Starting phenix.real_space_refine on Wed May 28 17:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a99_15273/05_2025/8a99_15273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a99_15273/05_2025/8a99_15273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a99_15273/05_2025/8a99_15273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a99_15273/05_2025/8a99_15273.map" model { file = "/net/cci-nas-00/data/ceres_data/8a99_15273/05_2025/8a99_15273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a99_15273/05_2025/8a99_15273.cif" } resolution = 2.5 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= 0.004 sd= 0.085 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 135 5.16 5 C 19619 2.51 5 N 5070 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30897 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8292 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8289 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8238 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 14, 'RTV': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 14, 'RTV': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 18.57, per 1000 atoms: 0.60 Number of scatterers: 30897 At special positions: 0 Unit cell: (159.58, 167.66, 204.02, 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 135 16.00 O 6073 8.00 N 5070 7.00 C 19619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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=2.02 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " 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 " RTV G 1 " - " NAG G 2 " " RTV H 1 " - " NAG H 2 " " RTV I 1 " - " NAG I 2 " " RTV J 1 " - " NAG J 2 " " RTV K 1 " - " NAG K 2 " " RTV L 1 " - " NAG L 2 " " RTV M 1 " - " NAG M 2 " " RTV N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 149 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 801 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 603 " " NAG B1315 " - " ASN B 801 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 149 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 234 " " NAG C1316 " - " ASN C 801 " Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 4.1 seconds 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7182 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 64 sheets defined 20.6% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.922A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.673A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.891A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.338A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.088A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.311A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.633A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.568A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 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 918 removed outlier: 4.034A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.733A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.514A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.294A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.600A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 479 through 483 removed outlier: 4.411A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.984A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 825 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: 4.033A 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 967 removed outlier: 3.544A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.790A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.201A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'R' and resid 27 through 32 removed outlier: 3.967A pdb=" N THR R 31 " --> pdb=" O GLY R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.935A pdb=" N THR R 91 " --> pdb=" O TYR R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.914A pdb=" N THR S 91 " --> pdb=" O TYR S 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 72 removed outlier: 3.681A pdb=" N PHE P 72 " --> pdb=" O SER P 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 32 removed outlier: 4.219A pdb=" N THR T 31 " --> pdb=" O GLY T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 3.975A pdb=" N THR T 91 " --> pdb=" O TYR T 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 32 removed outlier: 4.278A pdb=" N SER Q 32 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 9.316A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 9.316A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.789A 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 removed outlier: 3.906A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.433A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.704A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.509A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.522A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.886A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 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 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.991A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (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: 6.531A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.891A 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: 6.531A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.281A 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 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.523A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.909A 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: 3.699A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.739A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.037A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.777A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.433A 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: 3.715A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.715A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) 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 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.135A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.645A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.491A 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: 6.524A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.908A 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: 6.524A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.383A 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 27 through 30 removed outlier: 3.537A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.578A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.452A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 84 removed outlier: 5.753A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 114 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE C 133 " --> pdb=" O THR C 114 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.501A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.920A 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: 3.725A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (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 538 through 540 removed outlier: 3.606A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.964A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.355A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.911A 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: 6.355A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.502A 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 'R' and resid 9 through 11 removed outlier: 3.833A pdb=" N THR R 120 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN R 59 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.540A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AF6, first strand: chain 'O' and resid 45 through 49 removed outlier: 6.327A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL O 86 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 64 through 65 Processing sheet with id=AF8, first strand: chain 'S' and resid 9 through 11 removed outlier: 4.060A pdb=" N THR S 120 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE S 34 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 9 through 11 removed outlier: 4.060A pdb=" N THR S 120 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR S 112 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.525A pdb=" N VAL S 18 " --> pdb=" O LEU S 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET S 81 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AG3, first strand: chain 'P' and resid 45 through 50 removed outlier: 7.043A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 63 through 66 removed outlier: 4.204A pdb=" N THR P 73 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 90 through 91 Processing sheet with id=AG6, first strand: chain 'T' and resid 10 through 11 removed outlier: 4.182A pdb=" N THR T 120 " --> pdb=" O GLU T 10 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN T 59 " --> pdb=" O ARG T 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 18 through 23 removed outlier: 3.573A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET T 81 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR T 78 " --> pdb=" O ASP T 73 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AG9, first strand: chain 'Q' and resid 45 through 49 removed outlier: 6.385A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 63 through 64 1181 hydrogen bonds defined for protein. 3243 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: 15.52 Time building geometry restraints manager: 9.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6307 1.33 - 1.46: 9026 1.46 - 1.58: 16081 1.58 - 1.71: 6 1.71 - 1.84: 174 Bond restraints: 31594 Sorted by residual: bond pdb=" CG1 ILE C 402 " pdb=" CD1 ILE C 402 " ideal model delta sigma weight residual 1.513 1.293 0.220 3.90e-02 6.57e+02 3.18e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CB THR B 393 " pdb=" CG2 THR B 393 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.56e+01 bond pdb=" CA THR Q 10 " pdb=" CB THR Q 10 " ideal model delta sigma weight residual 1.531 1.579 -0.049 1.34e-02 5.57e+03 1.32e+01 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 31589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 42414 4.25 - 8.50: 491 8.50 - 12.74: 59 12.74 - 16.99: 15 16.99 - 21.24: 3 Bond angle restraints: 42982 Sorted by residual: angle pdb=" N PRO A 899 " pdb=" CA PRO A 899 " pdb=" CB PRO A 899 " ideal model delta sigma weight residual 103.25 110.88 -7.63 1.05e+00 9.07e-01 5.28e+01 angle pdb=" C LEU C 518 " pdb=" N HIS C 519 " pdb=" CA HIS C 519 " ideal model delta sigma weight residual 121.54 134.83 -13.29 1.91e+00 2.74e-01 4.84e+01 angle pdb=" N PRO C 899 " pdb=" CA PRO C 899 " pdb=" CB PRO C 899 " ideal model delta sigma weight residual 103.25 110.37 -7.12 1.05e+00 9.07e-01 4.59e+01 angle pdb=" N ARG B 78 " pdb=" CA ARG B 78 " pdb=" C ARG B 78 " ideal model delta sigma weight residual 111.39 120.05 -8.66 1.38e+00 5.25e-01 3.94e+01 angle pdb=" CA LEU C 492 " pdb=" CB LEU C 492 " pdb=" CG LEU C 492 " ideal model delta sigma weight residual 116.30 137.54 -21.24 3.50e+00 8.16e-02 3.68e+01 ... (remaining 42977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 18818 33.26 - 66.52: 511 66.52 - 99.77: 146 99.77 - 133.03: 37 133.03 - 166.29: 4 Dihedral angle restraints: 19516 sinusoidal: 8306 harmonic: 11210 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 168.87 -75.87 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.04 -61.04 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.45 -60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 19513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.002: 4978 1.002 - 2.004: 1 2.004 - 3.006: 0 3.006 - 4.008: 0 4.008 - 5.010: 11 Chirality restraints: 4990 Sorted by residual: chirality pdb=" C2 RTV C1311 " pdb=" C1 RTV C1311 " pdb=" C3 RTV C1311 " pdb=" N2 RTV C1311 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C2 RTV B1314 " pdb=" C1 RTV B1314 " pdb=" C3 RTV B1314 " pdb=" N2 RTV B1314 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.27e+02 chirality pdb=" C2 RTV I 1 " pdb=" C1 RTV I 1 " pdb=" C3 RTV I 1 " pdb=" N2 RTV I 1 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.27e+02 ... (remaining 4987 not shown) Planarity restraints: 5530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 508 " 0.065 2.00e-02 2.50e+03 4.51e-02 4.07e+01 pdb=" CG TYR C 508 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 TYR C 508 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 508 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 508 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 508 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 508 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 508 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " -0.083 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO A 139 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 342 " 0.035 2.00e-02 2.50e+03 3.34e-02 1.95e+01 pdb=" CG PHE A 342 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 342 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 342 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 342 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 342 " 0.025 2.00e-02 2.50e+03 pdb=" CZ PHE A 342 " -0.003 2.00e-02 2.50e+03 ... (remaining 5527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2655 2.75 - 3.29: 29423 3.29 - 3.83: 52885 3.83 - 4.36: 61534 4.36 - 4.90: 106199 Nonbonded interactions: 252696 Sorted by model distance: nonbonded pdb=" O TYR P 50 " pdb=" OG SER P 54 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR R 120 " pdb=" O SER R 122 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR S 120 " pdb=" O SER S 122 " model vdw 2.225 3.040 nonbonded pdb=" O PHE B 464 " pdb=" O6 NAG C1315 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR T 120 " pdb=" O SER T 122 " model vdw 2.245 3.040 ... (remaining 252691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 531 or (resid 532 through 533 and (name N or na \ me CA or name C or name O or name CB )) or resid 534 through 577 or resid 584 th \ rough 1146 or resid 1301 through 1310 or resid 1313)) selection = (chain 'B' and (resid 14 through 532 or (resid 533 and (name N or name CA or nam \ e C or name O or name CB )) or resid 534 through 577 or resid 584 through 1146 o \ r resid 1301 through 1310 or resid 1313)) selection = (chain 'C' and (resid 14 through 1146 or resid 1301 through 1310 or resid 1313)) \ } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 75.210 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.210 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 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 : 0.007 0.220 31686 Z= 0.333 Angle : 1.254 21.241 43215 Z= 0.661 Chirality : 0.248 5.010 4990 Planarity : 0.008 0.129 5489 Dihedral : 17.405 166.291 12205 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 0.21 % Allowed : 0.87 % Favored : 98.92 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 3814 helix: 2.14 (0.20), residues: 688 sheet: 0.48 (0.18), residues: 848 loop : -1.06 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP C 886 HIS 0.014 0.002 HIS C 245 PHE 0.073 0.004 PHE A 342 TYR 0.108 0.004 TYR C 508 ARG 0.054 0.001 ARG T 98 Details of bonding type rmsd link_NAG-ASN : bond 0.01346 ( 41) link_NAG-ASN : angle 4.45765 ( 123) link_BETA1-4 : bond 0.00660 ( 8) link_BETA1-4 : angle 2.18700 ( 24) hydrogen bonds : bond 0.20214 ( 1111) hydrogen bonds : angle 8.58664 ( 3243) SS BOND : bond 0.00713 ( 43) SS BOND : angle 2.60907 ( 86) covalent geometry : bond 0.00714 (31594) covalent geometry : angle 1.22815 (42982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 521 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 866 THR cc_start: 0.7610 (p) cc_final: 0.7282 (t) REVERT: R 102 TYR cc_start: 0.4275 (m-80) cc_final: 0.3954 (m-80) REVERT: S 69 THR cc_start: 0.9106 (m) cc_final: 0.8876 (p) REVERT: P 48 LEU cc_start: 0.8224 (mp) cc_final: 0.8023 (pp) REVERT: P 49 ILE cc_start: 0.7517 (pt) cc_final: 0.7122 (pt) REVERT: P 72 PHE cc_start: 0.8818 (p90) cc_final: 0.8448 (p90) outliers start: 7 outliers final: 4 residues processed: 526 average time/residue: 1.1425 time to fit residues: 731.3074 Evaluate side-chains 286 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain O residue 92 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 20.0000 chunk 290 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 182 optimal weight: 0.5980 chunk 223 optimal weight: 0.6980 chunk 347 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 450 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 954 GLN B1002 GLN B1005 GLN B1058 HIS C 394 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 965 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 ASN P 39 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN T 6 GLN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.199520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.154425 restraints weight = 60367.343| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 4.25 r_work: 0.3926 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31686 Z= 0.190 Angle : 0.787 13.050 43215 Z= 0.389 Chirality : 0.053 0.551 4990 Planarity : 0.005 0.074 5489 Dihedral : 12.654 149.078 5431 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 2.50 % Allowed : 12.21 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 3814 helix: 1.87 (0.20), residues: 671 sheet: 0.29 (0.17), residues: 914 loop : -1.07 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 152 HIS 0.009 0.001 HIS C 519 PHE 0.031 0.002 PHE C 168 TYR 0.027 0.002 TYR C 170 ARG 0.012 0.001 ARG P 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 41) link_NAG-ASN : angle 2.89448 ( 123) link_BETA1-4 : bond 0.00555 ( 8) link_BETA1-4 : angle 2.24123 ( 24) hydrogen bonds : bond 0.05212 ( 1111) hydrogen bonds : angle 6.56313 ( 3243) SS BOND : bond 0.00616 ( 43) SS BOND : angle 1.50684 ( 86) covalent geometry : bond 0.00418 (31594) covalent geometry : angle 0.76870 (42982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 298 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.3336 (m-10) cc_final: 0.3032 (m-10) REVERT: A 81 ASN cc_start: 0.7784 (m-40) cc_final: 0.7243 (p0) REVERT: A 177 MET cc_start: 0.2975 (mpp) cc_final: 0.2732 (mpp) REVERT: A 646 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6496 (mtm-85) REVERT: A 988 GLU cc_start: 0.8400 (mp0) cc_final: 0.8033 (mp0) REVERT: B 380 TYR cc_start: 0.7862 (m-80) cc_final: 0.7653 (m-80) REVERT: B 392 PHE cc_start: 0.8404 (m-80) cc_final: 0.7824 (m-80) REVERT: B 508 TYR cc_start: 0.8061 (m-10) cc_final: 0.7827 (m-10) REVERT: B 795 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6035 (mtpp) REVERT: B 985 ASP cc_start: 0.8533 (p0) cc_final: 0.8169 (p0) REVERT: B 988 GLU cc_start: 0.8425 (mp0) cc_final: 0.8163 (mp0) REVERT: C 200 TYR cc_start: 0.7317 (m-80) cc_final: 0.7068 (m-80) REVERT: C 990 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6861 (mm-30) REVERT: S 20 VAL cc_start: 0.7003 (t) cc_final: 0.6777 (t) REVERT: S 39 GLN cc_start: 0.8182 (tt0) cc_final: 0.7928 (tt0) REVERT: S 45 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6243 (mt) REVERT: S 82 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7896 (tm-30) REVERT: S 83 LEU cc_start: 0.9009 (mm) cc_final: 0.8417 (pp) REVERT: P 72 PHE cc_start: 0.8962 (p90) cc_final: 0.8689 (p90) REVERT: T 36 TRP cc_start: 0.7102 (t-100) cc_final: 0.6893 (t-100) outliers start: 83 outliers final: 33 residues processed: 346 average time/residue: 1.1045 time to fit residues: 472.2128 Evaluate side-chains 273 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 3.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 32 TYR Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain P residue 50 TYR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain Q residue 77 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 23 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 222 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 367 optimal weight: 20.0000 chunk 134 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 381 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1088 HIS B 655 HIS B1058 HIS B1106 GLN C 81 ASN C 196 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 919 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN T 6 GLN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.194557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.149396 restraints weight = 58935.425| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 4.19 r_work: 0.3794 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 31686 Z= 0.245 Angle : 0.817 13.861 43215 Z= 0.409 Chirality : 0.057 0.547 4990 Planarity : 0.006 0.106 5489 Dihedral : 10.430 137.424 5423 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 3.43 % Allowed : 15.22 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3814 helix: 1.43 (0.19), residues: 663 sheet: 0.09 (0.17), residues: 890 loop : -1.19 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 152 HIS 0.033 0.002 HIS B1058 PHE 0.030 0.003 PHE A 906 TYR 0.027 0.002 TYR A 265 ARG 0.015 0.001 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 41) link_NAG-ASN : angle 3.35168 ( 123) link_BETA1-4 : bond 0.00626 ( 8) link_BETA1-4 : angle 2.28423 ( 24) hydrogen bonds : bond 0.05682 ( 1111) hydrogen bonds : angle 6.57327 ( 3243) SS BOND : bond 0.00923 ( 43) SS BOND : angle 1.52495 ( 86) covalent geometry : bond 0.00556 (31594) covalent geometry : angle 0.79461 (42982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 272 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8319 (mm) cc_final: 0.8027 (mm) REVERT: A 201 PHE cc_start: 0.7955 (t80) cc_final: 0.7635 (t80) REVERT: A 269 TYR cc_start: 0.7508 (m-80) cc_final: 0.7283 (m-80) REVERT: A 275 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.6421 (t80) REVERT: A 646 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7329 (mtm-85) REVERT: A 780 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: A 988 GLU cc_start: 0.8420 (mp0) cc_final: 0.8051 (mp0) REVERT: B 79 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: B 258 TRP cc_start: 0.4507 (p-90) cc_final: 0.4225 (p-90) REVERT: B 298 GLU cc_start: 0.7939 (tt0) cc_final: 0.7705 (mm-30) REVERT: B 310 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7440 (tttm) REVERT: B 377 PHE cc_start: 0.8905 (t80) cc_final: 0.8552 (t80) REVERT: B 388 ASN cc_start: 0.8109 (p0) cc_final: 0.7843 (p0) REVERT: B 392 PHE cc_start: 0.8431 (m-80) cc_final: 0.7889 (m-80) REVERT: B 508 TYR cc_start: 0.8160 (m-10) cc_final: 0.7950 (m-10) REVERT: B 795 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6402 (mtpp) REVERT: C 878 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8188 (mm) REVERT: C 964 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8462 (tmtm) REVERT: S 20 VAL cc_start: 0.6843 (t) cc_final: 0.6433 (t) REVERT: S 30 ASN cc_start: 0.8562 (p0) cc_final: 0.7701 (p0) REVERT: S 48 MET cc_start: 0.6850 (ptt) cc_final: 0.6157 (mpp) REVERT: S 54 MET cc_start: 0.8956 (ttp) cc_final: 0.8744 (ptm) REVERT: S 83 LEU cc_start: 0.8501 (mm) cc_final: 0.8130 (pp) REVERT: P 33 TYR cc_start: 0.7725 (m-80) cc_final: 0.7334 (m-10) REVERT: P 72 PHE cc_start: 0.8753 (p90) cc_final: 0.8440 (p90) outliers start: 114 outliers final: 37 residues processed: 359 average time/residue: 0.9882 time to fit residues: 449.1468 Evaluate side-chains 260 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain P residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 99 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 348 optimal weight: 30.0000 chunk 200 optimal weight: 0.7980 chunk 47 optimal weight: 30.0000 chunk 282 optimal weight: 0.9990 chunk 309 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 297 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 134 GLN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 804 GLN C 935 GLN O 39 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 GLN P 94 ASN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.194503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.149783 restraints weight = 59280.641| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 4.28 r_work: 0.3794 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31686 Z= 0.162 Angle : 0.703 12.745 43215 Z= 0.348 Chirality : 0.050 0.459 4990 Planarity : 0.005 0.065 5489 Dihedral : 9.211 133.471 5421 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 3.31 % Allowed : 17.30 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 3814 helix: 1.60 (0.19), residues: 674 sheet: -0.02 (0.17), residues: 879 loop : -1.12 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 436 HIS 0.009 0.001 HIS C 655 PHE 0.039 0.002 PHE A 342 TYR 0.025 0.002 TYR O 92 ARG 0.006 0.001 ARG S 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 41) link_NAG-ASN : angle 3.08326 ( 123) link_BETA1-4 : bond 0.00627 ( 8) link_BETA1-4 : angle 2.19648 ( 24) hydrogen bonds : bond 0.04583 ( 1111) hydrogen bonds : angle 6.16889 ( 3243) SS BOND : bond 0.00750 ( 43) SS BOND : angle 1.19006 ( 86) covalent geometry : bond 0.00361 (31594) covalent geometry : angle 0.68093 (42982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 243 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.4452 (m-80) cc_final: 0.3985 (m-80) REVERT: A 54 LEU cc_start: 0.8336 (mm) cc_final: 0.8083 (mm) REVERT: A 189 LEU cc_start: 0.7506 (tt) cc_final: 0.7295 (tp) REVERT: A 201 PHE cc_start: 0.7748 (t80) cc_final: 0.7533 (t80) REVERT: A 298 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 646 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.7121 (mtm-85) REVERT: A 780 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: A 988 GLU cc_start: 0.8466 (mp0) cc_final: 0.8103 (mp0) REVERT: B 172 SER cc_start: 0.6165 (t) cc_final: 0.5955 (t) REVERT: B 392 PHE cc_start: 0.8499 (m-80) cc_final: 0.8231 (m-80) REVERT: B 436 TRP cc_start: 0.8708 (p-90) cc_final: 0.8312 (p-90) REVERT: B 795 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.6371 (mtpp) REVERT: B 988 GLU cc_start: 0.8611 (mp0) cc_final: 0.8410 (mp0) REVERT: B 990 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8281 (pp20) REVERT: C 191 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: C 859 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7998 (p) REVERT: C 878 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8182 (mm) REVERT: C 950 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: C 964 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8545 (tmtm) REVERT: R 112 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6659 (p90) REVERT: S 30 ASN cc_start: 0.8331 (p0) cc_final: 0.7891 (p0) REVERT: S 48 MET cc_start: 0.7839 (ptt) cc_final: 0.6505 (ptt) REVERT: S 73 ASP cc_start: 0.8096 (t0) cc_final: 0.7685 (p0) REVERT: S 82 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7764 (tm-30) REVERT: S 83 LEU cc_start: 0.8475 (mm) cc_final: 0.8035 (pp) REVERT: P 33 TYR cc_start: 0.7752 (m-80) cc_final: 0.7227 (m-10) REVERT: P 72 PHE cc_start: 0.8889 (p90) cc_final: 0.8580 (p90) REVERT: P 91 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8601 (tp-100) REVERT: T 28 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8133 (p) outliers start: 110 outliers final: 40 residues processed: 327 average time/residue: 0.9856 time to fit residues: 410.3662 Evaluate side-chains 258 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 112 TYR Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 160 optimal weight: 0.0670 chunk 174 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 346 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 283 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 81 ASN A 87 ASN A 540 ASN A 762 GLN A 804 GLN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 935 GLN O 90 GLN O 91 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.192625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.148895 restraints weight = 58392.787| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 4.28 r_work: 0.3753 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31686 Z= 0.213 Angle : 0.740 16.241 43215 Z= 0.367 Chirality : 0.051 0.442 4990 Planarity : 0.005 0.067 5489 Dihedral : 8.477 118.937 5421 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 4.03 % Allowed : 17.99 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 3814 helix: 1.53 (0.20), residues: 672 sheet: -0.07 (0.17), residues: 876 loop : -1.13 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 36 HIS 0.011 0.001 HIS C 655 PHE 0.038 0.002 PHE A 565 TYR 0.025 0.002 TYR B1067 ARG 0.007 0.001 ARG S 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 41) link_NAG-ASN : angle 3.08843 ( 123) link_BETA1-4 : bond 0.00667 ( 8) link_BETA1-4 : angle 1.79734 ( 24) hydrogen bonds : bond 0.04968 ( 1111) hydrogen bonds : angle 6.18380 ( 3243) SS BOND : bond 0.00814 ( 43) SS BOND : angle 1.29234 ( 86) covalent geometry : bond 0.00488 (31594) covalent geometry : angle 0.71933 (42982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 218 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8276 (mm) cc_final: 0.7991 (mm) REVERT: A 189 LEU cc_start: 0.7976 (tt) cc_final: 0.7735 (tp) REVERT: A 275 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.6276 (t80) REVERT: A 298 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: A 646 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7071 (mtm-85) REVERT: A 780 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 988 GLU cc_start: 0.8525 (mp0) cc_final: 0.7993 (mp0) REVERT: B 79 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.5057 (m-80) REVERT: B 392 PHE cc_start: 0.8542 (m-80) cc_final: 0.8179 (m-80) REVERT: B 417 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9181 (tppp) REVERT: B 436 TRP cc_start: 0.8859 (p-90) cc_final: 0.8500 (p-90) REVERT: B 456 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6419 (p90) REVERT: B 473 TYR cc_start: 0.8542 (t80) cc_final: 0.8302 (t80) REVERT: B 795 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.6445 (mtpp) REVERT: B 947 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7657 (mttt) REVERT: B 988 GLU cc_start: 0.8653 (mp0) cc_final: 0.8326 (mp0) REVERT: B 990 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8292 (pp20) REVERT: C 492 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7844 (tm) REVERT: C 693 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8506 (pp) REVERT: C 859 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8168 (p) REVERT: C 878 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8242 (mm) REVERT: C 950 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8035 (m-30) REVERT: C 964 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8630 (tmtm) REVERT: R 54 MET cc_start: 0.4485 (mpp) cc_final: 0.4269 (pmm) REVERT: R 112 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6280 (p90) REVERT: S 29 PHE cc_start: 0.7885 (p90) cc_final: 0.7676 (p90) REVERT: S 54 MET cc_start: 0.8892 (ptm) cc_final: 0.8587 (ptm) REVERT: S 73 ASP cc_start: 0.8060 (t0) cc_final: 0.7752 (p0) REVERT: S 83 LEU cc_start: 0.8211 (mm) cc_final: 0.7863 (pp) REVERT: P 63 PHE cc_start: 0.6983 (t80) cc_final: 0.6425 (m-80) REVERT: P 72 PHE cc_start: 0.8698 (p90) cc_final: 0.8379 (p90) REVERT: P 91 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8450 (tp-100) REVERT: T 28 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8033 (p) outliers start: 134 outliers final: 62 residues processed: 326 average time/residue: 0.9901 time to fit residues: 407.2090 Evaluate side-chains 278 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 112 TYR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain Q residue 10 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 105 optimal weight: 1.9990 chunk 208 optimal weight: 0.1980 chunk 371 optimal weight: 40.0000 chunk 18 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 276 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 293 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 762 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.192152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.146787 restraints weight = 58514.769| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 4.41 r_work: 0.3744 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31686 Z= 0.195 Angle : 0.719 13.765 43215 Z= 0.359 Chirality : 0.051 0.419 4990 Planarity : 0.005 0.069 5489 Dihedral : 7.873 105.769 5421 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 4.06 % Allowed : 18.35 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3814 helix: 1.62 (0.20), residues: 666 sheet: -0.12 (0.17), residues: 881 loop : -1.16 (0.12), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 353 HIS 0.009 0.001 HIS C 655 PHE 0.049 0.002 PHE A 392 TYR 0.027 0.002 TYR B 451 ARG 0.007 0.001 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00577 ( 41) link_NAG-ASN : angle 2.99393 ( 123) link_BETA1-4 : bond 0.00589 ( 8) link_BETA1-4 : angle 1.52066 ( 24) hydrogen bonds : bond 0.04845 ( 1111) hydrogen bonds : angle 6.11384 ( 3243) SS BOND : bond 0.00784 ( 43) SS BOND : angle 1.30177 ( 86) covalent geometry : bond 0.00445 (31594) covalent geometry : angle 0.69930 (42982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 212 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8304 (mm) cc_final: 0.8027 (mm) REVERT: A 189 LEU cc_start: 0.8048 (tt) cc_final: 0.7841 (tp) REVERT: A 200 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7535 (t80) REVERT: A 275 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: A 298 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: A 392 PHE cc_start: 0.7793 (t80) cc_final: 0.7577 (t80) REVERT: A 646 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7149 (mtm-85) REVERT: A 780 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: A 988 GLU cc_start: 0.8465 (mp0) cc_final: 0.7959 (mp0) REVERT: B 28 TYR cc_start: 0.7648 (m-10) cc_final: 0.7399 (m-80) REVERT: B 79 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.4813 (m-80) REVERT: B 392 PHE cc_start: 0.8581 (m-80) cc_final: 0.8184 (m-80) REVERT: B 436 TRP cc_start: 0.8802 (p-90) cc_final: 0.8412 (p-90) REVERT: B 613 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: B 795 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6662 (mtpp) REVERT: B 988 GLU cc_start: 0.8580 (mp0) cc_final: 0.8368 (mp0) REVERT: B 990 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8306 (pp20) REVERT: C 121 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6602 (t0) REVERT: C 492 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7882 (tm) REVERT: C 614 ASP cc_start: 0.7207 (m-30) cc_final: 0.6957 (p0) REVERT: C 693 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8663 (pt) REVERT: C 814 LYS cc_start: 0.6614 (mptt) cc_final: 0.6392 (tmmm) REVERT: C 878 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8182 (mm) REVERT: C 950 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: C 964 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8657 (tmtm) REVERT: R 81 MET cc_start: -0.0949 (OUTLIER) cc_final: -0.2245 (mpt) REVERT: R 112 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6964 (p90) REVERT: S 30 ASN cc_start: 0.8441 (p0) cc_final: 0.8208 (p0) REVERT: S 82 GLU cc_start: 0.8765 (tm-30) cc_final: 0.7935 (tp30) REVERT: S 83 LEU cc_start: 0.8766 (mm) cc_final: 0.7756 (pp) REVERT: P 33 TYR cc_start: 0.7265 (m-80) cc_final: 0.6875 (m-80) REVERT: P 63 PHE cc_start: 0.7224 (t80) cc_final: 0.6695 (m-80) REVERT: P 72 PHE cc_start: 0.8884 (p90) cc_final: 0.8586 (p90) REVERT: T 28 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8326 (p) outliers start: 135 outliers final: 68 residues processed: 321 average time/residue: 1.0039 time to fit residues: 409.0414 Evaluate side-chains 281 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 196 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 112 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain Q residue 10 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 325 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 225 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 279 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.192101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.146939 restraints weight = 58499.183| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 4.17 r_work: 0.3763 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31686 Z= 0.168 Angle : 0.719 15.286 43215 Z= 0.355 Chirality : 0.050 0.406 4990 Planarity : 0.005 0.065 5489 Dihedral : 7.593 97.283 5421 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.52 % Rotamer: Outliers : 3.46 % Allowed : 19.49 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 3814 helix: 1.69 (0.20), residues: 663 sheet: -0.11 (0.17), residues: 892 loop : -1.15 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 36 HIS 0.008 0.001 HIS C 655 PHE 0.044 0.002 PHE A 565 TYR 0.022 0.002 TYR B 508 ARG 0.008 0.000 ARG R 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 41) link_NAG-ASN : angle 3.54520 ( 123) link_BETA1-4 : bond 0.00534 ( 8) link_BETA1-4 : angle 1.28929 ( 24) hydrogen bonds : bond 0.04574 ( 1111) hydrogen bonds : angle 6.02086 ( 3243) SS BOND : bond 0.00681 ( 43) SS BOND : angle 1.40492 ( 86) covalent geometry : bond 0.00381 (31594) covalent geometry : angle 0.69224 (42982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 196 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8285 (mm) cc_final: 0.8014 (mm) REVERT: A 179 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.5474 (mm) REVERT: A 200 TYR cc_start: 0.8112 (m-80) cc_final: 0.7778 (t80) REVERT: A 275 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: A 298 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: A 646 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7101 (mtm-85) REVERT: A 780 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: A 988 GLU cc_start: 0.8300 (mp0) cc_final: 0.7882 (mp0) REVERT: B 79 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.4680 (m-80) REVERT: B 136 CYS cc_start: 0.4374 (OUTLIER) cc_final: 0.3949 (p) REVERT: B 172 SER cc_start: 0.6409 (t) cc_final: 0.5920 (p) REVERT: B 392 PHE cc_start: 0.8565 (m-80) cc_final: 0.8257 (m-80) REVERT: B 436 TRP cc_start: 0.8784 (p-90) cc_final: 0.8289 (p-90) REVERT: B 759 PHE cc_start: 0.8261 (m-80) cc_final: 0.8059 (m-80) REVERT: B 795 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.6802 (mtpp) REVERT: B 916 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 947 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7658 (mttt) REVERT: B 988 GLU cc_start: 0.8514 (mp0) cc_final: 0.8301 (mp0) REVERT: C 492 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7816 (tm) REVERT: C 614 ASP cc_start: 0.7236 (m-30) cc_final: 0.6934 (p0) REVERT: C 693 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8585 (pp) REVERT: C 814 LYS cc_start: 0.6685 (mptt) cc_final: 0.6472 (tmmm) REVERT: C 878 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8165 (mm) REVERT: R 81 MET cc_start: -0.0914 (OUTLIER) cc_final: -0.2121 (mpt) REVERT: R 112 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6429 (p90) REVERT: S 30 ASN cc_start: 0.8269 (p0) cc_final: 0.8027 (p0) REVERT: S 48 MET cc_start: 0.7333 (ptt) cc_final: 0.6515 (pmm) REVERT: S 73 ASP cc_start: 0.8042 (t0) cc_final: 0.7796 (p0) REVERT: S 82 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7554 (tp30) REVERT: S 83 LEU cc_start: 0.8225 (mm) cc_final: 0.7557 (pp) REVERT: P 33 TYR cc_start: 0.6984 (m-80) cc_final: 0.6660 (m-80) REVERT: P 63 PHE cc_start: 0.7133 (t80) cc_final: 0.6602 (m-80) REVERT: P 72 PHE cc_start: 0.8772 (p90) cc_final: 0.8437 (p90) REVERT: T 28 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8199 (p) outliers start: 115 outliers final: 58 residues processed: 288 average time/residue: 0.9259 time to fit residues: 340.9942 Evaluate side-chains 262 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 188 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 112 TYR Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain Q residue 10 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 126 optimal weight: 0.5980 chunk 285 optimal weight: 0.0980 chunk 161 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 333 optimal weight: 50.0000 chunk 73 optimal weight: 0.0370 chunk 229 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 87 ASN A 762 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 30 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.191871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.147182 restraints weight = 58504.368| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 4.35 r_work: 0.3743 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31686 Z= 0.166 Angle : 0.714 15.188 43215 Z= 0.352 Chirality : 0.050 0.393 4990 Planarity : 0.005 0.061 5489 Dihedral : 7.349 97.111 5421 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 3.79 % Allowed : 19.49 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 3814 helix: 1.55 (0.19), residues: 680 sheet: -0.07 (0.16), residues: 906 loop : -1.14 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP T 36 HIS 0.008 0.001 HIS C 655 PHE 0.032 0.002 PHE A 515 TYR 0.022 0.001 TYR B1067 ARG 0.010 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 41) link_NAG-ASN : angle 3.08256 ( 123) link_BETA1-4 : bond 0.00535 ( 8) link_BETA1-4 : angle 1.11761 ( 24) hydrogen bonds : bond 0.04534 ( 1111) hydrogen bonds : angle 5.95925 ( 3243) SS BOND : bond 0.00673 ( 43) SS BOND : angle 1.32525 ( 86) covalent geometry : bond 0.00376 (31594) covalent geometry : angle 0.69393 (42982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 203 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8291 (mm) cc_final: 0.8037 (mm) REVERT: A 179 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.5707 (mm) REVERT: A 275 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: A 298 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 780 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: A 988 GLU cc_start: 0.8374 (mp0) cc_final: 0.7923 (mp0) REVERT: B 66 HIS cc_start: 0.7059 (t-90) cc_final: 0.6417 (p90) REVERT: B 79 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.4747 (m-80) REVERT: B 136 CYS cc_start: 0.4318 (OUTLIER) cc_final: 0.3932 (p) REVERT: B 172 SER cc_start: 0.6394 (t) cc_final: 0.5884 (p) REVERT: B 203 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6895 (mp) REVERT: B 392 PHE cc_start: 0.8532 (m-80) cc_final: 0.8208 (m-80) REVERT: B 436 TRP cc_start: 0.8837 (p-90) cc_final: 0.8351 (p-90) REVERT: B 795 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7109 (mtpp) REVERT: B 900 MET cc_start: 0.8047 (mmm) cc_final: 0.7842 (mtp) REVERT: B 916 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8570 (tt) REVERT: B 947 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7646 (mttt) REVERT: B 988 GLU cc_start: 0.8648 (mp0) cc_final: 0.8402 (mp0) REVERT: C 492 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7826 (tm) REVERT: C 614 ASP cc_start: 0.7473 (m-30) cc_final: 0.7073 (p0) REVERT: C 693 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8626 (pp) REVERT: C 814 LYS cc_start: 0.6842 (mptt) cc_final: 0.6558 (tmmm) REVERT: C 878 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8174 (mm) REVERT: R 81 MET cc_start: -0.1146 (OUTLIER) cc_final: -0.2176 (mpt) REVERT: R 112 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6643 (p90) REVERT: O 91 GLN cc_start: 0.7066 (pm20) cc_final: 0.6824 (pm20) REVERT: S 81 MET cc_start: 0.7688 (mtt) cc_final: 0.6529 (tpp) REVERT: S 110 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7454 (tp) REVERT: P 33 TYR cc_start: 0.6966 (m-80) cc_final: 0.6623 (m-80) REVERT: P 63 PHE cc_start: 0.7325 (t80) cc_final: 0.6866 (m-80) REVERT: P 72 PHE cc_start: 0.8804 (p90) cc_final: 0.8475 (p90) REVERT: T 28 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (p) outliers start: 126 outliers final: 71 residues processed: 301 average time/residue: 0.9519 time to fit residues: 366.1697 Evaluate side-chains 276 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 188 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 112 TYR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain Q residue 10 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 16 optimal weight: 20.0000 chunk 248 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 323 optimal weight: 30.0000 chunk 250 optimal weight: 10.0000 chunk 296 optimal weight: 0.0980 chunk 256 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 378 optimal weight: 50.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.191329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.146010 restraints weight = 58042.658| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 4.54 r_work: 0.3727 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31686 Z= 0.184 Angle : 0.735 15.498 43215 Z= 0.362 Chirality : 0.050 0.385 4990 Planarity : 0.005 0.079 5489 Dihedral : 7.166 96.849 5421 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.23 % Rotamer: Outliers : 3.28 % Allowed : 20.22 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3814 helix: 1.50 (0.20), residues: 669 sheet: -0.14 (0.16), residues: 897 loop : -1.17 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP P 36 HIS 0.008 0.001 HIS C 655 PHE 0.049 0.002 PHE A 565 TYR 0.023 0.002 TYR B1067 ARG 0.013 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 41) link_NAG-ASN : angle 2.97803 ( 123) link_BETA1-4 : bond 0.00491 ( 8) link_BETA1-4 : angle 0.97920 ( 24) hydrogen bonds : bond 0.04700 ( 1111) hydrogen bonds : angle 5.98694 ( 3243) SS BOND : bond 0.00747 ( 43) SS BOND : angle 1.48731 ( 86) covalent geometry : bond 0.00421 (31594) covalent geometry : angle 0.71565 (42982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 197 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8330 (mm) cc_final: 0.8058 (mm) REVERT: A 179 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.5639 (mm) REVERT: A 275 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: A 298 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: A 780 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: A 988 GLU cc_start: 0.8371 (mp0) cc_final: 0.7926 (mp0) REVERT: B 66 HIS cc_start: 0.7092 (t-90) cc_final: 0.6519 (p90) REVERT: B 79 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.4731 (m-80) REVERT: B 136 CYS cc_start: 0.3868 (OUTLIER) cc_final: 0.3577 (p) REVERT: B 172 SER cc_start: 0.6247 (t) cc_final: 0.5699 (p) REVERT: B 203 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6928 (mp) REVERT: B 392 PHE cc_start: 0.8558 (m-80) cc_final: 0.8242 (m-80) REVERT: B 436 TRP cc_start: 0.8751 (p-90) cc_final: 0.8232 (p-90) REVERT: B 795 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7134 (mtpp) REVERT: B 900 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7801 (mtp) REVERT: B 916 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8561 (tt) REVERT: B 947 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7691 (mttt) REVERT: B 988 GLU cc_start: 0.8677 (mp0) cc_final: 0.8447 (mp0) REVERT: C 121 ASN cc_start: 0.6978 (OUTLIER) cc_final: 0.6495 (t0) REVERT: C 177 MET cc_start: 0.0812 (mmt) cc_final: -0.2961 (mtp) REVERT: C 492 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7823 (tm) REVERT: C 614 ASP cc_start: 0.7605 (m-30) cc_final: 0.7276 (p0) REVERT: C 693 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8710 (pt) REVERT: C 814 LYS cc_start: 0.6894 (mptt) cc_final: 0.6674 (tmmm) REVERT: C 817 PHE cc_start: 0.6260 (t80) cc_final: 0.5859 (t80) REVERT: C 878 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8185 (mm) REVERT: R 81 MET cc_start: -0.1075 (mpt) cc_final: -0.1796 (mpt) REVERT: R 112 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6870 (p90) REVERT: O 91 GLN cc_start: 0.7113 (pm20) cc_final: 0.6883 (pm20) REVERT: S 48 MET cc_start: 0.7170 (ptt) cc_final: 0.6140 (pmm) REVERT: S 81 MET cc_start: 0.7643 (mtt) cc_final: 0.6659 (tpt) REVERT: S 110 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7449 (tp) REVERT: P 33 TYR cc_start: 0.6916 (m-80) cc_final: 0.6586 (m-80) REVERT: P 63 PHE cc_start: 0.7305 (t80) cc_final: 0.6783 (m-80) REVERT: P 72 PHE cc_start: 0.8694 (p90) cc_final: 0.8348 (p90) REVERT: T 28 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8199 (p) REVERT: T 48 MET cc_start: 0.7833 (mmp) cc_final: 0.6928 (mpm) outliers start: 109 outliers final: 68 residues processed: 279 average time/residue: 0.9254 time to fit residues: 328.6516 Evaluate side-chains 274 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 112 TYR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain Q residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 203 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 310 optimal weight: 0.3980 chunk 360 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 313 optimal weight: 0.3980 chunk 222 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** P 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.191761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.147405 restraints weight = 58446.715| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 4.15 r_work: 0.3755 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31686 Z= 0.151 Angle : 0.711 15.706 43215 Z= 0.351 Chirality : 0.049 0.381 4990 Planarity : 0.005 0.077 5489 Dihedral : 6.899 96.207 5421 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.44 % Rotamer: Outliers : 2.89 % Allowed : 20.70 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 3814 helix: 1.59 (0.20), residues: 674 sheet: -0.20 (0.16), residues: 914 loop : -1.16 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.002 TRP T 36 HIS 0.007 0.001 HIS C 519 PHE 0.033 0.002 PHE A 392 TYR 0.020 0.001 TYR P 87 ARG 0.012 0.001 ARG R 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 41) link_NAG-ASN : angle 2.88539 ( 123) link_BETA1-4 : bond 0.00471 ( 8) link_BETA1-4 : angle 0.94179 ( 24) hydrogen bonds : bond 0.04405 ( 1111) hydrogen bonds : angle 5.87076 ( 3243) SS BOND : bond 0.00618 ( 43) SS BOND : angle 1.39957 ( 86) covalent geometry : bond 0.00341 (31594) covalent geometry : angle 0.69333 (42982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 195 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.5339 (m-80) cc_final: 0.4609 (m-80) REVERT: A 54 LEU cc_start: 0.8261 (mm) cc_final: 0.8008 (mm) REVERT: A 179 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.5730 (mm) REVERT: A 298 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: A 780 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: A 825 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7909 (mptp) REVERT: A 988 GLU cc_start: 0.8359 (mp0) cc_final: 0.7903 (mp0) REVERT: B 66 HIS cc_start: 0.7067 (t-90) cc_final: 0.6657 (p90) REVERT: B 79 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.4857 (m-80) REVERT: B 132 GLU cc_start: 0.7109 (pm20) cc_final: 0.6858 (pp20) REVERT: B 136 CYS cc_start: 0.3772 (OUTLIER) cc_final: 0.3541 (p) REVERT: B 203 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6954 (mp) REVERT: B 377 PHE cc_start: 0.8665 (t80) cc_final: 0.8454 (t80) REVERT: B 392 PHE cc_start: 0.8499 (m-80) cc_final: 0.8142 (m-80) REVERT: B 436 TRP cc_start: 0.8751 (p-90) cc_final: 0.8274 (p-90) REVERT: B 795 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7147 (mtpp) REVERT: B 947 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7644 (mttt) REVERT: B 988 GLU cc_start: 0.8664 (mp0) cc_final: 0.8421 (mp0) REVERT: C 121 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.6127 (t0) REVERT: C 177 MET cc_start: 0.0898 (mmt) cc_final: -0.2905 (mtp) REVERT: C 492 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7813 (tm) REVERT: C 614 ASP cc_start: 0.7560 (m-30) cc_final: 0.7274 (p0) REVERT: C 693 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8641 (pp) REVERT: C 814 LYS cc_start: 0.6863 (mptt) cc_final: 0.6634 (tmmm) REVERT: C 878 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8179 (mm) REVERT: R 81 MET cc_start: -0.1317 (OUTLIER) cc_final: -0.2132 (mpt) REVERT: R 112 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6962 (p90) REVERT: O 91 GLN cc_start: 0.7116 (pm20) cc_final: 0.6913 (pm20) REVERT: S 48 MET cc_start: 0.7544 (ptt) cc_final: 0.6307 (pmm) REVERT: S 81 MET cc_start: 0.7598 (mtt) cc_final: 0.6613 (tpt) REVERT: S 110 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7388 (tp) REVERT: P 33 TYR cc_start: 0.6963 (m-80) cc_final: 0.6634 (m-80) REVERT: P 63 PHE cc_start: 0.7200 (t80) cc_final: 0.6757 (m-80) REVERT: P 72 PHE cc_start: 0.8688 (p90) cc_final: 0.8346 (p90) REVERT: T 28 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8239 (p) REVERT: T 48 MET cc_start: 0.7667 (mmp) cc_final: 0.6748 (mpm) REVERT: Q 92 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7082 (p90) outliers start: 96 outliers final: 58 residues processed: 269 average time/residue: 0.9513 time to fit residues: 329.4996 Evaluate side-chains 261 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 185 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 112 TYR Chi-restraints excluded: chain S residue 29 PHE Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 92 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 287 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 345 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 296 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 121 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.191314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.145587 restraints weight = 58276.389| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.76 r_work: 0.3752 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31686 Z= 0.173 Angle : 0.724 15.779 43215 Z= 0.356 Chirality : 0.049 0.379 4990 Planarity : 0.005 0.076 5489 Dihedral : 6.826 95.813 5421 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 2.80 % Allowed : 21.21 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3814 helix: 1.52 (0.19), residues: 680 sheet: -0.19 (0.16), residues: 903 loop : -1.16 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP T 36 HIS 0.007 0.001 HIS C 655 PHE 0.040 0.002 PHE A 565 TYR 0.032 0.002 TYR B 508 ARG 0.011 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 41) link_NAG-ASN : angle 2.84865 ( 123) link_BETA1-4 : bond 0.00414 ( 8) link_BETA1-4 : angle 0.85431 ( 24) hydrogen bonds : bond 0.04503 ( 1111) hydrogen bonds : angle 5.90398 ( 3243) SS BOND : bond 0.00694 ( 43) SS BOND : angle 2.10247 ( 86) covalent geometry : bond 0.00396 (31594) covalent geometry : angle 0.70301 (42982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37840.00 seconds wall clock time: 649 minutes 7.73 seconds (38947.73 seconds total)