Starting phenix.real_space_refine on Fri Jun 27 05:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm3_27525/06_2025/8dm3_27525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm3_27525/06_2025/8dm3_27525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm3_27525/06_2025/8dm3_27525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm3_27525/06_2025/8dm3_27525.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm3_27525/06_2025/8dm3_27525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm3_27525/06_2025/8dm3_27525.cif" } resolution = 2.37 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= -0.001 sd= 0.024 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 150 5.16 5 C 19836 2.51 5 N 5109 2.21 5 O 6090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31185 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8291 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 55, 'TRANS': 1000} Chain breaks: 6 Chain: "B" Number of atoms: 8291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8291 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 55, 'TRANS': 1000} Chain breaks: 6 Chain: "C" Number of atoms: 8291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8291 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 55, 'TRANS': 1000} Chain breaks: 6 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "P" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "Q" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} 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: "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: "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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: 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: "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: 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 Time building chain proxies: 19.56, per 1000 atoms: 0.63 Number of scatterers: 31185 At special positions: 0 Unit cell: (202, 213, 199, 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 150 16.00 O 6090 8.00 N 5109 7.00 C 19836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 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=2.04 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 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.04 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 115 " distance=2.04 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 113 " distance=2.05 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 115 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 113 " 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 O 1 " - " NAG O 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG D 1 " - " ASN A 122 " " 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 122 " " NAG O 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 122 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 8.60 Conformation dependent library (CDL) restraints added in 4.1 seconds 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7248 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 65 sheets defined 20.4% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.763A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.683A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.788A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.080A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 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: 3.673A 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 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.083A 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 removed outlier: 3.964A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.001A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.918A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.676A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.861A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.742A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.059A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 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: 3.650A 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 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.156A 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 removed outlier: 3.622A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.510A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.072A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (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 371 removed outlier: 4.115A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.895A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.817A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.665A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.636A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.048A 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: 3.603A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.283A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.866A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 49 No H-bonds generated for 'chain 'M' and resid 47 through 49' Processing helix chain 'M' and resid 106 through 110 removed outlier: 4.101A pdb=" N THR M 110 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 49 No H-bonds generated for 'chain 'P' and resid 47 through 49' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.355A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.442A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.996A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.589A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.625A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.932A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.935A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.923A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.124A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.978A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.548A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.563A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.563A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.314A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.652A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.690A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.847A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.967A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.814A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.814A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.285A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.266A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.985A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.354A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.271A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.962A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.486A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.554A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.554A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.386A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.747A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.008A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.804A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.804A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.058A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.210A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.590A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.933A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.570A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.570A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.376A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'H' and resid 24 through 25 removed outlier: 3.714A pdb=" N LEU H 102 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.957A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 29 through 31 Processing sheet with id=AF6, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AF7, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AF8, first strand: chain 'L' and resid 30 through 32 removed outlier: 4.417A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 22 through 25 Processing sheet with id=AG1, first strand: chain 'M' and resid 29 through 31 removed outlier: 6.097A pdb=" N MET M 53 " --> pdb=" O PHE M 70 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ARG M 57 " --> pdb=" O TRP M 66 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N TRP M 66 " --> pdb=" O ARG M 57 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 29 through 31 Processing sheet with id=AG3, first strand: chain 'M' and resid 121 through 123 Processing sheet with id=AG4, first strand: chain 'N' and resid 24 through 27 Processing sheet with id=AG5, first strand: chain 'N' and resid 78 through 79 removed outlier: 4.113A pdb=" N ASN N 78 " --> pdb=" O TYR N 74 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR N 74 " --> pdb=" O ASN N 78 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU N 71 " --> pdb=" O GLN N 62 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN N 62 " --> pdb=" O LEU N 71 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 22 through 25 Processing sheet with id=AG7, first strand: chain 'P' and resid 29 through 31 removed outlier: 6.580A pdb=" N MET P 53 " --> pdb=" O GLY P 69 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY P 69 " --> pdb=" O MET P 53 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP P 55 " --> pdb=" O MET P 67 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 29 through 31 Processing sheet with id=AG9, first strand: chain 'P' and resid 121 through 123 Processing sheet with id=AH1, first strand: chain 'Q' and resid 24 through 27 Processing sheet with id=AH2, first strand: chain 'Q' and resid 30 through 32 removed outlier: 3.531A pdb=" N SER Q 31 " --> pdb=" O LYS Q 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP Q 130 " --> pdb=" O SER Q 31 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU Q 58 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR Q 74 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP Q 60 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3561 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: 18.11 Time building geometry restraints manager: 10.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9758 1.34 - 1.47: 8197 1.47 - 1.60: 13746 1.60 - 1.72: 0 1.72 - 1.85: 201 Bond restraints: 31902 Sorted by residual: bond pdb=" CG PRO P 72 " pdb=" CD PRO P 72 " ideal model delta sigma weight residual 1.503 1.382 0.121 3.40e-02 8.65e+02 1.26e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.49e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.47e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.11e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 31897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 42570 2.63 - 5.26: 716 5.26 - 7.89: 84 7.89 - 10.51: 17 10.51 - 13.14: 5 Bond angle restraints: 43392 Sorted by residual: angle pdb=" CA PRO P 72 " pdb=" N PRO P 72 " pdb=" CD PRO P 72 " ideal model delta sigma weight residual 112.00 99.61 12.39 1.40e+00 5.10e-01 7.83e+01 angle pdb=" N PRO P 72 " pdb=" CD PRO P 72 " pdb=" CG PRO P 72 " ideal model delta sigma weight residual 103.20 93.28 9.92 1.50e+00 4.44e-01 4.38e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.96 -7.26 1.22e+00 6.72e-01 3.54e+01 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.58 -7.12 1.41e+00 5.03e-01 2.55e+01 ... (remaining 43387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 18187 17.44 - 34.87: 1221 34.87 - 52.31: 216 52.31 - 69.75: 72 69.75 - 87.19: 44 Dihedral angle restraints: 19740 sinusoidal: 8445 harmonic: 11295 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -22.92 -63.08 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CA PHE C 392 " pdb=" C PHE C 392 " pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA PRO A 589 " pdb=" C PRO A 589 " pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 19737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4392 0.085 - 0.170: 624 0.170 - 0.256: 24 0.256 - 0.341: 2 0.341 - 0.426: 1 Chirality restraints: 5043 Sorted by residual: chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB ILE A 794 " pdb=" CA ILE A 794 " pdb=" CG1 ILE A 794 " pdb=" CG2 ILE A 794 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB ILE C 101 " pdb=" CA ILE C 101 " pdb=" CG1 ILE C 101 " pdb=" CG2 ILE C 101 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 5040 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP P 71 " -0.098 5.00e-02 4.00e+02 1.38e-01 3.07e+01 pdb=" N PRO P 72 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO P 72 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO P 72 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.088 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO C 561 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO C 463 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.064 5.00e-02 4.00e+02 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5562 2.78 - 3.31: 26543 3.31 - 3.84: 52743 3.84 - 4.37: 61141 4.37 - 4.90: 105660 Nonbonded interactions: 251649 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 605 " pdb=" OE1 GLN A 607 " model vdw 2.250 3.040 nonbonded pdb=" O SER L 45 " pdb=" OG1 THR L 94 " model vdw 2.276 3.040 nonbonded pdb=" OE2 GLU M 73 " pdb=" OH TYR M 132 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.290 3.040 ... (remaining 251644 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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: 8.350 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: 0.040 Extract box with map and model: 1.420 Check model and map are aligned: 0.220 Set scattering table: 0.320 Process input model: 82.580 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.121 32007 Z= 0.226 Angle : 0.849 13.142 43659 Z= 0.445 Chirality : 0.055 0.426 5043 Planarity : 0.008 0.138 5529 Dihedral : 12.925 87.185 12348 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.24 % Allowed : 0.77 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.56 (0.12), residues: 3834 helix: -0.01 (0.18), residues: 693 sheet: 0.41 (0.15), residues: 1029 loop : -0.88 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP P 66 HIS 0.010 0.001 HIS A 954 PHE 0.044 0.002 PHE A 906 TYR 0.028 0.002 TYR C1067 ARG 0.018 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 39) link_NAG-ASN : angle 2.28057 ( 117) link_BETA1-4 : bond 0.00669 ( 18) link_BETA1-4 : angle 1.70889 ( 54) hydrogen bonds : bond 0.11199 ( 1258) hydrogen bonds : angle 7.19678 ( 3561) SS BOND : bond 0.00378 ( 48) SS BOND : angle 1.48082 ( 96) covalent geometry : bond 0.00485 (31902) covalent geometry : angle 0.83869 (43392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 331 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7550 (mtmm) cc_final: 0.7269 (mttm) REVERT: A 140 PHE cc_start: 0.5851 (p90) cc_final: 0.5641 (p90) REVERT: A 201 PHE cc_start: 0.7628 (t80) cc_final: 0.7411 (t80) REVERT: A 237 ARG cc_start: 0.7458 (mtp180) cc_final: 0.7200 (mmt90) REVERT: A 238 PHE cc_start: 0.6360 (p90) cc_final: 0.6112 (p90) REVERT: A 326 ILE cc_start: 0.7381 (mm) cc_final: 0.6932 (pp) REVERT: B 238 PHE cc_start: 0.6914 (p90) cc_final: 0.6395 (p90) REVERT: B 242 LEU cc_start: 0.8053 (mt) cc_final: 0.7684 (mp) REVERT: B 392 PHE cc_start: 0.6177 (m-80) cc_final: 0.5875 (m-80) REVERT: B 467 ASP cc_start: 0.6377 (t0) cc_final: 0.5455 (t0) REVERT: C 121 ASN cc_start: 0.5628 (m-40) cc_final: 0.5392 (t0) REVERT: C 140 PHE cc_start: 0.5251 (p90) cc_final: 0.4706 (p90) REVERT: C 417 ASN cc_start: 0.7535 (t0) cc_final: 0.7207 (t0) REVERT: C 456 PHE cc_start: 0.7024 (m-10) cc_final: 0.6706 (m-80) REVERT: C 493 ARG cc_start: 0.6762 (mmt-90) cc_final: 0.6288 (mmp80) REVERT: C 512 VAL cc_start: 0.8444 (t) cc_final: 0.8073 (m) REVERT: C 988 GLU cc_start: 0.7114 (tp30) cc_final: 0.6781 (tp30) REVERT: M 39 VAL cc_start: 0.1423 (t) cc_final: 0.0992 (t) REVERT: M 52 SER cc_start: 0.1672 (m) cc_final: 0.1250 (p) REVERT: M 53 MET cc_start: 0.1579 (tpt) cc_final: 0.0180 (ttm) REVERT: M 121 VAL cc_start: 0.3794 (m) cc_final: 0.3466 (t) REVERT: N 24 MET cc_start: -0.0625 (mmt) cc_final: -0.1654 (ttp) outliers start: 8 outliers final: 4 residues processed: 337 average time/residue: 1.2917 time to fit residues: 528.1079 Evaluate side-chains 176 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 68 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 245 HIS A 536 ASN A 613 GLN A 755 GLN A 824 ASN A 907 ASN B 115 GLN B 245 HIS B 394 ASN B 564 GLN B 824 ASN B 856 ASN B 872 GLN B 926 GLN B 957 GLN B1005 GLN B1010 GLN B1011 GLN C 23 GLN C 245 HIS C 271 GLN C 417 ASN C 439 ASN C 824 ASN C 856 ASN C 907 ASN C 926 GLN L 63 GLN L 67 GLN L 78 ASN M 58 GLN P 58 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.159114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.098589 restraints weight = 64768.738| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.22 r_work: 0.3271 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32007 Z= 0.141 Angle : 0.593 12.645 43659 Z= 0.303 Chirality : 0.045 0.460 5043 Planarity : 0.005 0.078 5529 Dihedral : 6.745 86.153 5392 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.27 % Allowed : 6.76 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 3834 helix: 1.27 (0.19), residues: 709 sheet: 0.49 (0.15), residues: 1064 loop : -0.54 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 152 HIS 0.006 0.001 HIS H 54 PHE 0.021 0.001 PHE A 906 TYR 0.025 0.001 TYR C 170 ARG 0.006 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 39) link_NAG-ASN : angle 2.07594 ( 117) link_BETA1-4 : bond 0.00399 ( 18) link_BETA1-4 : angle 1.18922 ( 54) hydrogen bonds : bond 0.04213 ( 1258) hydrogen bonds : angle 5.72520 ( 3561) SS BOND : bond 0.00282 ( 48) SS BOND : angle 0.85965 ( 96) covalent geometry : bond 0.00319 (31902) covalent geometry : angle 0.58226 (43392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7700 (t80) cc_final: 0.7307 (t80) REVERT: A 214 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.8007 (tpt-90) REVERT: A 237 ARG cc_start: 0.7597 (mtp180) cc_final: 0.6986 (mmt90) REVERT: A 239 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6438 (mm110) REVERT: A 583 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: A 592 PHE cc_start: 0.7152 (p90) cc_final: 0.6753 (p90) REVERT: B 238 PHE cc_start: 0.7064 (p90) cc_final: 0.6519 (p90) REVERT: B 242 LEU cc_start: 0.8055 (mt) cc_final: 0.7634 (mp) REVERT: B 269 TYR cc_start: 0.7531 (m-10) cc_final: 0.7180 (m-80) REVERT: B 387 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6848 (mm) REVERT: B 558 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7975 (ptpt) REVERT: B 1142 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6988 (tp40) REVERT: C 140 PHE cc_start: 0.5468 (p90) cc_final: 0.4971 (p90) REVERT: C 200 TYR cc_start: 0.4996 (m-80) cc_final: 0.4772 (m-80) REVERT: C 456 PHE cc_start: 0.6923 (m-10) cc_final: 0.6554 (m-80) REVERT: C 512 VAL cc_start: 0.8392 (t) cc_final: 0.8058 (m) REVERT: C 988 GLU cc_start: 0.8453 (tp30) cc_final: 0.7511 (tp30) REVERT: M 134 MET cc_start: 0.1828 (tpp) cc_final: -0.0081 (mpt) REVERT: N 24 MET cc_start: 0.0677 (mmt) cc_final: -0.0665 (ttp) REVERT: P 89 MET cc_start: 0.3052 (tpt) cc_final: 0.0752 (ppp) REVERT: P 100 MET cc_start: -0.3016 (mmm) cc_final: -0.3823 (tpp) REVERT: Q 24 MET cc_start: 0.1316 (OUTLIER) cc_final: 0.1106 (mtt) outliers start: 43 outliers final: 13 residues processed: 226 average time/residue: 1.7104 time to fit residues: 481.0535 Evaluate side-chains 169 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 24 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 194 optimal weight: 8.9990 chunk 357 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 381 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 168 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 280 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS C 460 ASN C 505 HIS ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.167776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.110958 restraints weight = 60210.106| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.02 r_work: 0.3204 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32007 Z= 0.182 Angle : 0.587 11.105 43659 Z= 0.300 Chirality : 0.045 0.193 5043 Planarity : 0.004 0.068 5529 Dihedral : 6.190 64.361 5390 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.68 % Allowed : 8.35 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.27 (0.13), residues: 3834 helix: 1.61 (0.19), residues: 717 sheet: 0.46 (0.15), residues: 1057 loop : -0.45 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 152 HIS 0.005 0.001 HIS C1058 PHE 0.030 0.002 PHE C 168 TYR 0.028 0.002 TYR B 170 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 39) link_NAG-ASN : angle 2.01976 ( 117) link_BETA1-4 : bond 0.00335 ( 18) link_BETA1-4 : angle 1.25923 ( 54) hydrogen bonds : bond 0.04345 ( 1258) hydrogen bonds : angle 5.56969 ( 3561) SS BOND : bond 0.00253 ( 48) SS BOND : angle 0.90772 ( 96) covalent geometry : bond 0.00418 (31902) covalent geometry : angle 0.57613 (43392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.7718 (t80) cc_final: 0.7307 (t80) REVERT: A 237 ARG cc_start: 0.7535 (mtp180) cc_final: 0.6972 (mmt90) REVERT: A 581 THR cc_start: 0.8590 (p) cc_final: 0.8092 (p) REVERT: A 583 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7295 (pm20) REVERT: A 586 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: A 1010 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: B 18 LEU cc_start: 0.5212 (tp) cc_final: 0.4938 (tt) REVERT: B 238 PHE cc_start: 0.7247 (p90) cc_final: 0.6809 (p90) REVERT: B 242 LEU cc_start: 0.8023 (mt) cc_final: 0.7665 (mp) REVERT: B 244 LEU cc_start: 0.5785 (mm) cc_final: 0.5561 (mm) REVERT: B 269 TYR cc_start: 0.7610 (m-10) cc_final: 0.7384 (m-80) REVERT: B 439 ASN cc_start: 0.6469 (m-40) cc_final: 0.6109 (m-40) REVERT: B 558 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8044 (ptpt) REVERT: B 902 MET cc_start: 0.9214 (tpp) cc_final: 0.9012 (mmm) REVERT: B 1142 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7434 (tp40) REVERT: C 140 PHE cc_start: 0.5637 (p90) cc_final: 0.5114 (p90) REVERT: C 340 GLU cc_start: 0.8297 (mp0) cc_final: 0.8045 (mp0) REVERT: C 357 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6952 (tpt170) REVERT: C 456 PHE cc_start: 0.6963 (m-10) cc_final: 0.6584 (m-80) REVERT: C 556 ASN cc_start: 0.7415 (p0) cc_final: 0.7211 (p0) REVERT: C 869 MET cc_start: 0.9075 (mtm) cc_final: 0.8855 (mtp) REVERT: C 988 GLU cc_start: 0.8447 (tp30) cc_final: 0.7564 (tp30) REVERT: M 134 MET cc_start: 0.1620 (OUTLIER) cc_final: -0.0140 (mpt) REVERT: N 24 MET cc_start: 0.0728 (mmt) cc_final: -0.1069 (tmt) REVERT: P 67 MET cc_start: 0.1575 (mtt) cc_final: 0.0619 (tpp) outliers start: 57 outliers final: 24 residues processed: 204 average time/residue: 1.1834 time to fit residues: 298.6457 Evaluate side-chains 173 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain L residue 67 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 134 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 43 optimal weight: 0.0060 chunk 153 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 173 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.157593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096754 restraints weight = 64495.527| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.10 r_work: 0.3226 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32007 Z= 0.122 Angle : 0.538 11.105 43659 Z= 0.275 Chirality : 0.044 0.195 5043 Planarity : 0.004 0.064 5529 Dihedral : 5.749 59.463 5384 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.59 % Allowed : 9.59 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.41 (0.13), residues: 3834 helix: 1.88 (0.20), residues: 716 sheet: 0.49 (0.15), residues: 1042 loop : -0.38 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.003 0.001 HIS B 69 PHE 0.020 0.001 PHE C 392 TYR 0.022 0.001 TYR A1067 ARG 0.005 0.000 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 39) link_NAG-ASN : angle 1.80752 ( 117) link_BETA1-4 : bond 0.00279 ( 18) link_BETA1-4 : angle 1.14568 ( 54) hydrogen bonds : bond 0.03845 ( 1258) hydrogen bonds : angle 5.37014 ( 3561) SS BOND : bond 0.00208 ( 48) SS BOND : angle 0.83326 ( 96) covalent geometry : bond 0.00272 (31902) covalent geometry : angle 0.52835 (43392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7556 (mtp180) cc_final: 0.6974 (mmt90) REVERT: A 581 THR cc_start: 0.8643 (p) cc_final: 0.8173 (p) REVERT: A 583 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: A 586 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: B 18 LEU cc_start: 0.5349 (tp) cc_final: 0.5064 (tt) REVERT: B 68 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7892 (tp) REVERT: B 439 ASN cc_start: 0.6520 (m-40) cc_final: 0.6267 (m-40) REVERT: B 515 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7279 (m-10) REVERT: B 558 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8013 (ptpt) REVERT: B 1142 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7087 (tp40) REVERT: C 140 PHE cc_start: 0.5557 (p90) cc_final: 0.5076 (p90) REVERT: C 177 MET cc_start: 0.5871 (pmm) cc_final: 0.5039 (ppp) REVERT: C 237 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7125 (ttp-110) REVERT: C 340 GLU cc_start: 0.8376 (mp0) cc_final: 0.8077 (mp0) REVERT: C 456 PHE cc_start: 0.7089 (m-10) cc_final: 0.6725 (m-80) REVERT: C 556 ASN cc_start: 0.7496 (p0) cc_final: 0.7240 (p0) REVERT: C 988 GLU cc_start: 0.8455 (tp30) cc_final: 0.7557 (tp30) REVERT: M 89 MET cc_start: -0.2091 (ptm) cc_final: -0.2341 (ptp) REVERT: M 134 MET cc_start: 0.1520 (OUTLIER) cc_final: -0.0191 (mpt) REVERT: N 24 MET cc_start: 0.0891 (mmt) cc_final: -0.0948 (tmt) REVERT: P 67 MET cc_start: 0.1771 (mtt) cc_final: 0.0752 (tpp) REVERT: Q 24 MET cc_start: 0.1379 (mtt) cc_final: 0.0902 (mtp) outliers start: 54 outliers final: 22 residues processed: 188 average time/residue: 1.1688 time to fit residues: 272.6958 Evaluate side-chains 171 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain M residue 134 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 303 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 383 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 361 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 856 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.153015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.093929 restraints weight = 64582.389| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.94 r_work: 0.3182 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 32007 Z= 0.279 Angle : 0.667 12.518 43659 Z= 0.339 Chirality : 0.049 0.233 5043 Planarity : 0.005 0.065 5529 Dihedral : 6.169 59.156 5384 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.48 % Allowed : 10.03 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.17 (0.13), residues: 3834 helix: 1.64 (0.20), residues: 704 sheet: 0.30 (0.15), residues: 1078 loop : -0.49 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 104 HIS 0.006 0.001 HIS C1058 PHE 0.026 0.002 PHE A 238 TYR 0.027 0.002 TYR A1067 ARG 0.004 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 39) link_NAG-ASN : angle 2.37533 ( 117) link_BETA1-4 : bond 0.00268 ( 18) link_BETA1-4 : angle 1.35725 ( 54) hydrogen bonds : bond 0.04938 ( 1258) hydrogen bonds : angle 5.81060 ( 3561) SS BOND : bond 0.00414 ( 48) SS BOND : angle 1.03751 ( 96) covalent geometry : bond 0.00651 (31902) covalent geometry : angle 0.65430 (43392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 136 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8395 (tt0) cc_final: 0.7869 (tm-30) REVERT: A 220 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7259 (t80) REVERT: A 237 ARG cc_start: 0.7691 (mtp180) cc_final: 0.7014 (mmt90) REVERT: A 558 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8012 (mmpt) REVERT: A 586 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6687 (m-30) REVERT: B 347 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6355 (m-10) REVERT: B 558 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8141 (ptpt) REVERT: C 140 PHE cc_start: 0.5956 (p90) cc_final: 0.5436 (p90) REVERT: C 177 MET cc_start: 0.5991 (pmm) cc_final: 0.4957 (ppp) REVERT: C 237 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7421 (ttp-110) REVERT: C 340 GLU cc_start: 0.8486 (mp0) cc_final: 0.8189 (mp0) REVERT: C 357 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7583 (tpm-80) REVERT: C 456 PHE cc_start: 0.7402 (m-10) cc_final: 0.7117 (m-80) REVERT: C 869 MET cc_start: 0.9164 (mtm) cc_final: 0.8903 (mtp) REVERT: C 988 GLU cc_start: 0.8610 (tp30) cc_final: 0.7637 (tp30) REVERT: C 1092 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8263 (tm-30) REVERT: H 53 MET cc_start: 0.2217 (ppp) cc_final: 0.1562 (ttt) REVERT: M 53 MET cc_start: 0.2135 (tpt) cc_final: 0.1611 (mtm) REVERT: M 134 MET cc_start: 0.1587 (OUTLIER) cc_final: 0.0033 (mpt) REVERT: N 24 MET cc_start: 0.0265 (mmt) cc_final: -0.1873 (tmt) REVERT: P 67 MET cc_start: 0.1598 (mtt) cc_final: 0.0741 (tpp) REVERT: Q 24 MET cc_start: 0.1462 (mtt) cc_final: 0.0977 (mtp) outliers start: 84 outliers final: 38 residues processed: 204 average time/residue: 1.2378 time to fit residues: 313.7838 Evaluate side-chains 168 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain M residue 134 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 353 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 373 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 160 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.164010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.105236 restraints weight = 62030.353| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.43 r_work: 0.3205 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32007 Z= 0.171 Angle : 0.574 13.076 43659 Z= 0.291 Chirality : 0.045 0.214 5043 Planarity : 0.004 0.063 5529 Dihedral : 5.800 57.089 5384 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.21 % Allowed : 10.88 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.30 (0.13), residues: 3834 helix: 1.92 (0.20), residues: 705 sheet: 0.33 (0.15), residues: 1063 loop : -0.43 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.007 0.001 HIS B 69 PHE 0.020 0.001 PHE A 238 TYR 0.022 0.001 TYR C1067 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 39) link_NAG-ASN : angle 1.97585 ( 117) link_BETA1-4 : bond 0.00261 ( 18) link_BETA1-4 : angle 1.14115 ( 54) hydrogen bonds : bond 0.04152 ( 1258) hydrogen bonds : angle 5.53085 ( 3561) SS BOND : bond 0.00298 ( 48) SS BOND : angle 0.84835 ( 96) covalent geometry : bond 0.00393 (31902) covalent geometry : angle 0.56329 (43392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 129 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7610 (mtp180) cc_final: 0.7062 (mmt90) REVERT: A 558 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8002 (mmpt) REVERT: A 581 THR cc_start: 0.8741 (p) cc_final: 0.8496 (p) REVERT: A 586 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: B 177 MET cc_start: 0.6355 (pmm) cc_final: 0.6010 (pmm) REVERT: B 515 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7396 (m-10) REVERT: B 580 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7903 (mm110) REVERT: C 140 PHE cc_start: 0.5926 (p90) cc_final: 0.5439 (p90) REVERT: C 177 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5498 (ppp) REVERT: C 237 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7106 (ttp-110) REVERT: C 239 GLN cc_start: 0.7950 (tp40) cc_final: 0.7203 (mm110) REVERT: C 340 GLU cc_start: 0.8418 (mp0) cc_final: 0.8156 (mp0) REVERT: C 357 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7604 (tpm-80) REVERT: C 456 PHE cc_start: 0.7295 (m-10) cc_final: 0.7038 (m-80) REVERT: C 556 ASN cc_start: 0.7708 (p0) cc_final: 0.7386 (p0) REVERT: C 988 GLU cc_start: 0.8552 (tp30) cc_final: 0.7607 (tp30) REVERT: C 1092 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8274 (tm-30) REVERT: H 53 MET cc_start: 0.2340 (ppp) cc_final: 0.1651 (ttt) REVERT: M 53 MET cc_start: 0.2401 (tpt) cc_final: 0.1845 (mtm) REVERT: M 89 MET cc_start: -0.1788 (ptp) cc_final: -0.2153 (pmm) REVERT: N 24 MET cc_start: 0.0403 (mmt) cc_final: -0.1947 (tmt) REVERT: N 61 LEU cc_start: 0.0706 (OUTLIER) cc_final: -0.0066 (tt) REVERT: P 67 MET cc_start: 0.1638 (mtt) cc_final: 0.0826 (tpp) REVERT: P 89 MET cc_start: 0.2708 (OUTLIER) cc_final: 0.0435 (ppp) REVERT: P 100 MET cc_start: -0.3198 (mmm) cc_final: -0.3591 (tpp) REVERT: Q 24 MET cc_start: 0.1203 (mtt) cc_final: 0.0769 (mtp) outliers start: 75 outliers final: 42 residues processed: 189 average time/residue: 1.1411 time to fit residues: 267.9232 Evaluate side-chains 172 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 34 optimal weight: 9.9990 chunk 369 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 270 optimal weight: 0.0980 chunk 350 optimal weight: 0.6980 chunk 351 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.156237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.096316 restraints weight = 63919.834| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.05 r_work: 0.3193 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32007 Z= 0.122 Angle : 0.544 11.983 43659 Z= 0.275 Chirality : 0.044 0.215 5043 Planarity : 0.004 0.061 5529 Dihedral : 5.454 59.040 5384 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.92 % Allowed : 11.71 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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 (0.13), residues: 3834 helix: 2.15 (0.20), residues: 699 sheet: 0.32 (0.15), residues: 1049 loop : -0.41 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 137 HIS 0.005 0.001 HIS H 54 PHE 0.025 0.001 PHE C 168 TYR 0.024 0.001 TYR A 170 ARG 0.003 0.000 ARG M 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 39) link_NAG-ASN : angle 1.78569 ( 117) link_BETA1-4 : bond 0.00295 ( 18) link_BETA1-4 : angle 1.11995 ( 54) hydrogen bonds : bond 0.03781 ( 1258) hydrogen bonds : angle 5.33162 ( 3561) SS BOND : bond 0.00221 ( 48) SS BOND : angle 0.77929 ( 96) covalent geometry : bond 0.00274 (31902) covalent geometry : angle 0.53456 (43392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 5.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8438 (tt0) cc_final: 0.7854 (tm-30) REVERT: A 237 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7008 (mmt90) REVERT: A 558 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8074 (mmpt) REVERT: A 586 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: B 18 LEU cc_start: 0.5383 (tp) cc_final: 0.5087 (mt) REVERT: B 177 MET cc_start: 0.6245 (pmm) cc_final: 0.5847 (pmm) REVERT: B 244 LEU cc_start: 0.6419 (mm) cc_final: 0.6150 (mt) REVERT: B 515 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: B 580 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7859 (mm110) REVERT: B 964 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8863 (mtpt) REVERT: B 1142 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7490 (tp40) REVERT: C 140 PHE cc_start: 0.5906 (p90) cc_final: 0.5358 (p90) REVERT: C 177 MET cc_start: 0.6211 (pmm) cc_final: 0.5541 (pp-130) REVERT: C 237 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7063 (ttp-110) REVERT: C 239 GLN cc_start: 0.7984 (tp40) cc_final: 0.7189 (mm110) REVERT: C 340 GLU cc_start: 0.8427 (mp0) cc_final: 0.8114 (mp0) REVERT: C 456 PHE cc_start: 0.7326 (m-10) cc_final: 0.7049 (m-80) REVERT: C 532 ASN cc_start: 0.8652 (t0) cc_final: 0.8008 (t0) REVERT: C 556 ASN cc_start: 0.7623 (p0) cc_final: 0.7290 (p0) REVERT: C 988 GLU cc_start: 0.8541 (tp30) cc_final: 0.7584 (tp30) REVERT: C 1092 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8238 (tm-30) REVERT: H 53 MET cc_start: 0.2238 (ppp) cc_final: 0.1753 (ttt) REVERT: M 53 MET cc_start: 0.2510 (tpt) cc_final: 0.1996 (mtm) REVERT: M 89 MET cc_start: -0.1457 (ptp) cc_final: -0.1739 (pmm) REVERT: N 24 MET cc_start: 0.1493 (mmt) cc_final: -0.1162 (tmt) REVERT: N 61 LEU cc_start: 0.0745 (OUTLIER) cc_final: -0.0088 (tt) REVERT: Q 24 MET cc_start: 0.2155 (mtt) cc_final: 0.1742 (mtp) outliers start: 65 outliers final: 35 residues processed: 184 average time/residue: 1.2195 time to fit residues: 281.6239 Evaluate side-chains 166 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 274 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 332 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 378 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.155212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.095502 restraints weight = 63316.253| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.96 r_work: 0.3182 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32007 Z= 0.166 Angle : 0.571 11.310 43659 Z= 0.289 Chirality : 0.045 0.216 5043 Planarity : 0.004 0.061 5529 Dihedral : 5.412 54.336 5384 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.92 % Allowed : 11.95 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.34 (0.13), residues: 3834 helix: 2.01 (0.20), residues: 711 sheet: 0.30 (0.15), residues: 1061 loop : -0.42 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 137 HIS 0.003 0.001 HIS B1058 PHE 0.020 0.001 PHE C 392 TYR 0.024 0.001 TYR C1067 ARG 0.006 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 39) link_NAG-ASN : angle 1.86691 ( 117) link_BETA1-4 : bond 0.00250 ( 18) link_BETA1-4 : angle 1.14297 ( 54) hydrogen bonds : bond 0.04037 ( 1258) hydrogen bonds : angle 5.37723 ( 3561) SS BOND : bond 0.00253 ( 48) SS BOND : angle 0.80496 ( 96) covalent geometry : bond 0.00382 (31902) covalent geometry : angle 0.56136 (43392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 127 time to evaluate : 9.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8451 (tt0) cc_final: 0.7903 (tm-30) REVERT: A 237 ARG cc_start: 0.7608 (mtp180) cc_final: 0.6987 (mmt90) REVERT: A 558 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8081 (mmpt) REVERT: A 586 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: B 177 MET cc_start: 0.6297 (pmm) cc_final: 0.5889 (pmm) REVERT: B 244 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6275 (mt) REVERT: B 515 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: B 558 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8111 (ptpt) REVERT: B 580 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7898 (mm110) REVERT: C 140 PHE cc_start: 0.5898 (p90) cc_final: 0.5345 (p90) REVERT: C 177 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5615 (pp-130) REVERT: C 237 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7094 (ttp-110) REVERT: C 357 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7551 (tpm-80) REVERT: C 456 PHE cc_start: 0.7480 (m-10) cc_final: 0.7207 (m-80) REVERT: C 556 ASN cc_start: 0.7665 (p0) cc_final: 0.7357 (p0) REVERT: C 988 GLU cc_start: 0.8531 (tp30) cc_final: 0.7563 (tp30) REVERT: M 53 MET cc_start: 0.2642 (tpt) cc_final: 0.1908 (mtm) REVERT: M 89 MET cc_start: -0.1516 (ptp) cc_final: -0.1829 (pmm) REVERT: M 134 MET cc_start: 0.0741 (tpp) cc_final: -0.0893 (mpt) REVERT: N 24 MET cc_start: 0.1229 (mmt) cc_final: -0.1400 (tmt) REVERT: N 61 LEU cc_start: 0.0661 (OUTLIER) cc_final: -0.0153 (tt) REVERT: Q 24 MET cc_start: 0.1770 (mtt) cc_final: 0.1345 (mtp) outliers start: 65 outliers final: 42 residues processed: 180 average time/residue: 1.5502 time to fit residues: 352.4929 Evaluate side-chains 174 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 178 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 253 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.155205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.094106 restraints weight = 63098.030| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.16 r_work: 0.3165 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32007 Z= 0.219 Angle : 0.619 14.765 43659 Z= 0.311 Chirality : 0.046 0.217 5043 Planarity : 0.004 0.061 5529 Dihedral : 5.532 54.118 5382 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.98 % Allowed : 12.15 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.28 (0.13), residues: 3834 helix: 1.92 (0.20), residues: 705 sheet: 0.30 (0.15), residues: 1052 loop : -0.45 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 152 HIS 0.009 0.001 HIS B 69 PHE 0.033 0.002 PHE C 168 TYR 0.026 0.002 TYR A 170 ARG 0.008 0.001 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 39) link_NAG-ASN : angle 2.02189 ( 117) link_BETA1-4 : bond 0.00244 ( 18) link_BETA1-4 : angle 1.18916 ( 54) hydrogen bonds : bond 0.04372 ( 1258) hydrogen bonds : angle 5.53188 ( 3561) SS BOND : bond 0.00302 ( 48) SS BOND : angle 0.89371 ( 96) covalent geometry : bond 0.00509 (31902) covalent geometry : angle 0.60919 (43392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8463 (tt0) cc_final: 0.7906 (tm-30) REVERT: A 237 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7027 (mmt90) REVERT: A 239 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6233 (mp10) REVERT: A 581 THR cc_start: 0.8594 (p) cc_final: 0.8348 (p) REVERT: B 462 LYS cc_start: 0.6460 (mptt) cc_final: 0.6025 (mttt) REVERT: B 580 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7889 (mm110) REVERT: C 140 PHE cc_start: 0.6084 (p90) cc_final: 0.5567 (p90) REVERT: C 177 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5568 (ppp) REVERT: C 237 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7074 (ttp-110) REVERT: C 239 GLN cc_start: 0.8117 (tp40) cc_final: 0.7289 (mm110) REVERT: C 357 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7229 (tpt170) REVERT: C 456 PHE cc_start: 0.7537 (m-10) cc_final: 0.7250 (m-80) REVERT: C 532 ASN cc_start: 0.8720 (t0) cc_final: 0.8142 (t0) REVERT: C 869 MET cc_start: 0.9112 (mtm) cc_final: 0.8864 (mtp) REVERT: C 988 GLU cc_start: 0.8594 (tp30) cc_final: 0.7615 (tp30) REVERT: H 53 MET cc_start: 0.2632 (ppp) cc_final: 0.1978 (tmt) REVERT: L 24 MET cc_start: 0.3769 (OUTLIER) cc_final: 0.3261 (pmm) REVERT: M 53 MET cc_start: 0.2504 (tpt) cc_final: 0.1598 (mtm) REVERT: M 89 MET cc_start: -0.1645 (ptp) cc_final: -0.1962 (pmm) REVERT: M 134 MET cc_start: 0.0701 (tpp) cc_final: -0.0851 (mpt) REVERT: N 24 MET cc_start: 0.0809 (mmt) cc_final: -0.1739 (tmt) REVERT: N 61 LEU cc_start: 0.0538 (OUTLIER) cc_final: -0.0342 (tt) REVERT: P 89 MET cc_start: 0.1205 (tpt) cc_final: -0.0935 (ptm) REVERT: P 100 MET cc_start: -0.2262 (tpp) cc_final: -0.2516 (tpp) outliers start: 67 outliers final: 43 residues processed: 183 average time/residue: 1.3228 time to fit residues: 298.2519 Evaluate side-chains 172 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 247 optimal weight: 0.3980 chunk 217 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 147 optimal weight: 0.2980 chunk 376 optimal weight: 7.9990 chunk 77 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 460 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.155795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.096272 restraints weight = 63814.825| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.28 r_work: 0.3186 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32007 Z= 0.119 Angle : 0.567 13.105 43659 Z= 0.285 Chirality : 0.044 0.226 5043 Planarity : 0.004 0.060 5529 Dihedral : 5.226 54.540 5382 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.45 % Allowed : 12.98 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.36 (0.13), residues: 3834 helix: 2.10 (0.20), residues: 711 sheet: 0.30 (0.15), residues: 1045 loop : -0.43 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 152 HIS 0.005 0.001 HIS B 245 PHE 0.020 0.001 PHE C 392 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 39) link_NAG-ASN : angle 1.73695 ( 117) link_BETA1-4 : bond 0.00332 ( 18) link_BETA1-4 : angle 1.10370 ( 54) hydrogen bonds : bond 0.03767 ( 1258) hydrogen bonds : angle 5.30478 ( 3561) SS BOND : bond 0.00214 ( 48) SS BOND : angle 0.77553 ( 96) covalent geometry : bond 0.00268 (31902) covalent geometry : angle 0.55924 (43392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8475 (tt0) cc_final: 0.7905 (tm-30) REVERT: A 237 ARG cc_start: 0.7542 (mtp180) cc_final: 0.6945 (mmt90) REVERT: A 239 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5954 (mp10) REVERT: A 581 THR cc_start: 0.8534 (p) cc_final: 0.8317 (p) REVERT: B 177 MET cc_start: 0.6356 (pmm) cc_final: 0.5785 (pmm) REVERT: B 462 LYS cc_start: 0.6697 (mptt) cc_final: 0.6236 (mttt) REVERT: B 515 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: C 117 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5963 (tp) REVERT: C 140 PHE cc_start: 0.5883 (p90) cc_final: 0.5371 (p90) REVERT: C 177 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.5773 (pp-130) REVERT: C 237 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6993 (ttp-110) REVERT: C 239 GLN cc_start: 0.8055 (tp40) cc_final: 0.7222 (mm110) REVERT: C 357 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7094 (tpt170) REVERT: C 456 PHE cc_start: 0.7428 (m-10) cc_final: 0.7191 (m-80) REVERT: C 532 ASN cc_start: 0.8668 (t0) cc_final: 0.8077 (t0) REVERT: C 988 GLU cc_start: 0.8536 (tp30) cc_final: 0.7571 (tp30) REVERT: H 53 MET cc_start: 0.2358 (ppp) cc_final: 0.1851 (ttt) REVERT: L 24 MET cc_start: 0.4222 (OUTLIER) cc_final: 0.3780 (pmm) REVERT: M 53 MET cc_start: 0.2595 (tpt) cc_final: 0.1792 (mtm) REVERT: M 89 MET cc_start: -0.1585 (ptp) cc_final: -0.1847 (pmm) REVERT: N 24 MET cc_start: 0.1196 (mmt) cc_final: -0.1508 (tmt) REVERT: N 61 LEU cc_start: 0.0676 (OUTLIER) cc_final: -0.0276 (tt) REVERT: P 89 MET cc_start: 0.1929 (OUTLIER) cc_final: -0.0393 (ppp) REVERT: P 100 MET cc_start: -0.2382 (tpp) cc_final: -0.2910 (tpp) REVERT: P 144 THR cc_start: 0.2087 (OUTLIER) cc_final: 0.1794 (p) REVERT: Q 24 MET cc_start: 0.1663 (mtt) cc_final: 0.1195 (mtp) outliers start: 49 outliers final: 34 residues processed: 165 average time/residue: 1.1806 time to fit residues: 243.7066 Evaluate side-chains 169 residues out of total 3390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 56 VAL Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 144 THR Chi-restraints excluded: chain Q residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 8 optimal weight: 10.0000 chunk 335 optimal weight: 8.9990 chunk 268 optimal weight: 0.5980 chunk 244 optimal weight: 0.4980 chunk 182 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 351 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.165965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.106013 restraints weight = 59315.968| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.05 r_work: 0.3221 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32007 Z= 0.140 Angle : 0.572 11.931 43659 Z= 0.287 Chirality : 0.044 0.224 5043 Planarity : 0.004 0.060 5529 Dihedral : 5.195 53.987 5382 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.47 % Allowed : 12.95 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.37 (0.13), residues: 3834 helix: 2.10 (0.20), residues: 711 sheet: 0.32 (0.15), residues: 1043 loop : -0.41 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 152 HIS 0.003 0.001 HIS B 245 PHE 0.028 0.001 PHE C 168 TYR 0.026 0.001 TYR A 170 ARG 0.003 0.000 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 39) link_NAG-ASN : angle 1.75654 ( 117) link_BETA1-4 : bond 0.00284 ( 18) link_BETA1-4 : angle 1.10937 ( 54) hydrogen bonds : bond 0.03857 ( 1258) hydrogen bonds : angle 5.31568 ( 3561) SS BOND : bond 0.00227 ( 48) SS BOND : angle 0.82516 ( 96) covalent geometry : bond 0.00322 (31902) covalent geometry : angle 0.56405 (43392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51650.68 seconds wall clock time: 893 minutes 38.42 seconds (53618.42 seconds total)