Starting phenix.real_space_refine on Wed May 28 15:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a94_15269/05_2025/8a94_15269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a94_15269/05_2025/8a94_15269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a94_15269/05_2025/8a94_15269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a94_15269/05_2025/8a94_15269.map" model { file = "/net/cci-nas-00/data/ceres_data/8a94_15269/05_2025/8a94_15269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a94_15269/05_2025/8a94_15269.cif" } resolution = 2.4 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= 0.086 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 19598 2.51 5 N 5069 2.21 5 O 6060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 2.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30862 Number of models: 1 Model: "" Number of chains: 19 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: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8290 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8244 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 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: "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: "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: "K" 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: "E" 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': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} 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': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 19.86, per 1000 atoms: 0.64 Number of scatterers: 30862 At special positions: 0 Unit cell: (159.58, 161.6, 229.27, 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 6060 8.00 N 5069 7.00 C 19598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 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=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 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 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " 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 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 C1311 " - " ASN C 331 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 234 " " NAG C1316 " - " ASN C 801 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 234 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN C 17 " Time building additional restraints: 7.82 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 63 sheets defined 20.7% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.42 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 365 through 372 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' 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 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.582A 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: 3.879A 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 940 removed outlier: 4.351A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) 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 removed outlier: 3.754A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.031A 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: 4.307A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.649A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 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 891 removed outlier: 3.703A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.075A 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: 3.766A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.511A 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 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.972A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.928A 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 826 removed outlier: 3.538A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.596A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.940A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'R' and resid 27 through 32 removed outlier: 4.097A pdb=" N THR R 31 " --> pdb=" O GLY R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 4.184A pdb=" N THR R 91 " --> pdb=" O TYR R 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 32 removed outlier: 4.037A pdb=" N THR T 31 " --> pdb=" O GLY T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 4.166A pdb=" N THR T 91 " --> pdb=" O TYR T 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 33 removed outlier: 4.029A pdb=" N SER Q 32 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR Q 33 " --> pdb=" O SER Q 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 29 through 33' Processing helix chain 'K' and resid 27 through 32 removed outlier: 4.208A pdb=" N THR K 31 " --> pdb=" O GLY K 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 32 removed outlier: 3.681A pdb=" N SER E 32 " --> pdb=" O VAL E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.813A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.576A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.969A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.604A 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: 3.882A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.634A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.616A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.640A 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: 3.665A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.524A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.885A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.569A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.362A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.147A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.125A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.773A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 126 through 128 removed outlier: 5.892A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.638A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.439A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.607A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 554 removed outlier: 4.944A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.102A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.763A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.492A 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 712 through 728 removed outlier: 6.572A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.375A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.372A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.219A 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 85 removed outlier: 13.140A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.500A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.664A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.848A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.462A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.164A 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: 3.613A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.264A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.626A 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: 6.347A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.936A 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: 6.347A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.145A 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: 4.535A 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: 3.861A pdb=" N THR R 120 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL R 37 " --> pdb=" O TYR R 95 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE R 34 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 18 through 19 removed outlier: 3.604A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 18 through 19 removed outlier: 3.604A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.507A pdb=" N LEU O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 9 through 11 removed outlier: 3.875A pdb=" N THR T 120 " --> pdb=" O GLU T 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL T 37 " --> pdb=" O TYR T 95 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE T 34 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG T 50 " --> pdb=" O ILE T 34 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP T 36 " --> pdb=" O MET T 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 9 through 11 removed outlier: 3.875A pdb=" N THR T 120 " --> pdb=" O GLU T 10 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR T 112 " --> pdb=" O ARG T 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 18 through 19 removed outlier: 3.617A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 18 through 19 removed outlier: 3.617A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.502A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.592A pdb=" N THR K 120 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.592A pdb=" N THR K 120 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR K 112 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.674A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AG8, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.642A pdb=" N SER E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 63 through 65 1161 hydrogen bonds defined for protein. 3177 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: 17.13 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8424 1.33 - 1.46: 9044 1.46 - 1.59: 13915 1.59 - 1.72: 2 1.72 - 1.85: 173 Bond restraints: 31558 Sorted by residual: bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.335 1.404 -0.068 1.30e-02 5.92e+03 2.77e+01 bond pdb=" CB PRO B 230 " pdb=" CG PRO B 230 " ideal model delta sigma weight residual 1.492 1.274 0.218 5.00e-02 4.00e+02 1.91e+01 bond pdb=" N GLY A 431 " pdb=" CA GLY A 431 " ideal model delta sigma weight residual 1.445 1.476 -0.031 8.30e-03 1.45e+04 1.40e+01 bond pdb=" N VAL B 16 " pdb=" CA VAL B 16 " ideal model delta sigma weight residual 1.456 1.497 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" C LYS B 462 " pdb=" N PRO B 463 " ideal model delta sigma weight residual 1.330 1.373 -0.042 1.19e-02 7.06e+03 1.27e+01 ... (remaining 31553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 42497 4.10 - 8.20: 392 8.20 - 12.30: 36 12.30 - 16.40: 4 16.40 - 20.50: 3 Bond angle restraints: 42932 Sorted by residual: angle pdb=" N ALA A 522 " pdb=" CA ALA A 522 " pdb=" C ALA A 522 " ideal model delta sigma weight residual 111.24 121.13 -9.89 1.38e+00 5.25e-01 5.14e+01 angle pdb=" N PRO A 899 " pdb=" CA PRO A 899 " pdb=" CB PRO A 899 " ideal model delta sigma weight residual 103.25 110.70 -7.45 1.05e+00 9.07e-01 5.03e+01 angle pdb=" CG1 ILE A 402 " pdb=" CB ILE A 402 " pdb=" CG2 ILE A 402 " ideal model delta sigma weight residual 110.70 90.20 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" N PRO B 899 " pdb=" CA PRO B 899 " pdb=" CB PRO B 899 " ideal model delta sigma weight residual 103.51 109.87 -6.36 9.60e-01 1.09e+00 4.39e+01 angle pdb=" C GLN E 101 " pdb=" N GLY E 102 " pdb=" CA GLY E 102 " ideal model delta sigma weight residual 121.41 108.54 12.87 1.96e+00 2.60e-01 4.31e+01 ... (remaining 42927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 18052 21.33 - 42.65: 1134 42.65 - 63.98: 197 63.98 - 85.31: 54 85.31 - 106.64: 27 Dihedral angle restraints: 19464 sinusoidal: 8254 harmonic: 11210 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -174.44 88.44 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -148.95 62.95 1 1.00e+01 1.00e-02 5.23e+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 -27.79 -58.21 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 19461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 4933 0.225 - 0.449: 46 0.449 - 0.674: 3 0.674 - 0.898: 0 0.898 - 1.123: 1 Chirality restraints: 4983 Sorted by residual: chirality pdb=" CB THR A 523 " pdb=" CA THR A 523 " pdb=" OG1 THR A 523 " pdb=" CG2 THR A 523 " both_signs ideal model delta sigma weight residual False 2.55 1.43 1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.45e+00 ... (remaining 4980 not shown) Planarity restraints: 5533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.350 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C1301 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.528 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG C1303 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.505 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1302 " 0.294 2.00e-02 2.50e+03 2.52e-01 7.91e+02 pdb=" C7 NAG C1302 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1302 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG C1302 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG C1302 " 0.042 2.00e-02 2.50e+03 ... (remaining 5530 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 332 2.62 - 3.19: 25363 3.19 - 3.76: 48515 3.76 - 4.33: 67018 4.33 - 4.90: 110489 Nonbonded interactions: 251717 Sorted by model distance: nonbonded pdb=" O PRO C 600 " pdb=" CG2 THR C 604 " model vdw 2.046 3.460 nonbonded pdb=" O TYR E 50 " pdb=" OG SER E 54 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR T 120 " pdb=" O SER T 122 " model vdw 2.230 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.262 3.040 ... (remaining 251712 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 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 577 or resid 584 through 1146 o \ r resid 1301 through 1313)) selection = (chain 'B' and (resid 14 through 577 or resid 584 through 1146 or resid 1301 thr \ ough 1313)) selection = (chain 'C' and (resid 14 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 1146 or resid 1301 through 1313 \ )) } ncs_group { reference = chain 'E' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'R' 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: 8.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.350 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 76.850 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 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 0.218 31653 Z= 0.359 Angle : 1.145 20.859 43175 Z= 0.618 Chirality : 0.073 1.123 4983 Planarity : 0.010 0.299 5487 Dihedral : 14.510 106.635 12156 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 0.66 % Allowed : 0.96 % Favored : 98.38 % Cbeta Deviations : 0.03 % 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: -0.60 (0.13), residues: 3814 helix: 2.09 (0.20), residues: 678 sheet: -0.30 (0.17), residues: 944 loop : -1.30 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 886 HIS 0.012 0.002 HIS C1048 PHE 0.068 0.004 PHE B 377 TYR 0.058 0.003 TYR B 508 ARG 0.021 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01241 ( 46) link_NAG-ASN : angle 5.21307 ( 138) link_BETA1-4 : bond 0.00768 ( 7) link_BETA1-4 : angle 3.44454 ( 21) hydrogen bonds : bond 0.16986 ( 1123) hydrogen bonds : angle 7.71087 ( 3177) SS BOND : bond 0.00746 ( 42) SS BOND : angle 1.91563 ( 84) covalent geometry : bond 0.00740 (31558) covalent geometry : angle 1.10351 (42932) *********************** 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 596 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 574 time to evaluate : 3.123 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: symmetry clash revert: symmetry clash REVERT: A 919 ASN cc_start: 0.5895 (m-40) cc_final: 0.5563 (m110) REVERT: C 177 MET cc_start: 0.1518 (ttt) cc_final: 0.0923 (mpt) REVERT: C 384 PRO cc_start: 0.5205 (Cg_endo) cc_final: 0.4681 (Cg_exo) REVERT: T 82 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8297 (tm-30) REVERT: T 110 LEU cc_start: 0.7766 (mt) cc_final: 0.7486 (mt) outliers start: 22 outliers final: 4 residues processed: 594 average time/residue: 1.1491 time to fit residues: 830.3786 Evaluate side-chains 298 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 294 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 7.9990 chunk 290 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 223 optimal weight: 8.9990 chunk 347 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 774 GLN A 901 GLN A 954 GLN A 969 ASN B 49 HIS B 81 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 954 GLN B 957 GLN B1106 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C1002 GLN C1106 GLN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.207846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.146252 restraints weight = 56925.849| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.91 r_work: 0.3750 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 31653 Z= 0.220 Angle : 0.802 15.215 43175 Z= 0.398 Chirality : 0.053 0.488 4983 Planarity : 0.006 0.068 5487 Dihedral : 9.253 77.491 5376 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 2.71 % Allowed : 12.69 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.69 (0.13), residues: 3814 helix: 1.90 (0.20), residues: 656 sheet: -0.27 (0.16), residues: 951 loop : -1.33 (0.12), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 886 HIS 0.007 0.001 HIS A1048 PHE 0.040 0.003 PHE B 898 TYR 0.027 0.002 TYR C1067 ARG 0.010 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.01308 ( 46) link_NAG-ASN : angle 3.97218 ( 138) link_BETA1-4 : bond 0.01339 ( 7) link_BETA1-4 : angle 3.21575 ( 21) hydrogen bonds : bond 0.04797 ( 1123) hydrogen bonds : angle 6.26141 ( 3177) SS BOND : bond 0.00727 ( 42) SS BOND : angle 1.28496 ( 84) covalent geometry : bond 0.00487 (31558) covalent geometry : angle 0.76671 (42932) *********************** 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 429 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 339 time to evaluate : 3.503 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: A 100 ILE cc_start: 0.9093 (mp) cc_final: 0.8810 (mm) REVERT: A 226 LEU cc_start: 0.7982 (tt) cc_final: 0.7777 (mm) REVERT: A 451 TYR cc_start: 0.7010 (m-80) cc_final: 0.6397 (m-10) REVERT: A 453 TYR cc_start: 0.9515 (p90) cc_final: 0.9212 (p90) REVERT: A 774 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7111 (mm-40) REVERT: A 859 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8502 (t) REVERT: A 919 ASN cc_start: 0.7449 (m-40) cc_final: 0.7245 (m110) REVERT: B 44 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5789 (mtm-85) REVERT: B 49 HIS cc_start: 0.5633 (t70) cc_final: 0.5412 (t-90) REVERT: B 223 LEU cc_start: 0.3926 (OUTLIER) cc_final: 0.3707 (tp) REVERT: B 308 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7979 (p) REVERT: B 558 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6528 (mmmm) REVERT: B 918 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: B 1010 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: B 1106 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: C 133 PHE cc_start: 0.7865 (m-80) cc_final: 0.7594 (m-10) REVERT: C 177 MET cc_start: 0.2809 (ttt) cc_final: 0.0803 (mpt) REVERT: C 269 TYR cc_start: 0.7149 (m-10) cc_final: 0.6836 (m-80) REVERT: C 325 SER cc_start: 0.8747 (t) cc_final: 0.8479 (p) REVERT: C 360 ASN cc_start: 0.8602 (t0) cc_final: 0.8394 (t0) REVERT: C 394 ASN cc_start: 0.7364 (t0) cc_final: 0.6704 (t0) REVERT: C 495 TYR cc_start: 0.8028 (m-10) cc_final: 0.7812 (m-80) REVERT: C 786 LYS cc_start: 0.7372 (pttm) cc_final: 0.7041 (mmmt) REVERT: C 976 VAL cc_start: 0.6873 (p) cc_final: 0.6657 (m) REVERT: C 1077 THR cc_start: 0.7885 (p) cc_final: 0.6906 (t) REVERT: R 48 MET cc_start: 0.8825 (mtp) cc_final: 0.8536 (ptp) REVERT: R 54 MET cc_start: 0.8977 (mmp) cc_final: 0.8516 (mpp) REVERT: R 98 ARG cc_start: 0.8596 (mmp80) cc_final: 0.8235 (tpm170) REVERT: T 12 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.7874 (ttmt) REVERT: T 19 LYS cc_start: 0.9323 (tppt) cc_final: 0.9064 (tppt) REVERT: T 23 LYS cc_start: 0.9390 (tptp) cc_final: 0.9120 (tppt) REVERT: T 45 LEU cc_start: 0.8332 (mt) cc_final: 0.8085 (mm) REVERT: T 52 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7900 (pp) REVERT: T 54 MET cc_start: 0.9036 (mmp) cc_final: 0.8750 (mmp) REVERT: Q 21 LEU cc_start: 0.8394 (mt) cc_final: 0.8150 (mm) REVERT: Q 62 ARG cc_start: 0.9120 (ptt-90) cc_final: 0.8258 (ppt-90) REVERT: Q 63 PHE cc_start: 0.9074 (m-80) cc_final: 0.8237 (m-80) REVERT: Q 75 THR cc_start: 0.7833 (p) cc_final: 0.7436 (t) REVERT: Q 76 ILE cc_start: 0.8465 (tp) cc_final: 0.7902 (tp) REVERT: Q 88 TYR cc_start: 0.8703 (m-80) cc_final: 0.8230 (m-80) REVERT: K 54 MET cc_start: 0.7858 (pmm) cc_final: 0.7610 (pmm) outliers start: 90 outliers final: 33 residues processed: 407 average time/residue: 1.0785 time to fit residues: 542.8083 Evaluate side-chains 311 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 295 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 367 optimal weight: 40.0000 chunk 263 optimal weight: 0.7980 chunk 272 optimal weight: 0.1980 chunk 254 optimal weight: 9.9990 chunk 270 optimal weight: 0.5980 chunk 356 optimal weight: 7.9990 chunk 328 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1011 GLN B1106 GLN C 146 HIS C 493 GLN C 751 ASN C 777 ASN C1002 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 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 = 0.4793 r_free = 0.4793 target = 0.199932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.137790 restraints weight = 57501.597| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.43 r_work: 0.3691 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31653 Z= 0.176 Angle : 0.720 15.327 43175 Z= 0.357 Chirality : 0.051 0.667 4983 Planarity : 0.005 0.053 5487 Dihedral : 8.267 71.700 5370 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 3.40 % Allowed : 15.12 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.13), residues: 3814 helix: 1.95 (0.20), residues: 647 sheet: -0.33 (0.17), residues: 944 loop : -1.32 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 104 HIS 0.003 0.001 HIS A1083 PHE 0.026 0.002 PHE C 565 TYR 0.022 0.002 TYR C1067 ARG 0.009 0.001 ARG B 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00922 ( 46) link_NAG-ASN : angle 3.63309 ( 138) link_BETA1-4 : bond 0.00484 ( 7) link_BETA1-4 : angle 2.46419 ( 21) hydrogen bonds : bond 0.04622 ( 1123) hydrogen bonds : angle 6.05818 ( 3177) SS BOND : bond 0.00849 ( 42) SS BOND : angle 1.36021 ( 84) covalent geometry : bond 0.00389 (31558) covalent geometry : angle 0.68678 (42932) *********************** 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 425 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 312 time to evaluate : 3.284 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9011 (mp) cc_final: 0.8756 (mp) REVERT: A 229 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (mm) REVERT: A 453 TYR cc_start: 0.9568 (p90) cc_final: 0.9235 (p90) REVERT: A 919 ASN cc_start: 0.7385 (m-40) cc_final: 0.7175 (m110) REVERT: A 1111 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: B 14 GLN cc_start: 0.4749 (OUTLIER) cc_final: 0.4537 (pp30) REVERT: B 104 TRP cc_start: 0.3546 (m-10) cc_final: 0.3340 (m-10) REVERT: B 136 CYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6303 (t) REVERT: B 177 MET cc_start: 0.1152 (ttt) cc_final: -0.0164 (mmt) REVERT: B 308 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8108 (p) REVERT: B 558 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6526 (mmmm) REVERT: B 577 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6130 (ptp-170) REVERT: B 587 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7499 (pp) REVERT: B 988 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7738 (mp0) REVERT: B 1010 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: C 160 TYR cc_start: 0.6336 (p90) cc_final: 0.6052 (p90) REVERT: C 177 MET cc_start: 0.2666 (ttt) cc_final: 0.0450 (mpt) REVERT: C 325 SER cc_start: 0.8729 (t) cc_final: 0.8479 (p) REVERT: C 356 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7909 (ttpp) REVERT: C 505 TYR cc_start: 0.8000 (t80) cc_final: 0.7554 (t80) REVERT: C 735 SER cc_start: 0.8116 (t) cc_final: 0.7872 (t) REVERT: C 786 LYS cc_start: 0.7570 (pttm) cc_final: 0.7220 (mmmt) REVERT: C 988 GLU cc_start: 0.8190 (mp0) cc_final: 0.7788 (mp0) REVERT: C 1038 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7882 (mptp) REVERT: C 1077 THR cc_start: 0.8348 (p) cc_final: 0.8083 (p) REVERT: R 54 MET cc_start: 0.9055 (mmp) cc_final: 0.8212 (pmm) REVERT: R 98 ARG cc_start: 0.8727 (mmp80) cc_final: 0.8419 (mmp-170) REVERT: T 23 LYS cc_start: 0.9401 (tptp) cc_final: 0.9157 (tppt) REVERT: T 48 MET cc_start: 0.8383 (mpt) cc_final: 0.8148 (mpt) REVERT: T 54 MET cc_start: 0.9136 (mmp) cc_final: 0.8921 (mmp) REVERT: T 81 MET cc_start: 0.8108 (mtp) cc_final: 0.7865 (mtp) REVERT: T 82 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8403 (tp30) REVERT: Q 63 PHE cc_start: 0.9055 (m-80) cc_final: 0.8633 (m-80) REVERT: Q 75 THR cc_start: 0.7978 (p) cc_final: 0.7639 (t) REVERT: K 48 MET cc_start: 0.4494 (ptp) cc_final: 0.3944 (ptt) REVERT: K 60 TYR cc_start: 0.5832 (m-80) cc_final: 0.5369 (t80) REVERT: K 102 TYR cc_start: 0.2962 (m-80) cc_final: 0.1790 (m-80) outliers start: 113 outliers final: 47 residues processed: 392 average time/residue: 1.1472 time to fit residues: 556.4164 Evaluate side-chains 320 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 201 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 318 optimal weight: 0.4980 chunk 334 optimal weight: 9.9990 chunk 260 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 303 optimal weight: 0.5980 chunk 305 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 409 GLN B 542 ASN B 920 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.213622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.155379 restraints weight = 54413.434| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 4.63 r_work: 0.3580 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 31653 Z= 0.179 Angle : 0.708 13.944 43175 Z= 0.356 Chirality : 0.050 0.478 4983 Planarity : 0.005 0.060 5487 Dihedral : 7.481 66.132 5370 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 4.06 % Allowed : 16.42 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.13), residues: 3814 helix: 1.90 (0.20), residues: 652 sheet: -0.40 (0.16), residues: 976 loop : -1.35 (0.12), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 104 HIS 0.003 0.001 HIS A1083 PHE 0.028 0.002 PHE A 541 TYR 0.023 0.002 TYR K 101 ARG 0.009 0.001 ARG Q 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 46) link_NAG-ASN : angle 3.24884 ( 138) link_BETA1-4 : bond 0.00461 ( 7) link_BETA1-4 : angle 1.99057 ( 21) hydrogen bonds : bond 0.04503 ( 1123) hydrogen bonds : angle 6.03123 ( 3177) SS BOND : bond 0.00867 ( 42) SS BOND : angle 1.31184 ( 84) covalent geometry : bond 0.00402 (31558) covalent geometry : angle 0.68213 (42932) *********************** 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 416 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 281 time to evaluate : 3.270 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: A 100 ILE cc_start: 0.8974 (mp) cc_final: 0.8750 (mp) REVERT: A 298 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: A 451 TYR cc_start: 0.7029 (m-80) cc_final: 0.6664 (m-80) REVERT: A 453 TYR cc_start: 0.9509 (p90) cc_final: 0.9108 (p90) REVERT: A 774 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.8019 (mm-40) REVERT: A 936 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.6350 (t0) REVERT: B 14 GLN cc_start: 0.4086 (OUTLIER) cc_final: 0.3788 (pp30) REVERT: B 177 MET cc_start: 0.1180 (ttt) cc_final: -0.0210 (mmt) REVERT: B 306 PHE cc_start: 0.6799 (t80) cc_final: 0.6507 (t80) REVERT: B 558 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6740 (mmmm) REVERT: B 577 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6228 (ptp-170) REVERT: B 762 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: B 988 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7842 (mp0) REVERT: B 990 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7887 (mm-30) REVERT: B 1010 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: B 1113 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: C 160 TYR cc_start: 0.6738 (p90) cc_final: 0.6386 (p90) REVERT: C 177 MET cc_start: 0.2390 (ttt) cc_final: 0.0351 (mpt) REVERT: C 325 SER cc_start: 0.8743 (t) cc_final: 0.8501 (p) REVERT: C 349 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7532 (t) REVERT: C 505 TYR cc_start: 0.7925 (t80) cc_final: 0.7457 (t80) REVERT: C 735 SER cc_start: 0.8182 (t) cc_final: 0.7962 (t) REVERT: C 988 GLU cc_start: 0.8219 (mp0) cc_final: 0.7826 (mp0) REVERT: C 1113 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: R 48 MET cc_start: 0.8130 (ptp) cc_final: 0.7455 (mpp) REVERT: R 54 MET cc_start: 0.8761 (mmp) cc_final: 0.8151 (pmm) REVERT: R 98 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8228 (mmp-170) REVERT: T 23 LYS cc_start: 0.9366 (tptp) cc_final: 0.9133 (tppt) REVERT: T 48 MET cc_start: 0.8282 (mpt) cc_final: 0.7934 (mpt) REVERT: T 54 MET cc_start: 0.9163 (mmp) cc_final: 0.8444 (mmm) REVERT: T 82 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8336 (tp30) REVERT: T 118 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7597 (mm) REVERT: Q 75 THR cc_start: 0.7888 (p) cc_final: 0.7441 (t) REVERT: Q 79 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8388 (mp) REVERT: Q 88 TYR cc_start: 0.8642 (m-80) cc_final: 0.8101 (m-80) REVERT: K 60 TYR cc_start: 0.5730 (m-80) cc_final: 0.5325 (t80) REVERT: K 102 TYR cc_start: 0.2181 (m-80) cc_final: 0.0492 (m-80) outliers start: 135 outliers final: 55 residues processed: 374 average time/residue: 1.0515 time to fit residues: 487.7120 Evaluate side-chains 319 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 328 optimal weight: 0.7980 chunk 358 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 332 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 308 optimal weight: 0.0170 chunk 172 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 245 HIS ** O 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 = 0.4830 r_free = 0.4830 target = 0.205733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.139342 restraints weight = 55663.016| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.41 r_work: 0.3663 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 31653 Z= 0.165 Angle : 0.699 14.702 43175 Z= 0.349 Chirality : 0.049 0.463 4983 Planarity : 0.005 0.173 5487 Dihedral : 7.139 62.449 5370 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 3.88 % Allowed : 17.23 % Favored : 78.89 % 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: -0.77 (0.13), residues: 3814 helix: 1.90 (0.20), residues: 662 sheet: -0.44 (0.16), residues: 970 loop : -1.36 (0.12), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 104 HIS 0.002 0.001 HIS A1058 PHE 0.033 0.002 PHE B 140 TYR 0.024 0.002 TYR Q 37 ARG 0.014 0.001 ARG O 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00718 ( 46) link_NAG-ASN : angle 3.14586 ( 138) link_BETA1-4 : bond 0.00298 ( 7) link_BETA1-4 : angle 1.93970 ( 21) hydrogen bonds : bond 0.04365 ( 1123) hydrogen bonds : angle 5.99821 ( 3177) SS BOND : bond 0.00743 ( 42) SS BOND : angle 2.04262 ( 84) covalent geometry : bond 0.00375 (31558) covalent geometry : angle 0.67080 (42932) *********************** 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 388 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 259 time to evaluate : 3.225 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: A 298 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: A 451 TYR cc_start: 0.7141 (m-80) cc_final: 0.6851 (m-80) REVERT: A 453 TYR cc_start: 0.9572 (p90) cc_final: 0.9205 (p90) REVERT: A 900 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6936 (mtp) REVERT: A 988 GLU cc_start: 0.8108 (mp0) cc_final: 0.7337 (tp30) REVERT: A 1077 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8090 (p) REVERT: B 134 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7260 (pp30) REVERT: B 306 PHE cc_start: 0.7185 (t80) cc_final: 0.6820 (t80) REVERT: B 558 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6649 (mmmm) REVERT: B 762 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: B 1010 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: B 1113 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: C 41 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7061 (mmtp) REVERT: C 98 SER cc_start: 0.8823 (p) cc_final: 0.8170 (m) REVERT: C 117 LEU cc_start: 0.6554 (tt) cc_final: 0.5736 (mt) REVERT: C 160 TYR cc_start: 0.6835 (p90) cc_final: 0.6484 (p90) REVERT: C 177 MET cc_start: 0.2680 (ttt) cc_final: 0.0474 (mpt) REVERT: C 325 SER cc_start: 0.8719 (t) cc_final: 0.8494 (p) REVERT: C 349 SER cc_start: 0.7845 (OUTLIER) cc_final: 0.7425 (t) REVERT: C 374 PHE cc_start: 0.7546 (m-80) cc_final: 0.7128 (m-80) REVERT: C 462 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8657 (mmmm) REVERT: C 505 TYR cc_start: 0.8258 (t80) cc_final: 0.7734 (t80) REVERT: C 735 SER cc_start: 0.8365 (t) cc_final: 0.8152 (t) REVERT: C 740 MET cc_start: 0.8329 (ttt) cc_final: 0.8103 (ttm) REVERT: C 780 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6641 (pp20) REVERT: C 983 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.8037 (ttm110) REVERT: C 988 GLU cc_start: 0.8300 (mp0) cc_final: 0.7820 (mp0) REVERT: R 48 MET cc_start: 0.8116 (ptp) cc_final: 0.7348 (mpp) REVERT: R 54 MET cc_start: 0.8952 (mmp) cc_final: 0.8744 (mpp) REVERT: R 81 MET cc_start: -0.0596 (mmm) cc_final: -0.0923 (mmm) REVERT: R 98 ARG cc_start: 0.8521 (mmp80) cc_final: 0.8238 (mmp-170) REVERT: T 12 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7524 (tttt) REVERT: T 23 LYS cc_start: 0.9408 (tptp) cc_final: 0.9204 (tppt) REVERT: T 30 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.8987 (p0) REVERT: T 48 MET cc_start: 0.8362 (mpt) cc_final: 0.7794 (mpt) REVERT: T 54 MET cc_start: 0.9149 (mmp) cc_final: 0.8589 (mpm) REVERT: T 118 LEU cc_start: 0.8368 (tm) cc_final: 0.7558 (mm) REVERT: Q 75 THR cc_start: 0.7901 (p) cc_final: 0.7534 (t) REVERT: Q 79 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8313 (mm) REVERT: K 48 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.3577 (pmm) REVERT: K 60 TYR cc_start: 0.6096 (m-80) cc_final: 0.5613 (t80) outliers start: 129 outliers final: 62 residues processed: 356 average time/residue: 1.1028 time to fit residues: 487.9878 Evaluate side-chains 308 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 231 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 20 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 48 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 268 optimal weight: 0.4980 chunk 195 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 365 optimal weight: 10.0000 chunk 160 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 196 optimal weight: 0.0050 chunk 311 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 278 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN C 755 GLN C1002 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 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 = 0.4808 r_free = 0.4808 target = 0.198070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.132740 restraints weight = 56558.984| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.54 r_work: 0.3645 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31653 Z= 0.146 Angle : 0.672 12.524 43175 Z= 0.335 Chirality : 0.048 0.452 4983 Planarity : 0.005 0.139 5487 Dihedral : 6.905 59.471 5370 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 3.91 % Allowed : 17.65 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.75 (0.13), residues: 3814 helix: 1.95 (0.20), residues: 669 sheet: -0.49 (0.16), residues: 966 loop : -1.33 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 104 HIS 0.002 0.001 HIS A1088 PHE 0.023 0.002 PHE C 565 TYR 0.021 0.001 TYR Q 37 ARG 0.014 0.000 ARG T 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 46) link_NAG-ASN : angle 3.03798 ( 138) link_BETA1-4 : bond 0.00457 ( 7) link_BETA1-4 : angle 1.86360 ( 21) hydrogen bonds : bond 0.04172 ( 1123) hydrogen bonds : angle 5.90371 ( 3177) SS BOND : bond 0.00695 ( 42) SS BOND : angle 1.45621 ( 84) covalent geometry : bond 0.00327 (31558) covalent geometry : angle 0.64655 (42932) *********************** 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 385 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 255 time to evaluate : 3.421 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: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7615 (tp30) REVERT: A 453 TYR cc_start: 0.9610 (p90) cc_final: 0.9266 (p90) REVERT: A 900 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6929 (mtp) REVERT: B 14 GLN cc_start: 0.4883 (OUTLIER) cc_final: 0.4288 (pp30) REVERT: B 177 MET cc_start: 0.1085 (ttt) cc_final: -0.0462 (mmt) REVERT: B 558 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6694 (mmmm) REVERT: B 756 TYR cc_start: 0.7615 (t80) cc_final: 0.7152 (m-80) REVERT: B 762 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: B 990 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7746 (mm-30) REVERT: B 1010 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: C 41 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7015 (mmtp) REVERT: C 117 LEU cc_start: 0.6579 (tt) cc_final: 0.5812 (mt) REVERT: C 160 TYR cc_start: 0.6800 (p90) cc_final: 0.6446 (p90) REVERT: C 177 MET cc_start: 0.2647 (ttt) cc_final: 0.0589 (mpt) REVERT: C 325 SER cc_start: 0.8696 (t) cc_final: 0.8465 (p) REVERT: C 349 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7511 (t) REVERT: C 374 PHE cc_start: 0.7622 (m-80) cc_final: 0.7177 (m-80) REVERT: C 462 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8673 (mmmm) REVERT: C 505 TYR cc_start: 0.8253 (t80) cc_final: 0.7721 (t80) REVERT: C 656 VAL cc_start: 0.9029 (p) cc_final: 0.8829 (m) REVERT: C 735 SER cc_start: 0.8393 (t) cc_final: 0.8184 (t) REVERT: C 740 MET cc_start: 0.8432 (ttt) cc_final: 0.8147 (ttm) REVERT: C 780 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: C 988 GLU cc_start: 0.8406 (mp0) cc_final: 0.8013 (mp0) REVERT: R 48 MET cc_start: 0.8134 (ptp) cc_final: 0.7415 (mpp) REVERT: R 54 MET cc_start: 0.9090 (mmp) cc_final: 0.8874 (mpp) REVERT: R 81 MET cc_start: -0.0655 (mmm) cc_final: -0.1004 (mmm) REVERT: T 12 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7569 (tttt) REVERT: T 23 LYS cc_start: 0.9451 (tptp) cc_final: 0.9221 (tppt) REVERT: T 30 ASN cc_start: 0.9297 (OUTLIER) cc_final: 0.8978 (p0) REVERT: T 48 MET cc_start: 0.8387 (mpt) cc_final: 0.7904 (mpt) REVERT: T 54 MET cc_start: 0.9105 (mmp) cc_final: 0.8627 (mpm) REVERT: T 118 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7629 (mm) REVERT: Q 75 THR cc_start: 0.8019 (p) cc_final: 0.7610 (t) REVERT: Q 88 TYR cc_start: 0.8802 (m-80) cc_final: 0.8314 (m-80) REVERT: K 48 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.3944 (pmm) REVERT: K 60 TYR cc_start: 0.6114 (m-80) cc_final: 0.5692 (t80) REVERT: K 102 TYR cc_start: 0.2376 (m-80) cc_final: 0.1433 (m-80) outliers start: 130 outliers final: 72 residues processed: 349 average time/residue: 1.0188 time to fit residues: 446.5339 Evaluate side-chains 322 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 237 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 67 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 chunk 353 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 365 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 306 optimal weight: 0.1980 chunk 239 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 901 GLN A 919 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 703 ASN C 146 HIS C 196 ASN C 613 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.195508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.126668 restraints weight = 55080.671| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 3.18 r_work: 0.3589 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31653 Z= 0.237 Angle : 0.768 13.008 43175 Z= 0.390 Chirality : 0.052 0.431 4983 Planarity : 0.005 0.093 5487 Dihedral : 6.986 59.708 5370 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 4.27 % Allowed : 18.55 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.02 (0.13), residues: 3814 helix: 1.36 (0.19), residues: 677 sheet: -0.56 (0.16), residues: 962 loop : -1.43 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 104 HIS 0.011 0.001 HIS C 245 PHE 0.047 0.003 PHE T 64 TYR 0.024 0.002 TYR B1067 ARG 0.009 0.001 ARG Q 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 46) link_NAG-ASN : angle 3.10996 ( 138) link_BETA1-4 : bond 0.00409 ( 7) link_BETA1-4 : angle 1.82290 ( 21) hydrogen bonds : bond 0.05091 ( 1123) hydrogen bonds : angle 6.34685 ( 3177) SS BOND : bond 0.01011 ( 42) SS BOND : angle 1.75483 ( 84) covalent geometry : bond 0.00536 (31558) covalent geometry : angle 0.74424 (42932) *********************** 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 413 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 271 time to evaluate : 3.458 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 PHE cc_start: 0.6524 (p90) cc_final: 0.6063 (p90) REVERT: A 936 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6733 (t0) REVERT: B 195 LYS cc_start: 0.6178 (mtmt) cc_final: 0.5951 (mttm) REVERT: B 218 GLN cc_start: 0.0274 (OUTLIER) cc_final: -0.1215 (pm20) REVERT: B 266 TYR cc_start: 0.2893 (OUTLIER) cc_final: 0.2457 (m-10) REVERT: B 558 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6977 (mmmm) REVERT: B 756 TYR cc_start: 0.8034 (t80) cc_final: 0.7818 (m-80) REVERT: B 762 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: B 814 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7818 (mmmt) REVERT: B 983 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8463 (mtm110) REVERT: B 990 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7787 (mm-30) REVERT: B 1010 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: C 41 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6915 (mmtp) REVERT: C 160 TYR cc_start: 0.6818 (p90) cc_final: 0.6432 (p90) REVERT: C 177 MET cc_start: 0.2521 (ttt) cc_final: 0.0715 (mpt) REVERT: C 293 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8020 (tp) REVERT: C 349 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7706 (t) REVERT: C 740 MET cc_start: 0.8580 (ttt) cc_final: 0.8358 (ttm) REVERT: C 780 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6804 (pp20) REVERT: C 988 GLU cc_start: 0.8363 (mp0) cc_final: 0.8110 (mp0) REVERT: R 48 MET cc_start: 0.8039 (ptp) cc_final: 0.7147 (mpp) REVERT: R 54 MET cc_start: 0.8968 (mmp) cc_final: 0.8418 (pmm) REVERT: R 81 MET cc_start: -0.0556 (mmm) cc_final: -0.0930 (mmm) REVERT: T 12 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7219 (tttt) REVERT: T 23 LYS cc_start: 0.9404 (tptp) cc_final: 0.9180 (tppt) REVERT: T 39 GLN cc_start: 0.7689 (mm110) cc_final: 0.7110 (mt0) REVERT: T 46 GLU cc_start: 0.6681 (pp20) cc_final: 0.6475 (pp20) REVERT: T 48 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8063 (mpt) REVERT: T 54 MET cc_start: 0.9018 (mmp) cc_final: 0.8611 (mpm) REVERT: T 118 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7445 (mm) REVERT: Q 75 THR cc_start: 0.7931 (p) cc_final: 0.7459 (t) REVERT: Q 88 TYR cc_start: 0.8742 (m-80) cc_final: 0.8533 (m-80) REVERT: K 48 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.3673 (pmm) REVERT: K 60 TYR cc_start: 0.5900 (m-80) cc_final: 0.5611 (t80) REVERT: K 102 TYR cc_start: 0.1860 (m-80) cc_final: 0.0950 (m-80) outliers start: 142 outliers final: 72 residues processed: 374 average time/residue: 1.0393 time to fit residues: 487.7282 Evaluate side-chains 320 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 234 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 48 MET Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 48 MET Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 78 optimal weight: 0.6980 chunk 133 optimal weight: 0.0870 chunk 379 optimal weight: 50.0000 chunk 335 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 248 optimal weight: 8.9990 chunk 360 optimal weight: 0.1980 chunk 67 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 542 ASN B 755 GLN B1058 HIS B1113 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.195872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.130119 restraints weight = 55807.906| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.32 r_work: 0.3616 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31653 Z= 0.140 Angle : 0.686 14.756 43175 Z= 0.343 Chirality : 0.048 0.416 4983 Planarity : 0.005 0.172 5487 Dihedral : 6.654 59.434 5369 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 3.13 % Allowed : 20.11 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3814 helix: 1.68 (0.20), residues: 674 sheet: -0.55 (0.16), residues: 981 loop : -1.40 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP K 113 HIS 0.003 0.001 HIS B1058 PHE 0.027 0.002 PHE T 55 TYR 0.031 0.001 TYR K 112 ARG 0.010 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 46) link_NAG-ASN : angle 2.92099 ( 138) link_BETA1-4 : bond 0.00487 ( 7) link_BETA1-4 : angle 1.76089 ( 21) hydrogen bonds : bond 0.04198 ( 1123) hydrogen bonds : angle 5.99116 ( 3177) SS BOND : bond 0.00564 ( 42) SS BOND : angle 1.39091 ( 84) covalent geometry : bond 0.00312 (31558) covalent geometry : angle 0.66339 (42932) *********************** 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 350 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 246 time to evaluate : 3.143 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: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.7266 (m-80) cc_final: 0.6173 (m-10) REVERT: A 565 PHE cc_start: 0.6526 (p90) cc_final: 0.6162 (p90) REVERT: A 900 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7171 (mtp) REVERT: A 988 GLU cc_start: 0.7975 (mp0) cc_final: 0.7738 (mp0) REVERT: A 1074 ASN cc_start: 0.7525 (m110) cc_final: 0.7236 (t0) REVERT: B 44 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.7039 (ttm110) REVERT: B 180 GLU cc_start: 0.0429 (OUTLIER) cc_final: -0.0881 (mt-10) REVERT: B 195 LYS cc_start: 0.6167 (mtmt) cc_final: 0.5894 (mttm) REVERT: B 558 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6926 (mmmm) REVERT: B 756 TYR cc_start: 0.8036 (t80) cc_final: 0.7794 (m-80) REVERT: B 814 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7816 (mmmt) REVERT: B 983 ARG cc_start: 0.8719 (ttm110) cc_final: 0.8502 (mtm180) REVERT: B 990 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7741 (mm-30) REVERT: B 1010 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: C 41 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7161 (mmtm) REVERT: C 160 TYR cc_start: 0.6789 (p90) cc_final: 0.6383 (p90) REVERT: C 177 MET cc_start: 0.2573 (ttt) cc_final: 0.0237 (mpp) REVERT: C 200 TYR cc_start: 0.7520 (t80) cc_final: 0.7128 (t80) REVERT: C 217 PRO cc_start: 0.8205 (Cg_endo) cc_final: 0.8004 (Cg_exo) REVERT: C 349 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7627 (t) REVERT: C 462 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8593 (mmmm) REVERT: C 490 PHE cc_start: 0.7380 (t80) cc_final: 0.7173 (t80) REVERT: C 780 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6687 (pp20) REVERT: R 48 MET cc_start: 0.8168 (ptp) cc_final: 0.7351 (mpp) REVERT: R 54 MET cc_start: 0.8998 (mmp) cc_final: 0.8788 (mpp) REVERT: R 81 MET cc_start: -0.0439 (mmm) cc_final: -0.0763 (mmm) REVERT: T 12 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7357 (tttt) REVERT: T 23 LYS cc_start: 0.9483 (tptp) cc_final: 0.9264 (tppt) REVERT: T 30 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.8988 (p0) REVERT: T 36 TRP cc_start: 0.7632 (m100) cc_final: 0.7285 (m100) REVERT: T 48 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (mpt) REVERT: T 54 MET cc_start: 0.9009 (mmp) cc_final: 0.8420 (mpm) REVERT: T 118 LEU cc_start: 0.8326 (tm) cc_final: 0.7530 (mm) REVERT: Q 75 THR cc_start: 0.7978 (p) cc_final: 0.7541 (t) REVERT: Q 88 TYR cc_start: 0.8835 (m-80) cc_final: 0.8612 (m-80) REVERT: K 60 TYR cc_start: 0.5923 (m-80) cc_final: 0.5648 (t80) REVERT: K 102 TYR cc_start: 0.1632 (m-80) cc_final: 0.0899 (m-80) outliers start: 104 outliers final: 58 residues processed: 320 average time/residue: 1.0356 time to fit residues: 413.1918 Evaluate side-chains 299 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 230 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 48 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 306 optimal weight: 0.9990 chunk 337 optimal weight: 20.0000 chunk 287 optimal weight: 0.9980 chunk 370 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 352 optimal weight: 0.0670 chunk 336 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 268 optimal weight: 0.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 955 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 703 ASN B1058 HIS B1113 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.194629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.125060 restraints weight = 54974.161| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.77 r_work: 0.3635 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31653 Z= 0.184 Angle : 0.726 15.330 43175 Z= 0.368 Chirality : 0.049 0.424 4983 Planarity : 0.005 0.101 5487 Dihedral : 6.616 59.646 5369 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.10 % Rotamer: Outliers : 3.10 % Allowed : 20.57 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3814 helix: 1.64 (0.20), residues: 678 sheet: -0.60 (0.16), residues: 989 loop : -1.38 (0.12), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 113 HIS 0.004 0.001 HIS B1058 PHE 0.084 0.002 PHE B 543 TYR 0.048 0.002 TYR K 94 ARG 0.011 0.001 ARG Q 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 46) link_NAG-ASN : angle 2.90701 ( 138) link_BETA1-4 : bond 0.00421 ( 7) link_BETA1-4 : angle 1.76192 ( 21) hydrogen bonds : bond 0.04519 ( 1123) hydrogen bonds : angle 6.08502 ( 3177) SS BOND : bond 0.00788 ( 42) SS BOND : angle 1.48741 ( 84) covalent geometry : bond 0.00418 (31558) covalent geometry : angle 0.70510 (42932) *********************** 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 343 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 240 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: 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 396 TYR cc_start: 0.7310 (m-80) cc_final: 0.6165 (m-10) REVERT: A 565 PHE cc_start: 0.6553 (p90) cc_final: 0.6191 (p90) REVERT: A 900 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7272 (mtp) REVERT: A 988 GLU cc_start: 0.8020 (mp0) cc_final: 0.7816 (pm20) REVERT: B 136 CYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6147 (t) REVERT: B 180 GLU cc_start: 0.0680 (OUTLIER) cc_final: -0.0847 (mt-10) REVERT: B 195 LYS cc_start: 0.6160 (mtmt) cc_final: 0.5899 (mttm) REVERT: B 558 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6989 (mmmm) REVERT: B 580 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6860 (mm110) REVERT: B 814 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7860 (mmmt) REVERT: B 990 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7816 (mm-30) REVERT: B 1010 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: C 41 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7227 (mmtm) REVERT: C 160 TYR cc_start: 0.6745 (p90) cc_final: 0.6346 (p90) REVERT: C 177 MET cc_start: 0.2593 (ttt) cc_final: 0.0364 (mpp) REVERT: C 217 PRO cc_start: 0.8280 (Cg_endo) cc_final: 0.8068 (Cg_exo) REVERT: C 349 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7536 (t) REVERT: C 403 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6651 (mtp-110) REVERT: C 462 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8551 (mmmm) REVERT: C 780 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6737 (pp20) REVERT: C 988 GLU cc_start: 0.8292 (mp0) cc_final: 0.8078 (mp0) REVERT: R 48 MET cc_start: 0.8261 (ptp) cc_final: 0.7505 (mpp) REVERT: R 81 MET cc_start: -0.0472 (mmm) cc_final: -0.0696 (mmm) REVERT: O 88 TYR cc_start: 0.8102 (m-80) cc_final: 0.7765 (m-80) REVERT: T 12 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6970 (tttt) REVERT: T 18 VAL cc_start: 0.8135 (p) cc_final: 0.7823 (p) REVERT: T 23 LYS cc_start: 0.9413 (tptp) cc_final: 0.9184 (tppt) REVERT: T 30 ASN cc_start: 0.9324 (OUTLIER) cc_final: 0.8977 (p0) REVERT: T 39 GLN cc_start: 0.7619 (mm110) cc_final: 0.6966 (mt0) REVERT: T 48 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7904 (mpt) REVERT: T 54 MET cc_start: 0.8866 (mmp) cc_final: 0.8520 (mpm) REVERT: T 118 LEU cc_start: 0.8189 (tm) cc_final: 0.7354 (mt) REVERT: Q 24 ARG cc_start: 0.8962 (tpp-160) cc_final: 0.7942 (mmp80) REVERT: Q 75 THR cc_start: 0.7852 (p) cc_final: 0.7421 (t) REVERT: Q 88 TYR cc_start: 0.8705 (m-80) cc_final: 0.8445 (m-80) REVERT: K 32 TYR cc_start: 0.6123 (t80) cc_final: 0.5649 (t80) REVERT: K 48 MET cc_start: 0.7001 (pmm) cc_final: 0.5057 (pmt) REVERT: K 60 TYR cc_start: 0.6025 (m-80) cc_final: 0.5778 (t80) outliers start: 103 outliers final: 70 residues processed: 319 average time/residue: 1.0871 time to fit residues: 435.6135 Evaluate side-chains 312 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 229 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 48 MET Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 88 TYR Chi-restraints excluded: chain K residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 96 optimal weight: 0.6980 chunk 352 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 139 optimal weight: 40.0000 chunk 345 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 326 optimal weight: 40.0000 chunk 110 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1113 GLN C 314 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 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 = 0.4772 r_free = 0.4772 target = 0.194034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.127327 restraints weight = 55265.814| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.12 r_work: 0.3600 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31653 Z= 0.185 Angle : 0.723 16.067 43175 Z= 0.365 Chirality : 0.049 0.430 4983 Planarity : 0.005 0.083 5487 Dihedral : 6.532 59.677 5369 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 2.83 % Allowed : 20.93 % Favored : 76.25 % 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: -0.92 (0.13), residues: 3814 helix: 1.61 (0.20), residues: 678 sheet: -0.56 (0.16), residues: 954 loop : -1.40 (0.12), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP T 36 HIS 0.004 0.001 HIS B1058 PHE 0.036 0.002 PHE T 70 TYR 0.034 0.002 TYR K 112 ARG 0.011 0.001 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 46) link_NAG-ASN : angle 2.88466 ( 138) link_BETA1-4 : bond 0.00450 ( 7) link_BETA1-4 : angle 1.71619 ( 21) hydrogen bonds : bond 0.04462 ( 1123) hydrogen bonds : angle 6.08650 ( 3177) SS BOND : bond 0.00713 ( 42) SS BOND : angle 1.46442 ( 84) covalent geometry : bond 0.00422 (31558) covalent geometry : angle 0.70203 (42932) ********************** 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 325 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 231 time to evaluate : 3.270 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7942 (m-80) cc_final: 0.7370 (t80) REVERT: A 396 TYR cc_start: 0.7289 (m-80) cc_final: 0.6174 (m-10) REVERT: A 565 PHE cc_start: 0.6789 (p90) cc_final: 0.6356 (p90) REVERT: A 900 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7301 (mtp) REVERT: B 136 CYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6488 (p) REVERT: B 180 GLU cc_start: 0.0366 (OUTLIER) cc_final: -0.1103 (mt-10) REVERT: B 195 LYS cc_start: 0.6285 (mtmt) cc_final: 0.6045 (mttm) REVERT: B 266 TYR cc_start: 0.3054 (OUTLIER) cc_final: 0.2727 (m-10) REVERT: B 297 SER cc_start: 0.7470 (m) cc_final: 0.7031 (p) REVERT: B 558 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7012 (mmmm) REVERT: B 580 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6770 (mm110) REVERT: B 588 THR cc_start: 0.7405 (OUTLIER) cc_final: 0.7109 (p) REVERT: B 814 LYS cc_start: 0.8388 (mmtt) cc_final: 0.7846 (mmmt) REVERT: B 990 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7658 (mm-30) REVERT: B 1010 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: C 160 TYR cc_start: 0.6877 (p90) cc_final: 0.6428 (p90) REVERT: C 177 MET cc_start: 0.2520 (ttt) cc_final: 0.0318 (mpp) REVERT: C 200 TYR cc_start: 0.7264 (t80) cc_final: 0.6984 (t80) REVERT: C 217 PRO cc_start: 0.8310 (Cg_endo) cc_final: 0.8064 (Cg_exo) REVERT: C 349 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7636 (t) REVERT: C 403 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6325 (mtp-110) REVERT: C 462 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8561 (mmmm) REVERT: C 516 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7447 (tm-30) REVERT: C 780 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6759 (pp20) REVERT: C 796 ASP cc_start: 0.7004 (t0) cc_final: 0.6434 (p0) REVERT: C 988 GLU cc_start: 0.8371 (mp0) cc_final: 0.8168 (mp0) REVERT: R 48 MET cc_start: 0.8344 (ptp) cc_final: 0.7616 (mpp) REVERT: R 81 MET cc_start: -0.0499 (mmm) cc_final: -0.0752 (mmm) REVERT: O 88 TYR cc_start: 0.8237 (m-80) cc_final: 0.7915 (m-80) REVERT: T 12 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7153 (tttt) REVERT: T 18 VAL cc_start: 0.8369 (p) cc_final: 0.8072 (p) REVERT: T 23 LYS cc_start: 0.9435 (tptp) cc_final: 0.9199 (tppt) REVERT: T 30 ASN cc_start: 0.9354 (OUTLIER) cc_final: 0.9024 (p0) REVERT: T 38 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8188 (tmm160) REVERT: T 48 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8023 (mpt) REVERT: T 54 MET cc_start: 0.9068 (mmp) cc_final: 0.8535 (mpm) REVERT: Q 24 ARG cc_start: 0.8971 (tpp-160) cc_final: 0.7898 (mmp80) REVERT: Q 75 THR cc_start: 0.7907 (p) cc_final: 0.7450 (t) REVERT: Q 88 TYR cc_start: 0.8813 (m-80) cc_final: 0.8342 (m-80) REVERT: K 48 MET cc_start: 0.7367 (pmm) cc_final: 0.5365 (pmm) REVERT: K 60 TYR cc_start: 0.6103 (m-80) cc_final: 0.5880 (t80) REVERT: K 102 TYR cc_start: 0.1011 (m-80) cc_final: 0.0571 (m-80) outliers start: 94 outliers final: 67 residues processed: 305 average time/residue: 1.0430 time to fit residues: 399.1213 Evaluate side-chains 301 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 12 LYS Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 48 MET Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 88 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 172 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 372 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 153 optimal weight: 50.0000 chunk 80 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 703 ASN B 779 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1113 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.193549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.127930 restraints weight = 55508.735| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.17 r_work: 0.3596 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31653 Z= 0.174 Angle : 0.709 13.056 43175 Z= 0.359 Chirality : 0.049 0.436 4983 Planarity : 0.005 0.096 5487 Dihedral : 6.435 59.677 5369 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 20.78 % Favored : 76.19 % 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: -0.94 (0.13), residues: 3814 helix: 1.57 (0.20), residues: 678 sheet: -0.62 (0.16), residues: 981 loop : -1.38 (0.12), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP T 36 HIS 0.004 0.001 HIS B1058 PHE 0.028 0.002 PHE A 400 TYR 0.027 0.002 TYR C 200 ARG 0.011 0.001 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 46) link_NAG-ASN : angle 2.86354 ( 138) link_BETA1-4 : bond 0.00436 ( 7) link_BETA1-4 : angle 1.69493 ( 21) hydrogen bonds : bond 0.04391 ( 1123) hydrogen bonds : angle 6.03974 ( 3177) SS BOND : bond 0.00690 ( 42) SS BOND : angle 1.43776 ( 84) covalent geometry : bond 0.00396 (31558) covalent geometry : angle 0.68818 (42932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47831.49 seconds wall clock time: 818 minutes 3.69 seconds (49083.69 seconds total)