc_start: 0.7204 (mpp) cc_final: 0.6387 (tpt) REVERT: B 198 ASP cc_start: 0.8687 (m-30) cc_final: 0.7942 (p0) REVERT: B 200 TYR cc_start: 0.8491 (m-10) cc_final: 0.7856 (m-80) REVERT: B 240 THR cc_start: 0.7141 (m) cc_final: 0.6523 (t) REVERT: B 990 GLU cc_start: 0.8783 (tt0) cc_final: 0.8370 (tm-30) REVERT: C 421 TYR cc_start: 0.9041 (m-80) cc_final: 0.8652 (m-10) REVERT: C 434 ILE cc_start: 0.9217 (mt) cc_final: 0.8730 (pp) REVERT: C 455 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8043 (mt) REVERT: H 34 MET cc_start: 0.6686 (mmm) cc_final: 0.6368 (mmp) REVERT: H 82 MET cc_start: 0.6826 (ttt) cc_final: 0.6510 (tmt) REVERT: H 99 TRP cc_start: 0.7016 (t60) cc_final: 0.6653 (t60) outliers start: 24 outliers final: 9 residues processed: 96 average time/residue: 0.6385 time to fit residues: 72.3615 Evaluate side-chains 82 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 292 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 269 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN C 824 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.092041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055144 restraints weight = 75196.274| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.31 r_work: 0.2981 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24924 Z= 0.150 Angle : 0.520 10.391 34044 Z= 0.257 Chirality : 0.044 0.361 4020 Planarity : 0.003 0.044 4294 Dihedral : 5.438 58.319 4452 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.91 % Allowed : 7.61 % Favored : 91.48 % 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: 0.59 (0.15), residues: 2951 helix: 2.44 (0.20), residues: 654 sheet: 0.35 (0.20), residues: 651 loop : -0.42 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.020 0.001 TYR H 94 PHE 0.015 0.001 PHE A 898 TRP 0.025 0.002 TRP B 104 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00336 (24827) covalent geometry : angle 0.49610 (33791) SS BOND : bond 0.00121 ( 38) SS BOND : angle 0.54591 ( 76) hydrogen bonds : bond 0.04003 ( 901) hydrogen bonds : angle 5.29380 ( 2496) link_BETA1-4 : bond 0.00209 ( 18) link_BETA1-4 : angle 1.10768 ( 54) link_NAG-ASN : bond 0.00545 ( 41) link_NAG-ASN : angle 2.53067 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9050 (mtm) REVERT: B 153 MET cc_start: 0.7234 (mpp) cc_final: 0.6423 (tpt) REVERT: B 240 THR cc_start: 0.6870 (m) cc_final: 0.6109 (t) REVERT: B 740 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.9018 (tpp) REVERT: B 990 GLU cc_start: 0.8789 (tt0) cc_final: 0.8376 (tm-30) REVERT: C 421 TYR cc_start: 0.9000 (m-80) cc_final: 0.8650 (m-10) REVERT: C 434 ILE cc_start: 0.9224 (mt) cc_final: 0.8742 (pp) REVERT: H 34 MET cc_start: 0.6735 (mmm) cc_final: 0.6456 (mmp) REVERT: H 82 MET cc_start: 0.6931 (ttt) cc_final: 0.6612 (tmt) REVERT: H 99 TRP cc_start: 0.7009 (t60) cc_final: 0.6756 (t60) outliers start: 24 outliers final: 8 residues processed: 92 average time/residue: 0.6022 time to fit residues: 66.2435 Evaluate side-chains 79 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 196 ASN B 245 HIS B 824 ASN C 955 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.091998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055174 restraints weight = 74795.878| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.33 r_work: 0.2961 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24924 Z= 0.142 Angle : 0.508 10.311 34044 Z= 0.251 Chirality : 0.044 0.355 4020 Planarity : 0.003 0.041 4294 Dihedral : 5.121 56.552 4452 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.91 % Allowed : 8.22 % Favored : 90.87 % 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: 0.62 (0.15), residues: 2951 helix: 2.52 (0.20), residues: 654 sheet: 0.31 (0.20), residues: 654 loop : -0.40 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.021 0.001 TYR H 94 PHE 0.014 0.001 PHE A 898 TRP 0.026 0.001 TRP C 104 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00317 (24827) covalent geometry : angle 0.48501 (33791) SS BOND : bond 0.00111 ( 38) SS BOND : angle 0.53097 ( 76) hydrogen bonds : bond 0.03909 ( 901) hydrogen bonds : angle 5.19196 ( 2496) link_BETA1-4 : bond 0.00235 ( 18) link_BETA1-4 : angle 1.09514 ( 54) link_NAG-ASN : bond 0.00529 ( 41) link_NAG-ASN : angle 2.48223 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9049 (mtm) REVERT: B 153 MET cc_start: 0.7205 (mpp) cc_final: 0.6389 (tpt) REVERT: B 240 THR cc_start: 0.6996 (m) cc_final: 0.6428 (t) REVERT: B 990 GLU cc_start: 0.8801 (tt0) cc_final: 0.8359 (tm-30) REVERT: C 421 TYR cc_start: 0.8924 (m-80) cc_final: 0.8563 (m-10) REVERT: C 434 ILE cc_start: 0.9174 (mt) cc_final: 0.8696 (pp) REVERT: H 82 MET cc_start: 0.6910 (ttt) cc_final: 0.6589 (tmt) REVERT: H 99 TRP cc_start: 0.6909 (t60) cc_final: 0.6458 (t60) outliers start: 24 outliers final: 9 residues processed: 89 average time/residue: 0.6211 time to fit residues: 65.8244 Evaluate side-chains 77 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 42 optimal weight: 30.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 824 ASN B 49 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.090729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053909 restraints weight = 75143.532| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.30 r_work: 0.2954 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24924 Z= 0.219 Angle : 0.560 10.226 34044 Z= 0.277 Chirality : 0.045 0.366 4020 Planarity : 0.004 0.039 4294 Dihedral : 5.213 55.034 4452 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.95 % Allowed : 8.67 % Favored : 90.38 % 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: 0.49 (0.15), residues: 2951 helix: 2.40 (0.20), residues: 654 sheet: 0.17 (0.20), residues: 654 loop : -0.45 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 246 TYR 0.020 0.001 TYR C1067 PHE 0.019 0.001 PHE A 898 TRP 0.029 0.002 TRP C 104 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00495 (24827) covalent geometry : angle 0.53690 (33791) SS BOND : bond 0.00186 ( 38) SS BOND : angle 0.56275 ( 76) hydrogen bonds : bond 0.04376 ( 901) hydrogen bonds : angle 5.29933 ( 2496) link_BETA1-4 : bond 0.00180 ( 18) link_BETA1-4 : angle 1.25416 ( 54) link_NAG-ASN : bond 0.00593 ( 41) link_NAG-ASN : angle 2.56768 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9109 (mtm) REVERT: B 153 MET cc_start: 0.7210 (mpp) cc_final: 0.6411 (tpt) REVERT: B 238 PHE cc_start: 0.7058 (p90) cc_final: 0.6797 (p90) REVERT: B 240 THR cc_start: 0.7285 (m) cc_final: 0.6862 (t) REVERT: B 990 GLU cc_start: 0.8877 (tt0) cc_final: 0.8585 (tm-30) REVERT: C 421 TYR cc_start: 0.8965 (m-80) cc_final: 0.8550 (m-10) REVERT: H 34 MET cc_start: 0.6757 (mmm) cc_final: 0.6512 (mmp) REVERT: H 82 MET cc_start: 0.6978 (ttt) cc_final: 0.6649 (tmt) REVERT: H 99 TRP cc_start: 0.7183 (t60) cc_final: 0.6704 (t60) outliers start: 25 outliers final: 12 residues processed: 87 average time/residue: 0.6497 time to fit residues: 66.7965 Evaluate side-chains 80 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 32 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 255 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.090608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.054111 restraints weight = 74640.178| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.25 r_work: 0.2961 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24924 Z= 0.199 Angle : 0.535 10.257 34044 Z= 0.265 Chirality : 0.045 0.374 4020 Planarity : 0.003 0.040 4294 Dihedral : 5.166 52.757 4452 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.80 % Allowed : 8.90 % Favored : 90.30 % 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: 0.45 (0.15), residues: 2951 helix: 2.45 (0.20), residues: 660 sheet: 0.05 (0.20), residues: 642 loop : -0.47 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.017 0.001 TYR C1067 PHE 0.021 0.001 PHE A 565 TRP 0.030 0.002 TRP C 104 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00452 (24827) covalent geometry : angle 0.51282 (33791) SS BOND : bond 0.00183 ( 38) SS BOND : angle 0.56409 ( 76) hydrogen bonds : bond 0.04150 ( 901) hydrogen bonds : angle 5.22658 ( 2496) link_BETA1-4 : bond 0.00233 ( 18) link_BETA1-4 : angle 1.12276 ( 54) link_NAG-ASN : bond 0.00561 ( 41) link_NAG-ASN : angle 2.51143 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9051 (mtm) REVERT: B 153 MET cc_start: 0.6956 (mpp) cc_final: 0.6151 (tpt) REVERT: B 240 THR cc_start: 0.7470 (m) cc_final: 0.7117 (t) REVERT: B 990 GLU cc_start: 0.8883 (tt0) cc_final: 0.8548 (tm-30) REVERT: C 421 TYR cc_start: 0.8984 (m-80) cc_final: 0.8529 (m-10) REVERT: C 740 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.8778 (tmm) REVERT: H 38 ARG cc_start: 0.6783 (ppp-140) cc_final: 0.6257 (ptm-80) REVERT: H 82 MET cc_start: 0.7025 (ttt) cc_final: 0.6705 (tmt) REVERT: H 99 TRP cc_start: 0.7073 (t60) cc_final: 0.6699 (t60) outliers start: 21 outliers final: 11 residues processed: 83 average time/residue: 0.6351 time to fit residues: 61.9814 Evaluate side-chains 76 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 116 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 284 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 907 ASN C1002 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.088907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051947 restraints weight = 75498.195| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.34 r_work: 0.2903 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 24924 Z= 0.373 Angle : 0.674 10.112 34044 Z= 0.333 Chirality : 0.049 0.416 4020 Planarity : 0.004 0.040 4294 Dihedral : 5.849 54.674 4452 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.80 % Allowed : 9.32 % Favored : 89.88 % 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 (0.15), residues: 2951 helix: 2.07 (0.20), residues: 665 sheet: -0.16 (0.19), residues: 719 loop : -0.69 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 765 TYR 0.023 0.002 TYR A 756 PHE 0.027 0.002 PHE A 898 TRP 0.031 0.002 TRP C 104 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00850 (24827) covalent geometry : angle 0.65155 (33791) SS BOND : bond 0.00309 ( 38) SS BOND : angle 0.71971 ( 76) hydrogen bonds : bond 0.05067 ( 901) hydrogen bonds : angle 5.59619 ( 2496) link_BETA1-4 : bond 0.00322 ( 18) link_BETA1-4 : angle 1.55388 ( 54) link_NAG-ASN : bond 0.00819 ( 41) link_NAG-ASN : angle 2.80646 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7160 (mpp) cc_final: 0.6449 (tpt) REVERT: B 216 LEU cc_start: 0.7734 (tp) cc_final: 0.7476 (mp) REVERT: B 990 GLU cc_start: 0.8930 (tt0) cc_final: 0.8601 (tm-30) REVERT: C 196 ASN cc_start: 0.8335 (t0) cc_final: 0.7986 (m-40) REVERT: C 198 ASP cc_start: 0.7906 (m-30) cc_final: 0.7532 (m-30) REVERT: C 646 ARG cc_start: 0.8614 (tpt-90) cc_final: 0.7869 (tpm170) REVERT: C 740 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.8695 (tmm) REVERT: H 38 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6670 (ppp-140) REVERT: H 99 TRP cc_start: 0.7092 (t60) cc_final: 0.6745 (t60) outliers start: 21 outliers final: 10 residues processed: 85 average time/residue: 0.6544 time to fit residues: 65.5116 Evaluate side-chains 77 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 203 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN B 196 ASN C 580 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.090701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054272 restraints weight = 74735.306| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.33 r_work: 0.2945 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24924 Z= 0.120 Angle : 0.526 10.399 34044 Z= 0.260 Chirality : 0.044 0.387 4020 Planarity : 0.003 0.040 4294 Dihedral : 5.345 52.779 4452 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.61 % Allowed : 9.66 % Favored : 89.73 % 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: 0.40 (0.15), residues: 2951 helix: 2.52 (0.20), residues: 659 sheet: -0.09 (0.20), residues: 690 loop : -0.51 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.016 0.001 TYR C1067 PHE 0.021 0.001 PHE A 565 TRP 0.032 0.002 TRP C 104 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00263 (24827) covalent geometry : angle 0.50352 (33791) SS BOND : bond 0.00105 ( 38) SS BOND : angle 0.55541 ( 76) hydrogen bonds : bond 0.03975 ( 901) hydrogen bonds : angle 5.24473 ( 2496) link_BETA1-4 : bond 0.00277 ( 18) link_BETA1-4 : angle 1.05349 ( 54) link_NAG-ASN : bond 0.00505 ( 41) link_NAG-ASN : angle 2.48141 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7019 (mpp) cc_final: 0.6257 (tpt) REVERT: B 990 GLU cc_start: 0.8880 (tt0) cc_final: 0.8519 (tm-30) REVERT: C 740 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.8847 (tmm) REVERT: H 38 ARG cc_start: 0.6833 (ppp-140) cc_final: 0.6573 (ptm-80) REVERT: H 99 TRP cc_start: 0.6911 (t60) cc_final: 0.6591 (t60) outliers start: 16 outliers final: 10 residues processed: 77 average time/residue: 0.7041 time to fit residues: 63.2353 Evaluate side-chains 69 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 285 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 32 optimal weight: 0.0010 chunk 108 optimal weight: 9.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052784 restraints weight = 75145.628| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.29 r_work: 0.2899 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24924 Z= 0.265 Angle : 0.597 10.351 34044 Z= 0.295 Chirality : 0.046 0.397 4020 Planarity : 0.004 0.040 4294 Dihedral : 5.475 55.327 4452 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.53 % Allowed : 9.89 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 2951 helix: 2.36 (0.20), residues: 666 sheet: -0.14 (0.19), residues: 715 loop : -0.61 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 765 TYR 0.021 0.001 TYR H 94 PHE 0.019 0.002 PHE A 898 TRP 0.026 0.002 TRP C 104 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00602 (24827) covalent geometry : angle 0.57555 (33791) SS BOND : bond 0.00230 ( 38) SS BOND : angle 0.60930 ( 76) hydrogen bonds : bond 0.04536 ( 901) hydrogen bonds : angle 5.41959 ( 2496) link_BETA1-4 : bond 0.00221 ( 18) link_BETA1-4 : angle 1.32614 ( 54) link_NAG-ASN : bond 0.00645 ( 41) link_NAG-ASN : angle 2.60149 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7145 (mpp) cc_final: 0.6489 (tpt) REVERT: B 990 GLU cc_start: 0.8922 (tt0) cc_final: 0.8642 (tm-30) REVERT: C 135 PHE cc_start: 0.7679 (m-80) cc_final: 0.6870 (p90) REVERT: C 196 ASN cc_start: 0.8274 (t0) cc_final: 0.7998 (m-40) REVERT: C 421 TYR cc_start: 0.8960 (m-80) cc_final: 0.8529 (m-10) REVERT: C 646 ARG cc_start: 0.8582 (tpt-90) cc_final: 0.7893 (tpm170) REVERT: C 740 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.8716 (tmm) REVERT: H 99 TRP cc_start: 0.6909 (t60) cc_final: 0.6596 (t60) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.6939 time to fit residues: 58.6221 Evaluate side-chains 74 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 135 optimal weight: 0.9980 chunk 238 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.089839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.053459 restraints weight = 75250.454| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.30 r_work: 0.2914 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24924 Z= 0.192 Angle : 0.549 10.354 34044 Z= 0.272 Chirality : 0.045 0.393 4020 Planarity : 0.003 0.040 4294 Dihedral : 5.326 57.422 4452 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.68 % Allowed : 9.97 % Favored : 89.35 % 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: 0.35 (0.15), residues: 2951 helix: 2.52 (0.20), residues: 659 sheet: -0.10 (0.20), residues: 690 loop : -0.58 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.021 0.001 TYR H 94 PHE 0.020 0.001 PHE A 565 TRP 0.027 0.002 TRP C 104 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00438 (24827) covalent geometry : angle 0.52755 (33791) SS BOND : bond 0.00145 ( 38) SS BOND : angle 0.58238 ( 76) hydrogen bonds : bond 0.04141 ( 901) hydrogen bonds : angle 5.30071 ( 2496) link_BETA1-4 : bond 0.00226 ( 18) link_BETA1-4 : angle 1.12458 ( 54) link_NAG-ASN : bond 0.00538 ( 41) link_NAG-ASN : angle 2.50721 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16241.23 seconds wall clock time: 275 minutes 43.59 seconds (16543.59 seconds total)