Starting phenix.real_space_refine on Sat Jun 21 05:38:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlx_27519/06_2025/8dlx_27519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlx_27519/06_2025/8dlx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlx_27519/06_2025/8dlx_27519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlx_27519/06_2025/8dlx_27519.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlx_27519/06_2025/8dlx_27519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlx_27519/06_2025/8dlx_27519.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.27, per 1000 atoms: 0.59 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: 6.38 Conformation dependent library (CDL) restraints added in 3.2 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: 3.34 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: 10.73 Time building geometry restraints manager: 7.53 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 1147 or resid 1301 thr \ ough 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 57.740 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.150 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (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 TRP 0.065 0.003 TRP H 99 HIS 0.013 0.001 HIS H 35 PHE 0.057 0.002 PHE C 486 TYR 0.031 0.002 TYR C1067 ARG 0.014 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00738 ( 41) link_NAG-ASN : angle 3.52487 ( 123) link_BETA1-4 : bond 0.00625 ( 18) link_BETA1-4 : angle 1.44673 ( 54) hydrogen bonds : bond 0.12787 ( 901) hydrogen bonds : angle 7.27238 ( 2496) SS BOND : bond 0.00290 ( 38) SS BOND : angle 1.32975 ( 76) covalent geometry : bond 0.00503 (24827) covalent geometry : angle 0.83228 (33791) *********************** 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 : 2.589 Fit side-chains revert: symmetry clash 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: 0.7706 (p0) REVERT: B 200 TYR cc_start: 0.8560 (m-10) cc_final: 0.7871 (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: H 34 MET cc_start: 0.7333 (mmm) cc_final: 0.6735 (mmt) REVERT: H 48 ILE cc_start: 0.8035 (mt) cc_final: 0.7617 (mt) REVERT: H 79 TYR cc_start: 0.8198 (m-10) cc_final: 0.7981 (m-80) REVERT: H 100 LEU cc_start: 0.8291 (mt) cc_final: 0.8007 (mp) REVERT: H 101 TYR cc_start: 0.8567 (m-80) cc_final: 0.8327 (m-80) outliers start: 2 outliers final: 1 residues processed: 182 average time/residue: 1.2667 time to fit residues: 269.7954 Evaluate side-chains 91 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 2.870 ------------------------------------------------------------------------------- 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 252 optimal weight: 2.9990 chunk 226 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 234 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 173 GLN B 218 GLN B 245 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 414 GLN C 580 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.093041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.056287 restraints weight = 74773.821| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.25 r_work: 0.2997 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24924 Z= 0.165 Angle : 0.569 10.845 34044 Z= 0.287 Chirality : 0.045 0.382 4020 Planarity : 0.004 0.060 4294 Dihedral : 6.747 58.525 4454 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.72 % Allowed : 5.97 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2951 helix: 1.96 (0.20), residues: 650 sheet: 0.45 (0.20), residues: 668 loop : -0.52 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 104 HIS 0.007 0.001 HIS B 245 PHE 0.019 0.001 PHE C 238 TYR 0.023 0.001 TYR H 94 ARG 0.006 0.001 ARG C 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 41) link_NAG-ASN : angle 2.73876 ( 123) link_BETA1-4 : bond 0.00076 ( 18) link_BETA1-4 : angle 1.19569 ( 54) hydrogen bonds : bond 0.04342 ( 901) hydrogen bonds : angle 5.81456 ( 2496) SS BOND : bond 0.00281 ( 38) SS BOND : angle 0.73518 ( 76) covalent geometry : bond 0.00369 (24827) covalent geometry : angle 0.54325 (33791) *********************** 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 117 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 2.586 Fit side-chains REVERT: B 85 PRO cc_start: 0.8788 (Cg_exo) cc_final: 0.8245 (Cg_endo) REVERT: B 153 MET cc_start: 0.7237 (mpp) cc_final: 0.6550 (tpt) REVERT: B 198 ASP cc_start: 0.8524 (m-30) cc_final: 0.7804 (p0) REVERT: B 200 TYR cc_start: 0.8553 (m-10) cc_final: 0.7919 (m-80) REVERT: B 240 THR cc_start: 0.7140 (m) cc_final: 0.6551 (t) REVERT: B 990 GLU cc_start: 0.8725 (tt0) cc_final: 0.8295 (tm-30) REVERT: C 97 LYS cc_start: 0.8371 (pttt) cc_final: 0.7948 (tptp) REVERT: C 392 PHE cc_start: 0.8446 (m-80) cc_final: 0.7968 (m-80) REVERT: C 421 TYR cc_start: 0.9010 (m-80) cc_final: 0.8611 (m-10) REVERT: C 740 MET cc_start: 0.9255 (tpp) cc_final: 0.9017 (tpp) REVERT: C 993 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9156 (mp) REVERT: H 59 TYR cc_start: 0.7548 (m-80) cc_final: 0.6981 (m-80) REVERT: H 82 MET cc_start: 0.6497 (tpt) cc_final: 0.6263 (tmt) REVERT: H 99 TRP cc_start: 0.7300 (t60) cc_final: 0.6872 (t60) outliers start: 19 outliers final: 3 residues processed: 107 average time/residue: 1.2199 time to fit residues: 154.8804 Evaluate side-chains 82 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 244 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A1002 GLN B 196 ASN B 901 GLN B 955 ASN C 121 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.093140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.056455 restraints weight = 74561.112| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.36 r_work: 0.3001 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24924 Z= 0.120 Angle : 0.523 10.538 34044 Z= 0.259 Chirality : 0.044 0.360 4020 Planarity : 0.004 0.051 4294 Dihedral : 5.927 58.437 4452 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.72 % Allowed : 6.88 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 2951 helix: 2.47 (0.21), residues: 639 sheet: 0.40 (0.20), residues: 660 loop : -0.44 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 104 HIS 0.004 0.001 HIS B 245 PHE 0.016 0.001 PHE C 238 TYR 0.024 0.001 TYR H 94 ARG 0.006 0.000 ARG C 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 41) link_NAG-ASN : angle 2.58005 ( 123) link_BETA1-4 : bond 0.00315 ( 18) link_BETA1-4 : angle 1.10807 ( 54) hydrogen bonds : bond 0.03936 ( 901) hydrogen bonds : angle 5.41635 ( 2496) SS BOND : bond 0.00121 ( 38) SS BOND : angle 0.59585 ( 76) covalent geometry : bond 0.00262 (24827) covalent geometry : angle 0.49842 (33791) *********************** 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: 19 poor density : 86 time to evaluate : 2.673 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9063 (mtm) REVERT: A 1010 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8891 (mp10) REVERT: B 85 PRO cc_start: 0.8991 (Cg_exo) cc_final: 0.8128 (Cg_endo) REVERT: B 104 TRP cc_start: 0.7777 (m100) cc_final: 0.7507 (m100) REVERT: B 153 MET cc_start: 0.7178 (mpp) cc_final: 0.6404 (tpt) REVERT: B 198 ASP cc_start: 0.8607 (m-30) cc_final: 0.7931 (p0) REVERT: B 200 TYR cc_start: 0.8517 (m-10) cc_final: 0.7873 (m-80) REVERT: B 238 PHE cc_start: 0.6150 (p90) cc_final: 0.5881 (p90) REVERT: B 240 THR cc_start: 0.6741 (m) cc_final: 0.6163 (t) REVERT: B 269 TYR cc_start: 0.8656 (m-80) cc_final: 0.8120 (m-80) REVERT: B 990 GLU cc_start: 0.8768 (tt0) cc_final: 0.8351 (tm-30) REVERT: B 1029 MET cc_start: 0.9651 (tpp) cc_final: 0.9365 (tpp) REVERT: C 421 TYR cc_start: 0.8984 (m-80) cc_final: 0.8634 (m-10) REVERT: C 993 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9122 (mp) REVERT: H 79 TYR cc_start: 0.7569 (m-10) cc_final: 0.7363 (m-80) REVERT: H 82 MET cc_start: 0.6366 (tpt) cc_final: 0.6095 (tmt) REVERT: H 99 TRP cc_start: 0.7242 (t60) cc_final: 0.6872 (t60) outliers start: 19 outliers final: 6 residues processed: 98 average time/residue: 1.1837 time to fit residues: 139.8578 Evaluate side-chains 82 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET 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 57 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 116 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 824 ASN A 957 GLN B 824 ASN C 779 GLN C 824 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.090409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.053114 restraints weight = 75833.078| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.32 r_work: 0.2935 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 24924 Z= 0.326 Angle : 0.652 10.437 34044 Z= 0.323 Chirality : 0.048 0.412 4020 Planarity : 0.004 0.052 4294 Dihedral : 5.982 58.831 4452 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.91 % Allowed : 7.76 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 2951 helix: 2.15 (0.20), residues: 650 sheet: 0.09 (0.19), residues: 664 loop : -0.50 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 104 HIS 0.005 0.001 HIS C1058 PHE 0.025 0.002 PHE B 275 TYR 0.024 0.002 TYR A 756 ARG 0.008 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 41) link_NAG-ASN : angle 2.78197 ( 123) link_BETA1-4 : bond 0.00244 ( 18) link_BETA1-4 : angle 1.38784 ( 54) hydrogen bonds : bond 0.04972 ( 901) hydrogen bonds : angle 5.60650 ( 2496) SS BOND : bond 0.00307 ( 38) SS BOND : angle 0.77668 ( 76) covalent geometry : bond 0.00738 (24827) covalent geometry : angle 0.62865 (33791) *********************** 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 98 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9157 (mtm) REVERT: A 1010 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8893 (mp10) REVERT: B 153 MET cc_start: 0.7243 (mpp) cc_final: 0.6525 (tpt) REVERT: B 240 THR cc_start: 0.7405 (m) cc_final: 0.6923 (t) REVERT: B 990 GLU cc_start: 0.8864 (tt0) cc_final: 0.8547 (tm-30) REVERT: C 421 TYR cc_start: 0.9067 (m-80) cc_final: 0.8716 (m-10) REVERT: H 79 TYR cc_start: 0.7379 (m-80) cc_final: 0.7178 (m-80) REVERT: H 82 MET cc_start: 0.6439 (tpt) cc_final: 0.6063 (tmt) REVERT: H 99 TRP cc_start: 0.7308 (t60) cc_final: 0.6799 (t-100) REVERT: H 101 TYR cc_start: 0.7970 (m-80) cc_final: 0.7767 (m-80) outliers start: 24 outliers final: 8 residues processed: 92 average time/residue: 1.3063 time to fit residues: 143.3203 Evaluate side-chains 74 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN 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 1010 GLN 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 206 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 289 optimal weight: 20.0000 chunk 214 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1002 GLN ** 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 = 0.4010 r_free = 0.4010 target = 0.091469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.054693 restraints weight = 75290.554| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.34 r_work: 0.2944 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24924 Z= 0.146 Angle : 0.527 10.304 34044 Z= 0.261 Chirality : 0.044 0.389 4020 Planarity : 0.003 0.048 4294 Dihedral : 5.533 55.259 4452 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.91 % Allowed : 8.33 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 2951 helix: 2.44 (0.20), residues: 651 sheet: 0.07 (0.20), residues: 636 loop : -0.45 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.003 0.001 HIS B 245 PHE 0.021 0.001 PHE C 238 TYR 0.018 0.001 TYR H 94 ARG 0.007 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 41) link_NAG-ASN : angle 2.55828 ( 123) link_BETA1-4 : bond 0.00256 ( 18) link_BETA1-4 : angle 1.06760 ( 54) hydrogen bonds : bond 0.04078 ( 901) hydrogen bonds : angle 5.31786 ( 2496) SS BOND : bond 0.00112 ( 38) SS BOND : angle 0.54612 ( 76) covalent geometry : bond 0.00327 (24827) covalent geometry : angle 0.50395 (33791) *********************** 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 100 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9027 (mtm) REVERT: B 153 MET cc_start: 0.7162 (mpp) cc_final: 0.6325 (tpt) REVERT: B 240 THR cc_start: 0.7080 (m) cc_final: 0.6319 (t) REVERT: B 990 GLU cc_start: 0.8835 (tt0) cc_final: 0.8471 (tm-30) REVERT: C 421 TYR cc_start: 0.9006 (m-80) cc_final: 0.8543 (m-10) REVERT: C 1145 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8272 (pt) REVERT: H 99 TRP cc_start: 0.7227 (t60) cc_final: 0.6796 (t60) outliers start: 24 outliers final: 8 residues processed: 93 average time/residue: 1.3710 time to fit residues: 153.7673 Evaluate side-chains 76 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 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 1010 GLN Chi-restraints excluded: chain C residue 1145 LEU 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 160 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 207 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 250 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 755 GLN B 49 HIS B 196 ASN B 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.091685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055075 restraints weight = 74976.047| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.33 r_work: 0.2977 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24924 Z= 0.125 Angle : 0.509 10.361 34044 Z= 0.251 Chirality : 0.044 0.369 4020 Planarity : 0.003 0.046 4294 Dihedral : 5.135 54.733 4452 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.84 % Allowed : 8.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 2951 helix: 2.61 (0.20), residues: 646 sheet: 0.08 (0.20), residues: 635 loop : -0.40 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 104 HIS 0.002 0.000 HIS H 35 PHE 0.019 0.001 PHE C 238 TYR 0.021 0.001 TYR H 94 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 41) link_NAG-ASN : angle 2.46457 ( 123) link_BETA1-4 : bond 0.00248 ( 18) link_BETA1-4 : angle 1.09376 ( 54) hydrogen bonds : bond 0.03857 ( 901) hydrogen bonds : angle 5.14037 ( 2496) SS BOND : bond 0.00105 ( 38) SS BOND : angle 0.52154 ( 76) covalent geometry : bond 0.00278 (24827) covalent geometry : angle 0.48608 (33791) *********************** 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 94 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9031 (mtm) REVERT: B 153 MET cc_start: 0.7203 (mpp) cc_final: 0.6336 (tpt) REVERT: B 200 TYR cc_start: 0.8480 (m-80) cc_final: 0.8234 (m-80) REVERT: B 240 THR cc_start: 0.6984 (m) cc_final: 0.6494 (t) REVERT: B 740 MET cc_start: 0.9362 (tpp) cc_final: 0.9122 (ttt) REVERT: B 990 GLU cc_start: 0.8852 (tt0) cc_final: 0.8501 (tm-30) REVERT: B 1029 MET cc_start: 0.9582 (tpp) cc_final: 0.9339 (tpp) REVERT: C 135 PHE cc_start: 0.7410 (m-80) cc_final: 0.6639 (p90) REVERT: C 421 TYR cc_start: 0.9000 (m-80) cc_final: 0.8594 (m-10) REVERT: H 34 MET cc_start: 0.6816 (mmp) cc_final: 0.6573 (mmm) REVERT: H 99 TRP cc_start: 0.7240 (t60) cc_final: 0.6725 (t-100) outliers start: 22 outliers final: 10 residues processed: 86 average time/residue: 1.3258 time to fit residues: 135.9862 Evaluate side-chains 74 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 2.799 ------------------------------------------------------------------------------- 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 1010 GLN 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 213 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.090262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.053444 restraints weight = 75555.619| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.34 r_work: 0.2942 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24924 Z= 0.250 Angle : 0.577 10.225 34044 Z= 0.286 Chirality : 0.046 0.380 4020 Planarity : 0.004 0.046 4294 Dihedral : 5.296 54.335 4452 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.76 % Allowed : 8.90 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 2951 helix: 2.44 (0.20), residues: 652 sheet: 0.01 (0.20), residues: 650 loop : -0.47 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 104 HIS 0.003 0.001 HIS C1058 PHE 0.019 0.001 PHE A 898 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00624 ( 41) link_NAG-ASN : angle 2.58298 ( 123) link_BETA1-4 : bond 0.00164 ( 18) link_BETA1-4 : angle 1.25776 ( 54) hydrogen bonds : bond 0.04452 ( 901) hydrogen bonds : angle 5.30107 ( 2496) SS BOND : bond 0.00197 ( 38) SS BOND : angle 0.57614 ( 76) covalent geometry : bond 0.00571 (24827) covalent geometry : angle 0.55490 (33791) *********************** 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 89 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.6992 (m-10) cc_final: 0.6723 (m-10) REVERT: A 900 MET cc_start: 0.9461 (OUTLIER) cc_final: 0.9124 (mtm) REVERT: B 153 MET cc_start: 0.6991 (mpp) cc_final: 0.6345 (tpt) REVERT: B 240 THR cc_start: 0.7299 (m) cc_final: 0.7075 (t) REVERT: B 740 MET cc_start: 0.9400 (tpp) cc_final: 0.8955 (ttt) REVERT: B 990 GLU cc_start: 0.8855 (tt0) cc_final: 0.8580 (tm-30) REVERT: C 135 PHE cc_start: 0.7529 (m-80) cc_final: 0.6689 (p90) REVERT: C 740 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.8715 (tmm) REVERT: H 34 MET cc_start: 0.6806 (mmp) cc_final: 0.6455 (mmm) REVERT: H 38 ARG cc_start: 0.6613 (ppp-140) cc_final: 0.6119 (ptm-80) REVERT: H 99 TRP cc_start: 0.7219 (t60) cc_final: 0.6816 (t-100) outliers start: 20 outliers final: 12 residues processed: 81 average time/residue: 1.4134 time to fit residues: 135.8215 Evaluate side-chains 77 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 582 LEU 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 1010 GLN 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 69 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 204 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 chunk 181 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.091219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.054519 restraints weight = 74901.828| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.35 r_work: 0.2951 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2798 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= 0.128 Angle : 0.516 10.323 34044 Z= 0.256 Chirality : 0.044 0.372 4020 Planarity : 0.003 0.043 4294 Dihedral : 5.082 52.439 4452 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.72 % Allowed : 9.21 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 2951 helix: 2.63 (0.20), residues: 652 sheet: 0.01 (0.20), residues: 654 loop : -0.39 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.013 0.001 HIS H 35 PHE 0.021 0.001 PHE A 565 TYR 0.016 0.001 TYR H 94 ARG 0.010 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 41) link_NAG-ASN : angle 2.44636 ( 123) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 1.06582 ( 54) hydrogen bonds : bond 0.03924 ( 901) hydrogen bonds : angle 5.13091 ( 2496) SS BOND : bond 0.00112 ( 38) SS BOND : angle 0.51693 ( 76) covalent geometry : bond 0.00286 (24827) covalent geometry : angle 0.49388 (33791) *********************** 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 86 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 2.659 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9027 (mtm) REVERT: B 153 MET cc_start: 0.6958 (mpp) cc_final: 0.6216 (tpt) REVERT: B 240 THR cc_start: 0.7339 (m) cc_final: 0.7022 (t) REVERT: B 740 MET cc_start: 0.9396 (tpp) cc_final: 0.8954 (ttt) REVERT: B 990 GLU cc_start: 0.8853 (tt0) cc_final: 0.8484 (tm-30) REVERT: C 740 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.8789 (tmm) REVERT: H 34 MET cc_start: 0.6655 (mmp) cc_final: 0.6420 (mmm) REVERT: H 99 TRP cc_start: 0.6784 (t60) cc_final: 0.6521 (t-100) outliers start: 19 outliers final: 9 residues processed: 79 average time/residue: 1.3320 time to fit residues: 124.4930 Evaluate side-chains 71 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 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 1010 GLN 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 294 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.091061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054342 restraints weight = 75190.089| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.30 r_work: 0.2963 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2860 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= 0.146 Angle : 0.519 10.303 34044 Z= 0.258 Chirality : 0.044 0.367 4020 Planarity : 0.004 0.117 4294 Dihedral : 4.988 52.174 4452 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.61 % Allowed : 9.47 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 2951 helix: 2.66 (0.20), residues: 652 sheet: 0.06 (0.20), residues: 658 loop : -0.38 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 104 HIS 0.003 0.000 HIS H 35 PHE 0.016 0.001 PHE C 238 TYR 0.024 0.001 TYR C 200 ARG 0.008 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 41) link_NAG-ASN : angle 2.42960 ( 123) link_BETA1-4 : bond 0.00206 ( 18) link_BETA1-4 : angle 1.10436 ( 54) hydrogen bonds : bond 0.03966 ( 901) hydrogen bonds : angle 5.10790 ( 2496) SS BOND : bond 0.00113 ( 38) SS BOND : angle 0.52043 ( 76) covalent geometry : bond 0.00328 (24827) covalent geometry : angle 0.49715 (33791) *********************** 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 81 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 3.005 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9043 (mtm) REVERT: B 153 MET cc_start: 0.6856 (mpp) cc_final: 0.6114 (tpt) REVERT: B 240 THR cc_start: 0.7405 (m) cc_final: 0.7146 (t) REVERT: B 990 GLU cc_start: 0.8871 (tt0) cc_final: 0.8517 (tm-30) REVERT: C 135 PHE cc_start: 0.7648 (m-80) cc_final: 0.6727 (p90) REVERT: C 458 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8706 (mmtm) REVERT: C 740 MET cc_start: 0.9480 (OUTLIER) cc_final: 0.8829 (tmm) REVERT: H 38 ARG cc_start: 0.6591 (ppp-140) cc_final: 0.6320 (ptm-80) REVERT: H 46 GLU cc_start: 0.7376 (pp20) cc_final: 0.7098 (pp20) REVERT: H 99 TRP cc_start: 0.6650 (t60) cc_final: 0.6353 (t-100) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 1.3477 time to fit residues: 119.1316 Evaluate side-chains 74 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 2.874 ------------------------------------------------------------------------------- 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 1010 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 71 optimal weight: 0.9990 chunk 100 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 262 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.091400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.054958 restraints weight = 75150.282| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.33 r_work: 0.2967 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24924 Z= 0.117 Angle : 0.502 10.371 34044 Z= 0.249 Chirality : 0.044 0.360 4020 Planarity : 0.003 0.063 4294 Dihedral : 4.788 52.783 4452 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 2951 helix: 2.78 (0.20), residues: 646 sheet: -0.05 (0.20), residues: 634 loop : -0.32 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 104 HIS 0.002 0.000 HIS B 245 PHE 0.021 0.001 PHE A 565 TYR 0.021 0.001 TYR H 94 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 41) link_NAG-ASN : angle 2.37173 ( 123) link_BETA1-4 : bond 0.00260 ( 18) link_BETA1-4 : angle 1.03567 ( 54) hydrogen bonds : bond 0.03738 ( 901) hydrogen bonds : angle 5.01500 ( 2496) SS BOND : bond 0.00116 ( 38) SS BOND : angle 0.51760 ( 76) covalent geometry : bond 0.00259 (24827) covalent geometry : angle 0.48099 (33791) ********************** 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 84 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 2.768 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.9037 (mtm) REVERT: B 153 MET cc_start: 0.6873 (mpp) cc_final: 0.6158 (tpt) REVERT: B 238 PHE cc_start: 0.6967 (p90) cc_final: 0.6373 (p90) REVERT: B 240 THR cc_start: 0.7419 (m) cc_final: 0.7036 (t) REVERT: B 990 GLU cc_start: 0.8862 (tt0) cc_final: 0.8497 (tm-30) REVERT: B 1029 MET cc_start: 0.9596 (tpp) cc_final: 0.9371 (tpp) REVERT: C 324 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.9017 (pm20) REVERT: C 458 LYS cc_start: 0.9045 (mmtt) cc_final: 0.8708 (mmtm) REVERT: C 740 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.8826 (tmm) REVERT: H 99 TRP cc_start: 0.6512 (t60) cc_final: 0.6215 (t-100) outliers start: 16 outliers final: 9 residues processed: 77 average time/residue: 1.3701 time to fit residues: 124.7916 Evaluate side-chains 75 residues out of total 2629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 2.647 ------------------------------------------------------------------------------- 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 C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU 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 1010 GLN Chi-restraints excluded: chain H residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 0 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 273 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.091303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.054795 restraints weight = 75019.739| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.36 r_work: 0.2965 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24924 Z= 0.124 Angle : 0.501 10.381 34044 Z= 0.249 Chirality : 0.044 0.354 4020 Planarity : 0.003 0.049 4294 Dihedral : 4.700 52.974 4452 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.53 % Allowed : 9.97 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 2951 helix: 2.79 (0.20), residues: 646 sheet: 0.04 (0.21), residues: 636 loop : -0.30 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 104 HIS 0.003 0.001 HIS H 53 PHE 0.015 0.001 PHE C 238 TYR 0.019 0.001 TYR H 94 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 41) link_NAG-ASN : angle 2.36784 ( 123) link_BETA1-4 : bond 0.00239 ( 18) link_BETA1-4 : angle 1.07305 ( 54) hydrogen bonds : bond 0.03765 ( 901) hydrogen bonds : angle 4.99279 ( 2496) SS BOND : bond 0.00097 ( 38) SS BOND : angle 0.50056 ( 76) covalent geometry : bond 0.00276 (24827) covalent geometry : angle 0.47984 (33791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37141.97 seconds wall clock time: 647 minutes 50.71 seconds (38870.71 seconds total)