Starting phenix.real_space_refine on Fri Mar 6 12:06:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a94_15269/03_2026/8a94_15269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a94_15269/03_2026/8a94_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_15269/03_2026/8a94_15269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a94_15269/03_2026/8a94_15269.map" model { file = "/net/cci-nas-00/data/ceres_data/8a94_15269/03_2026/8a94_15269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a94_15269/03_2026/8a94_15269.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 6.14, per 1000 atoms: 0.20 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: 1.90 Conformation dependent library (CDL) restraints added in 1.1 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: 1.21 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: 7.51 Time building geometry restraints manager: 2.53 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 1313)) \ selection = (chain 'B' and (resid 14 through 577 or resid 584 through 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 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: 9.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.830 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.580 ------------------------------------------------------------------------------- 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 : 6.59 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (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 ARG 0.021 0.001 ARG A 357 TYR 0.058 0.003 TYR B 508 PHE 0.068 0.004 PHE B 377 TRP 0.042 0.003 TRP A 886 HIS 0.012 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00740 (31558) covalent geometry : angle 1.10351 (42932) SS BOND : bond 0.00746 ( 42) SS BOND : angle 1.91563 ( 84) hydrogen bonds : bond 0.16986 ( 1123) hydrogen bonds : angle 7.71087 ( 3177) link_BETA1-4 : bond 0.00768 ( 7) link_BETA1-4 : angle 3.44454 ( 21) link_NAG-ASN : bond 0.01241 ( 46) link_NAG-ASN : angle 5.21307 ( 138) *********************** 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 : 1.115 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: 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) outliers start: 22 outliers final: 5 residues processed: 594 average time/residue: 0.5596 time to fit residues: 401.7578 Evaluate side-chains 294 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 T residue 3 GLN 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 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 0.8980 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B1071 GLN B1106 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1106 GLN C1113 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.207647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.162083 restraints weight = 60542.054| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 4.32 r_work: 0.3934 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 31653 Z= 0.154 Angle : 0.745 15.688 43175 Z= 0.366 Chirality : 0.051 0.501 4983 Planarity : 0.005 0.063 5487 Dihedral : 9.362 81.115 5379 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 2.62 % Allowed : 12.21 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 3814 helix: 2.35 (0.20), residues: 662 sheet: -0.21 (0.16), residues: 964 loop : -1.24 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 237 TYR 0.021 0.002 TYR T 60 PHE 0.036 0.002 PHE C 565 TRP 0.017 0.002 TRP T 113 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00330 (31558) covalent geometry : angle 0.71025 (42932) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.12113 ( 84) hydrogen bonds : bond 0.04375 ( 1123) hydrogen bonds : angle 6.11169 ( 3177) link_BETA1-4 : bond 0.01099 ( 7) link_BETA1-4 : angle 3.11725 ( 21) link_NAG-ASN : bond 0.00939 ( 46) link_NAG-ASN : angle 3.81077 ( 138) *********************** 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 413 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 326 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.9037 (mp) cc_final: 0.8727 (mm) REVERT: A 453 TYR cc_start: 0.9402 (p90) cc_final: 0.9085 (p90) REVERT: A 919 ASN cc_start: 0.6942 (m-40) cc_final: 0.6591 (m110) REVERT: A 1074 ASN cc_start: 0.6484 (m110) cc_final: 0.6249 (t0) REVERT: B 14 GLN cc_start: 0.5310 (OUTLIER) cc_final: 0.4484 (pm20) REVERT: B 91 TYR cc_start: 0.4138 (t80) cc_final: 0.3798 (t80) REVERT: B 558 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6110 (mmmm) REVERT: B 993 ILE cc_start: 0.8838 (mt) cc_final: 0.8628 (mm) REVERT: C 133 PHE cc_start: 0.7720 (m-80) cc_final: 0.7428 (m-10) REVERT: C 177 MET cc_start: 0.3023 (ttt) cc_final: 0.0822 (mpt) REVERT: C 226 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6779 (mt) REVERT: C 988 GLU cc_start: 0.8095 (mp0) cc_final: 0.7724 (mp0) REVERT: C 1077 THR cc_start: 0.5835 (p) cc_final: 0.4756 (t) REVERT: R 48 MET cc_start: 0.8761 (mtp) cc_final: 0.8466 (mtm) REVERT: R 54 MET cc_start: 0.8769 (mmp) cc_final: 0.8382 (mpp) REVERT: R 82 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7106 (tm-30) REVERT: T 45 LEU cc_start: 0.8330 (mt) cc_final: 0.7977 (mt) REVERT: T 48 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7820 (mpt) REVERT: T 52 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8034 (pp) REVERT: T 81 MET cc_start: 0.9009 (ttp) cc_final: 0.8741 (mtp) REVERT: T 82 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8822 (tm-30) REVERT: Q 80 GLU cc_start: 0.8036 (mp0) cc_final: 0.7666 (mp0) REVERT: Q 88 TYR cc_start: 0.8505 (m-80) cc_final: 0.8070 (m-80) REVERT: K 54 MET cc_start: 0.6227 (pmm) cc_final: 0.5892 (pmm) outliers start: 87 outliers final: 31 residues processed: 387 average time/residue: 0.5345 time to fit residues: 252.6268 Evaluate side-chains 283 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 231 ILE 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 747 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 1130 ILE Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 978 ASN 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 468 ILE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain R residue 55 PHE Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 48 MET 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 259 optimal weight: 3.9990 chunk 23 optimal weight: 30.0000 chunk 75 optimal weight: 1.9990 chunk 153 optimal weight: 30.0000 chunk 295 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 A 913 GLN A 955 ASN A 969 ASN B 49 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1002 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN Q 90 GLN ** 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 = 0.4807 r_free = 0.4807 target = 0.202615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.138709 restraints weight = 56571.621| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 3.49 r_work: 0.3655 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.261 31653 Z= 0.240 Angle : 0.810 15.495 43175 Z= 0.406 Chirality : 0.054 0.687 4983 Planarity : 0.006 0.062 5487 Dihedral : 8.343 70.873 5370 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Rotamer: Outliers : 3.37 % Allowed : 14.34 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 3814 helix: 1.70 (0.20), residues: 657 sheet: -0.33 (0.17), residues: 923 loop : -1.38 (0.12), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 87 TYR 0.026 0.002 TYR B1067 PHE 0.043 0.003 PHE B 898 TRP 0.033 0.002 TRP A 886 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00541 (31558) covalent geometry : angle 0.77988 (42932) SS BOND : bond 0.00988 ( 42) SS BOND : angle 1.79649 ( 84) hydrogen bonds : bond 0.05240 ( 1123) hydrogen bonds : angle 6.29331 ( 3177) link_BETA1-4 : bond 0.00549 ( 7) link_BETA1-4 : angle 2.48336 ( 21) link_NAG-ASN : bond 0.01041 ( 46) link_NAG-ASN : angle 3.61504 ( 138) *********************** 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 424 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 312 time to evaluate : 1.161 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 451 TYR cc_start: 0.6940 (m-80) cc_final: 0.6353 (m-80) REVERT: A 453 TYR cc_start: 0.9545 (p90) cc_final: 0.9231 (p90) REVERT: A 539 VAL cc_start: 0.5572 (OUTLIER) cc_final: 0.5289 (m) REVERT: A 646 ARG cc_start: 0.7301 (ptm-80) cc_final: 0.7079 (ptt-90) REVERT: A 774 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7864 (mm-40) REVERT: A 859 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8534 (t) REVERT: A 900 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7067 (mtp) REVERT: A 1138 TYR cc_start: 0.6393 (t80) cc_final: 0.6152 (t80) REVERT: B 14 GLN cc_start: 0.4874 (OUTLIER) cc_final: 0.4397 (pm20) REVERT: B 177 MET cc_start: 0.3672 (mmt) cc_final: 0.1255 (ttt) REVERT: B 308 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.8022 (p) REVERT: B 779 GLN cc_start: 0.8296 (tp40) cc_final: 0.8084 (mm-40) REVERT: B 918 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: B 988 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7714 (mp0) REVERT: B 990 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7775 (mm-30) REVERT: B 1045 LYS cc_start: 0.8574 (mptt) cc_final: 0.8121 (mmtm) REVERT: C 41 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7348 (mmtm) REVERT: C 177 MET cc_start: 0.2893 (ttt) cc_final: 0.0796 (mpt) REVERT: C 325 SER cc_start: 0.8733 (t) cc_final: 0.8500 (p) REVERT: C 349 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7538 (t) REVERT: C 495 TYR cc_start: 0.7386 (m-10) cc_final: 0.6405 (m-10) REVERT: C 511 VAL cc_start: 0.8981 (t) cc_final: 0.8773 (p) REVERT: C 786 LYS cc_start: 0.7638 (pttm) cc_final: 0.7266 (mmmt) REVERT: C 913 GLN cc_start: 0.7245 (mt0) cc_final: 0.6881 (pt0) REVERT: C 988 GLU cc_start: 0.8223 (mp0) cc_final: 0.7811 (mp0) REVERT: C 1077 THR cc_start: 0.8553 (p) cc_final: 0.8279 (p) REVERT: R 54 MET cc_start: 0.9053 (mmp) cc_final: 0.8741 (mpt) REVERT: T 45 LEU cc_start: 0.8419 (mt) cc_final: 0.7996 (mt) REVERT: T 54 MET cc_start: 0.9123 (mmp) cc_final: 0.8595 (mpm) REVERT: T 78 THR cc_start: 0.6749 (m) cc_final: 0.6415 (m) REVERT: Q 24 ARG cc_start: 0.9164 (tpp-160) cc_final: 0.8779 (mmp80) REVERT: Q 63 PHE cc_start: 0.9205 (m-80) cc_final: 0.8135 (m-80) REVERT: Q 75 THR cc_start: 0.7944 (p) cc_final: 0.7595 (t) REVERT: Q 79 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8128 (mm) REVERT: Q 88 TYR cc_start: 0.8567 (m-80) cc_final: 0.8259 (m-80) REVERT: K 54 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7735 (pmm) outliers start: 112 outliers final: 47 residues processed: 393 average time/residue: 0.5451 time to fit residues: 260.7826 Evaluate side-chains 307 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 213 VAL 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 512 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 602 THR 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 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 934 ILE 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 308 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain C residue 41 LYS 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 362 VAL Chi-restraints excluded: chain C residue 489 TYR 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 866 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain R residue 55 PHE 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 31 THR Chi-restraints excluded: chain T residue 88 TYR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 79 LEU 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 54 MET 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 164 optimal weight: 1.9990 chunk 324 optimal weight: 0.9980 chunk 314 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 275 optimal weight: 0.9990 chunk 375 optimal weight: 40.0000 chunk 167 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 243 optimal weight: 9.9990 chunk 284 optimal weight: 0.0670 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 774 GLN A 919 ASN B 134 GLN B 409 GLN B 542 ASN B 957 GLN B1071 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1002 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN T 30 ASN T 65 GLN ** 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 = 0.4820 r_free = 0.4820 target = 0.213313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.148369 restraints weight = 55219.874| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.59 r_work: 0.3661 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31653 Z= 0.153 Angle : 0.699 13.960 43175 Z= 0.347 Chirality : 0.049 0.474 4983 Planarity : 0.005 0.070 5487 Dihedral : 7.518 66.556 5370 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 3.31 % Allowed : 16.27 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 3814 helix: 1.85 (0.20), residues: 660 sheet: -0.47 (0.16), residues: 955 loop : -1.32 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 158 TYR 0.022 0.001 TYR Q 37 PHE 0.027 0.002 PHE Q 63 TRP 0.030 0.002 TRP B 104 HIS 0.002 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00341 (31558) covalent geometry : angle 0.67091 (42932) SS BOND : bond 0.00544 ( 42) SS BOND : angle 1.55590 ( 84) hydrogen bonds : bond 0.04330 ( 1123) hydrogen bonds : angle 5.96567 ( 3177) link_BETA1-4 : bond 0.00535 ( 7) link_BETA1-4 : angle 1.97605 ( 21) link_NAG-ASN : bond 0.00705 ( 46) link_NAG-ASN : angle 3.31228 ( 138) *********************** 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 386 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 276 time to evaluate : 1.107 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: 0.8965 (mm) cc_final: 0.8702 (mp) REVERT: A 298 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: A 451 TYR cc_start: 0.7067 (m-80) cc_final: 0.6526 (m-80) REVERT: A 453 TYR cc_start: 0.9569 (p90) cc_final: 0.9224 (p90) REVERT: A 646 ARG cc_start: 0.7248 (ptm-80) cc_final: 0.6979 (ptt-90) REVERT: A 900 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6796 (mtp) REVERT: B 14 GLN cc_start: 0.4302 (OUTLIER) cc_final: 0.3448 (pp30) REVERT: B 306 PHE cc_start: 0.6611 (t80) cc_final: 0.6241 (t80) REVERT: B 558 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6756 (mmmm) REVERT: B 988 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7833 (mp0) REVERT: B 994 ASP cc_start: 0.8492 (t70) cc_final: 0.8178 (t0) REVERT: B 1111 GLU cc_start: 0.8187 (tt0) cc_final: 0.7985 (tp30) REVERT: C 177 MET cc_start: 0.2857 (ttt) cc_final: 0.0650 (mpt) REVERT: C 237 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7637 (mmm160) REVERT: C 325 SER cc_start: 0.8730 (t) cc_final: 0.8503 (p) REVERT: C 349 SER cc_start: 0.8017 (OUTLIER) cc_final: 0.7547 (t) REVERT: C 508 TYR cc_start: 0.7235 (m-80) cc_final: 0.7000 (m-80) REVERT: C 511 VAL cc_start: 0.8951 (t) cc_final: 0.8744 (p) REVERT: C 786 LYS cc_start: 0.7665 (pttm) cc_final: 0.7295 (mmmt) REVERT: C 913 GLN cc_start: 0.7316 (mt0) cc_final: 0.6969 (mt0) REVERT: C 988 GLU cc_start: 0.8284 (mp0) cc_final: 0.7789 (mp0) REVERT: C 1113 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: R 48 MET cc_start: 0.8496 (ptp) cc_final: 0.7485 (mpp) REVERT: R 54 MET cc_start: 0.8915 (mmp) cc_final: 0.8686 (mpp) REVERT: T 23 LYS cc_start: 0.9391 (tptp) cc_final: 0.9148 (tppt) REVERT: T 30 ASN cc_start: 0.9264 (m110) cc_final: 0.9034 (p0) REVERT: T 45 LEU cc_start: 0.8485 (mt) cc_final: 0.8151 (mt) REVERT: T 54 MET cc_start: 0.9090 (mmp) cc_final: 0.8525 (mpm) REVERT: T 81 MET cc_start: 0.8768 (ttm) cc_final: 0.8445 (mtp) REVERT: T 82 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8698 (tp30) REVERT: Q 63 PHE cc_start: 0.9074 (m-10) cc_final: 0.8540 (m-80) REVERT: Q 75 THR cc_start: 0.7694 (p) cc_final: 0.7262 (t) REVERT: Q 88 TYR cc_start: 0.8575 (m-80) cc_final: 0.8254 (m-80) REVERT: K 54 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7722 (pmm) outliers start: 110 outliers final: 43 residues processed: 351 average time/residue: 0.5358 time to fit residues: 229.6977 Evaluate side-chains 285 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 551 VAL 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 B residue 14 GLN 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 740 MET Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 VAL 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 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 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1113 GLN 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 31 THR Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 94 ASN 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 54 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 256 optimal weight: 0.9980 chunk 278 optimal weight: 0.8980 chunk 349 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 133 optimal weight: 0.0170 chunk 112 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 336 optimal weight: 30.0000 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN B 134 GLN B 542 ASN B 957 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 493 GLN C 613 GLN C1002 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 65 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.197576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.133246 restraints weight = 55956.475| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.53 r_work: 0.3607 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31653 Z= 0.171 Angle : 0.705 17.689 43175 Z= 0.350 Chirality : 0.049 0.461 4983 Planarity : 0.005 0.080 5487 Dihedral : 7.071 62.182 5370 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 3.70 % Allowed : 17.02 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 3814 helix: 1.89 (0.20), residues: 656 sheet: -0.36 (0.16), residues: 928 loop : -1.34 (0.12), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 24 TYR 0.023 0.002 TYR Q 37 PHE 0.026 0.002 PHE C 592 TRP 0.031 0.002 TRP B 104 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00381 (31558) covalent geometry : angle 0.67725 (42932) SS BOND : bond 0.00846 ( 42) SS BOND : angle 1.88688 ( 84) hydrogen bonds : bond 0.04466 ( 1123) hydrogen bonds : angle 5.97378 ( 3177) link_BETA1-4 : bond 0.00490 ( 7) link_BETA1-4 : angle 1.87925 ( 21) link_NAG-ASN : bond 0.00703 ( 46) link_NAG-ASN : angle 3.19297 ( 138) *********************** 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 383 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 260 time to evaluate : 1.055 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: 0.8959 (mm) cc_final: 0.8713 (mp) REVERT: A 298 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7709 (tp30) REVERT: A 451 TYR cc_start: 0.6781 (m-80) cc_final: 0.5992 (m-10) REVERT: A 646 ARG cc_start: 0.7317 (ptm-80) cc_final: 0.7062 (ptp90) REVERT: A 900 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6871 (mtp) REVERT: A 988 GLU cc_start: 0.8121 (mp0) cc_final: 0.7424 (tp30) REVERT: B 177 MET cc_start: 0.3078 (mmt) cc_final: 0.0102 (ttt) REVERT: B 306 PHE cc_start: 0.7037 (t80) cc_final: 0.6759 (t80) REVERT: B 558 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6691 (mmmm) REVERT: B 762 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: B 779 GLN cc_start: 0.8298 (tp40) cc_final: 0.8039 (mm-40) REVERT: B 988 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7918 (mp0) REVERT: B 990 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7828 (mm-30) REVERT: B 994 ASP cc_start: 0.8558 (t70) cc_final: 0.8197 (t0) REVERT: B 1111 GLU cc_start: 0.8181 (tt0) cc_final: 0.7877 (tp30) REVERT: B 1113 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: C 117 LEU cc_start: 0.6604 (tt) cc_final: 0.5838 (mt) REVERT: C 177 MET cc_start: 0.2495 (ttt) cc_final: 0.0391 (mpt) REVERT: C 325 SER cc_start: 0.8709 (t) cc_final: 0.8490 (p) REVERT: C 349 SER cc_start: 0.7962 (OUTLIER) cc_final: 0.7528 (t) REVERT: C 365 TYR cc_start: 0.7230 (m-80) cc_final: 0.6981 (m-80) REVERT: C 462 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8647 (mmmm) REVERT: C 481 ASN cc_start: 0.8875 (m-40) cc_final: 0.8663 (p0) REVERT: C 508 TYR cc_start: 0.7248 (m-80) cc_final: 0.7020 (m-80) REVERT: C 786 LYS cc_start: 0.7899 (pttm) cc_final: 0.7445 (mmmt) REVERT: C 913 GLN cc_start: 0.7395 (mt0) cc_final: 0.7052 (mt0) REVERT: R 48 MET cc_start: 0.8396 (ptp) cc_final: 0.7565 (mpp) REVERT: R 54 MET cc_start: 0.9073 (mmp) cc_final: 0.8864 (mpp) REVERT: R 81 MET cc_start: -0.0153 (mmm) cc_final: -0.0870 (mmm) REVERT: O 48 LEU cc_start: 0.7710 (pp) cc_final: 0.7111 (pp) REVERT: T 23 LYS cc_start: 0.9442 (tptp) cc_final: 0.9237 (tppt) REVERT: T 30 ASN cc_start: 0.9319 (m110) cc_final: 0.9042 (p0) REVERT: T 48 MET cc_start: 0.8348 (mpt) cc_final: 0.8023 (mpt) REVERT: T 52 ILE cc_start: 0.8697 (tp) cc_final: 0.8399 (pp) REVERT: T 54 MET cc_start: 0.9004 (mmp) cc_final: 0.8516 (mpm) REVERT: T 81 MET cc_start: 0.8785 (ttm) cc_final: 0.8533 (mtp) REVERT: Q 63 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: Q 75 THR cc_start: 0.7980 (p) cc_final: 0.7516 (t) REVERT: K 48 MET cc_start: 0.5719 (pmm) cc_final: 0.5375 (pmm) REVERT: K 54 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8263 (pmm) outliers start: 123 outliers final: 57 residues processed: 349 average time/residue: 0.5190 time to fit residues: 223.5704 Evaluate side-chains 293 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 228 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 602 THR 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 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 136 CYS 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 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 THR 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 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 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain R residue 37 VAL 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 93 VAL Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 94 ASN 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 54 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 360 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 369 optimal weight: 20.0000 chunk 186 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 351 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 613 GLN C 755 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** 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 = 0.4744 r_free = 0.4744 target = 0.194087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.128864 restraints weight = 55883.007| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.40 r_work: 0.3553 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 31653 Z= 0.240 Angle : 0.758 16.207 43175 Z= 0.381 Chirality : 0.052 0.445 4983 Planarity : 0.005 0.083 5487 Dihedral : 6.957 59.822 5370 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.97 % Rotamer: Outliers : 3.88 % Allowed : 17.74 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3814 helix: 1.57 (0.19), residues: 670 sheet: -0.53 (0.16), residues: 968 loop : -1.45 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 237 TYR 0.030 0.002 TYR C 505 PHE 0.028 0.002 PHE B 898 TRP 0.035 0.002 TRP B 104 HIS 0.009 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00550 (31558) covalent geometry : angle 0.73190 (42932) SS BOND : bond 0.00957 ( 42) SS BOND : angle 1.68864 ( 84) hydrogen bonds : bond 0.04964 ( 1123) hydrogen bonds : angle 6.27320 ( 3177) link_BETA1-4 : bond 0.00425 ( 7) link_BETA1-4 : angle 1.83462 ( 21) link_NAG-ASN : bond 0.00745 ( 46) link_NAG-ASN : angle 3.29735 ( 138) *********************** 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 384 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 255 time to evaluate : 1.238 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: A 451 TYR cc_start: 0.7192 (m-80) cc_final: 0.6609 (m-80) REVERT: A 587 ILE cc_start: 0.6190 (mm) cc_final: 0.5824 (mm) REVERT: A 646 ARG cc_start: 0.7574 (ptm-80) cc_final: 0.7247 (ptt-90) REVERT: A 900 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7331 (mtp) REVERT: A 936 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6841 (t0) REVERT: A 1074 ASN cc_start: 0.7611 (m110) cc_final: 0.7374 (t0) REVERT: B 177 MET cc_start: 0.2821 (mmt) cc_final: -0.0357 (ttt) REVERT: B 558 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6906 (mmmm) REVERT: B 756 TYR cc_start: 0.7873 (t80) cc_final: 0.7563 (m-80) REVERT: B 762 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: B 779 GLN cc_start: 0.8345 (tp40) cc_final: 0.8116 (mm-40) REVERT: B 814 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7800 (mmmt) REVERT: B 957 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7836 (tp-100) REVERT: B 988 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7993 (mp0) REVERT: B 990 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7887 (mm-30) REVERT: B 994 ASP cc_start: 0.8526 (t70) cc_final: 0.8179 (t0) REVERT: B 1113 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: C 41 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7028 (mmtp) REVERT: C 153 MET cc_start: 0.9244 (ppp) cc_final: 0.8949 (pmm) REVERT: C 177 MET cc_start: 0.2565 (ttt) cc_final: 0.0594 (mpt) REVERT: C 349 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7700 (t) REVERT: C 356 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8034 (tppp) REVERT: C 365 TYR cc_start: 0.7377 (m-80) cc_final: 0.7060 (m-80) REVERT: C 508 TYR cc_start: 0.7296 (m-80) cc_final: 0.7026 (m-80) REVERT: C 786 LYS cc_start: 0.7920 (pttm) cc_final: 0.7598 (mmmt) REVERT: C 817 PHE cc_start: 0.6956 (m-80) cc_final: 0.6743 (m-80) REVERT: C 913 GLN cc_start: 0.7464 (mt0) cc_final: 0.7152 (mt0) REVERT: C 983 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.8132 (ttp-110) REVERT: C 988 GLU cc_start: 0.8365 (mp0) cc_final: 0.8122 (mp0) REVERT: R 48 MET cc_start: 0.8250 (ptp) cc_final: 0.7466 (mpp) REVERT: R 81 MET cc_start: -0.0173 (mmm) cc_final: -0.0805 (mmm) REVERT: O 88 TYR cc_start: 0.7990 (m-80) cc_final: 0.7637 (m-80) REVERT: T 39 GLN cc_start: 0.7837 (mm110) cc_final: 0.7591 (mt0) REVERT: T 48 MET cc_start: 0.8277 (mpt) cc_final: 0.7995 (mpt) REVERT: T 52 ILE cc_start: 0.8810 (tp) cc_final: 0.8549 (pp) REVERT: T 54 MET cc_start: 0.9079 (mmp) cc_final: 0.8578 (mpm) REVERT: T 55 PHE cc_start: 0.9010 (m-80) cc_final: 0.8720 (m-10) REVERT: T 82 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8916 (tp30) REVERT: Q 88 TYR cc_start: 0.8842 (m-80) cc_final: 0.8611 (m-80) REVERT: K 54 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7617 (pmm) outliers start: 129 outliers final: 69 residues processed: 358 average time/residue: 0.5031 time to fit residues: 223.0352 Evaluate side-chains 306 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 227 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain A residue 236 THR 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 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 602 THR 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 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 315 THR Chi-restraints excluded: chain B residue 539 VAL 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 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1058 HIS 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 208 THR 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 356 LYS 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 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 791 THR Chi-restraints excluded: chain C residue 859 THR 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 C residue 1132 ILE Chi-restraints excluded: chain R residue 71 THR 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 45 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 5 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 316 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 chunk 364 optimal weight: 50.0000 chunk 261 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 283 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 356 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN C 613 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.196207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.129359 restraints weight = 55405.719| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.53 r_work: 0.3612 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5835 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= 0.167 Angle : 0.706 14.941 43175 Z= 0.352 Chirality : 0.049 0.435 4983 Planarity : 0.005 0.058 5487 Dihedral : 6.725 59.382 5370 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.61 % Favored : 95.36 % Rotamer: Outliers : 3.22 % Allowed : 18.91 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 3814 helix: 1.61 (0.19), residues: 677 sheet: -0.53 (0.16), residues: 988 loop : -1.42 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 24 TYR 0.022 0.002 TYR C1067 PHE 0.038 0.002 PHE Q 63 TRP 0.039 0.002 TRP T 36 HIS 0.015 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00376 (31558) covalent geometry : angle 0.68135 (42932) SS BOND : bond 0.00710 ( 42) SS BOND : angle 1.59568 ( 84) hydrogen bonds : bond 0.04424 ( 1123) hydrogen bonds : angle 6.09211 ( 3177) link_BETA1-4 : bond 0.00455 ( 7) link_BETA1-4 : angle 1.81036 ( 21) link_NAG-ASN : bond 0.00653 ( 46) link_NAG-ASN : angle 3.05534 ( 138) *********************** 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 344 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 237 time to evaluate : 0.731 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: A 451 TYR cc_start: 0.7214 (m-80) cc_final: 0.6576 (m-80) REVERT: A 565 PHE cc_start: 0.6342 (p90) cc_final: 0.6116 (p90) REVERT: A 587 ILE cc_start: 0.6403 (mm) cc_final: 0.6041 (mm) REVERT: A 646 ARG cc_start: 0.7507 (ptm-80) cc_final: 0.7190 (ptp90) REVERT: A 900 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7094 (mtp) REVERT: A 1074 ASN cc_start: 0.7504 (m110) cc_final: 0.7184 (t0) REVERT: B 177 MET cc_start: 0.2784 (mmt) cc_final: -0.0214 (ttt) REVERT: B 558 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6818 (mmmm) REVERT: B 756 TYR cc_start: 0.7940 (t80) cc_final: 0.7680 (m-80) REVERT: B 762 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: B 779 GLN cc_start: 0.8282 (tp40) cc_final: 0.8016 (mm-40) REVERT: B 814 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7790 (mmmt) REVERT: B 900 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7996 (mtm) REVERT: B 988 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8094 (mp0) REVERT: B 990 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7849 (mm-30) REVERT: B 994 ASP cc_start: 0.8496 (t70) cc_final: 0.8168 (t0) REVERT: B 1113 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: C 41 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6980 (mmtp) REVERT: C 117 LEU cc_start: 0.6685 (tt) cc_final: 0.5802 (mt) REVERT: C 153 MET cc_start: 0.9247 (ppp) cc_final: 0.9002 (pmm) REVERT: C 177 MET cc_start: 0.2616 (ttt) cc_final: 0.0860 (mpt) REVERT: C 349 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7597 (t) REVERT: C 365 TYR cc_start: 0.7252 (m-80) cc_final: 0.6929 (m-80) REVERT: C 462 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8558 (mmmm) REVERT: C 508 TYR cc_start: 0.7241 (m-80) cc_final: 0.6912 (m-80) REVERT: C 786 LYS cc_start: 0.7863 (pttm) cc_final: 0.7472 (mmmt) REVERT: C 913 GLN cc_start: 0.7449 (mt0) cc_final: 0.7085 (mt0) REVERT: C 983 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8185 (ttp-110) REVERT: C 988 GLU cc_start: 0.8351 (mp0) cc_final: 0.8080 (mp0) REVERT: R 48 MET cc_start: 0.8213 (ptp) cc_final: 0.7434 (mpp) REVERT: R 81 MET cc_start: -0.0259 (mmm) cc_final: -0.0800 (mmm) REVERT: T 23 LYS cc_start: 0.9301 (tptt) cc_final: 0.9014 (tppt) REVERT: T 30 ASN cc_start: 0.9326 (m110) cc_final: 0.9069 (p0) REVERT: T 48 MET cc_start: 0.8278 (mpt) cc_final: 0.7931 (mpt) REVERT: T 52 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8483 (pp) REVERT: T 54 MET cc_start: 0.9101 (mmp) cc_final: 0.8574 (mpm) REVERT: Q 88 TYR cc_start: 0.8829 (m-80) cc_final: 0.8482 (m-80) REVERT: K 48 MET cc_start: 0.5636 (pmm) cc_final: 0.5326 (pmm) REVERT: K 54 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7787 (pmm) outliers start: 107 outliers final: 61 residues processed: 316 average time/residue: 0.5030 time to fit residues: 195.5854 Evaluate side-chains 293 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 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 602 THR 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 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1072 GLU 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 141 LEU Chi-restraints excluded: chain B residue 478 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 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 969 ASN 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 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 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 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain R residue 71 THR 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 52 ILE Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain Q residue 63 PHE Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 179 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 150 optimal weight: 40.0000 chunk 116 optimal weight: 3.9990 chunk 303 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 703 ASN C 99 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 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 = 0.4779 r_free = 0.4779 target = 0.195181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.127508 restraints weight = 55401.683| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.13 r_work: 0.3601 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31653 Z= 0.189 Angle : 0.720 12.489 43175 Z= 0.362 Chirality : 0.050 0.421 4983 Planarity : 0.005 0.091 5487 Dihedral : 6.571 59.316 5369 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 3.22 % Allowed : 19.72 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 3814 helix: 1.42 (0.19), residues: 696 sheet: -0.50 (0.16), residues: 974 loop : -1.46 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG T 87 TYR 0.028 0.002 TYR C 505 PHE 0.030 0.002 PHE Q 63 TRP 0.034 0.002 TRP B 104 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00430 (31558) covalent geometry : angle 0.69480 (42932) SS BOND : bond 0.00802 ( 42) SS BOND : angle 2.07222 ( 84) hydrogen bonds : bond 0.04541 ( 1123) hydrogen bonds : angle 6.10672 ( 3177) link_BETA1-4 : bond 0.00474 ( 7) link_BETA1-4 : angle 1.75892 ( 21) link_NAG-ASN : bond 0.00644 ( 46) link_NAG-ASN : angle 3.01119 ( 138) *********************** 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 348 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 241 time to evaluate : 0.847 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: A 451 TYR cc_start: 0.7203 (m-80) cc_final: 0.6503 (m-10) REVERT: A 565 PHE cc_start: 0.6469 (p90) cc_final: 0.6111 (p90) REVERT: A 646 ARG cc_start: 0.7508 (ptm-80) cc_final: 0.7221 (ptp90) REVERT: A 900 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7213 (mtp) REVERT: B 91 TYR cc_start: 0.5239 (t80) cc_final: 0.5002 (t80) REVERT: B 177 MET cc_start: 0.2802 (mmt) cc_final: -0.0648 (ttt) REVERT: B 218 GLN cc_start: 0.0165 (OUTLIER) cc_final: -0.1281 (pm20) REVERT: B 266 TYR cc_start: 0.2631 (OUTLIER) cc_final: 0.2200 (m-80) REVERT: B 558 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6912 (mmmm) REVERT: B 762 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: B 779 GLN cc_start: 0.8256 (tp40) cc_final: 0.7994 (mm-40) REVERT: B 814 LYS cc_start: 0.8385 (mmtt) cc_final: 0.7842 (mmmt) REVERT: B 983 ARG cc_start: 0.8657 (ttm110) cc_final: 0.8407 (mtm180) REVERT: B 988 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8162 (mp0) REVERT: B 990 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7845 (mm-30) REVERT: B 994 ASP cc_start: 0.8421 (t70) cc_final: 0.8201 (t0) REVERT: B 1113 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: C 41 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7194 (mmtm) REVERT: C 153 MET cc_start: 0.9228 (ppp) cc_final: 0.8977 (pmm) REVERT: C 177 MET cc_start: 0.2195 (ttt) cc_final: 0.0131 (mpt) REVERT: C 349 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7630 (t) REVERT: C 365 TYR cc_start: 0.7432 (m-80) cc_final: 0.7145 (m-80) REVERT: C 374 PHE cc_start: 0.7847 (m-80) cc_final: 0.7482 (m-80) REVERT: C 486 PHE cc_start: 0.8168 (t80) cc_final: 0.7482 (t80) REVERT: C 508 TYR cc_start: 0.7290 (m-80) cc_final: 0.6973 (m-80) REVERT: C 586 ASP cc_start: 0.7939 (m-30) cc_final: 0.7731 (m-30) REVERT: C 786 LYS cc_start: 0.7947 (pttm) cc_final: 0.7579 (mmmt) REVERT: C 913 GLN cc_start: 0.7375 (mt0) cc_final: 0.7066 (mt0) REVERT: C 988 GLU cc_start: 0.8311 (mp0) cc_final: 0.8090 (mp0) REVERT: R 48 MET cc_start: 0.8164 (ptp) cc_final: 0.7519 (mpp) REVERT: R 81 MET cc_start: -0.0105 (mmm) cc_final: -0.0605 (mmm) REVERT: O 97 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7640 (mtp180) REVERT: T 23 LYS cc_start: 0.9330 (tptt) cc_final: 0.9042 (tppt) REVERT: T 30 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.9062 (p0) REVERT: T 48 MET cc_start: 0.8308 (mpt) cc_final: 0.7810 (mpt) REVERT: T 52 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8432 (pp) REVERT: T 54 MET cc_start: 0.9064 (mmp) cc_final: 0.8516 (mpm) REVERT: T 55 PHE cc_start: 0.9027 (m-80) cc_final: 0.8802 (m-10) REVERT: T 82 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8756 (mp0) REVERT: Q 24 ARG cc_start: 0.8805 (mmm160) cc_final: 0.7876 (mmp80) REVERT: Q 88 TYR cc_start: 0.8833 (m-80) cc_final: 0.8541 (m-80) REVERT: K 48 MET cc_start: 0.6068 (pmm) cc_final: 0.5720 (pmm) REVERT: K 54 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7605 (pmm) outliers start: 107 outliers final: 69 residues processed: 323 average time/residue: 0.5100 time to fit residues: 203.0208 Evaluate side-chains 298 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 218 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 602 THR 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 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 141 LEU 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 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 735 SER Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1113 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 120 VAL Chi-restraints excluded: chain C residue 208 THR 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 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 735 SER Chi-restraints excluded: chain C residue 754 LEU 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 976 VAL 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 71 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 53 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 260 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 137 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 chunk 343 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 755 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 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 = 0.4780 r_free = 0.4780 target = 0.195556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.128372 restraints weight = 54895.841| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.23 r_work: 0.3597 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31653 Z= 0.174 Angle : 0.706 14.786 43175 Z= 0.355 Chirality : 0.050 0.423 4983 Planarity : 0.005 0.059 5487 Dihedral : 6.505 59.804 5369 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 2.98 % Allowed : 20.17 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3814 helix: 1.48 (0.19), residues: 696 sheet: -0.55 (0.16), residues: 968 loop : -1.45 (0.12), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 38 TYR 0.034 0.002 TYR O 88 PHE 0.027 0.002 PHE A 157 TRP 0.031 0.002 TRP T 36 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00393 (31558) covalent geometry : angle 0.68304 (42932) SS BOND : bond 0.00793 ( 42) SS BOND : angle 1.64920 ( 84) hydrogen bonds : bond 0.04391 ( 1123) hydrogen bonds : angle 6.05990 ( 3177) link_BETA1-4 : bond 0.00453 ( 7) link_BETA1-4 : angle 1.73896 ( 21) link_NAG-ASN : bond 0.00624 ( 46) link_NAG-ASN : angle 2.96136 ( 138) *********************** 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 326 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 227 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8038 (m-80) cc_final: 0.7375 (t80) REVERT: A 396 TYR cc_start: 0.7365 (m-80) cc_final: 0.6257 (m-10) REVERT: A 451 TYR cc_start: 0.7293 (m-80) cc_final: 0.6502 (m-10) REVERT: A 537 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6800 (tptp) REVERT: A 565 PHE cc_start: 0.6457 (p90) cc_final: 0.6134 (p90) REVERT: A 646 ARG cc_start: 0.7536 (ptm-80) cc_final: 0.7223 (ptp90) REVERT: A 900 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7129 (mtp) REVERT: B 91 TYR cc_start: 0.5368 (t80) cc_final: 0.5103 (t80) REVERT: B 177 MET cc_start: 0.2876 (mmt) cc_final: -0.0327 (ttt) REVERT: B 180 GLU cc_start: 0.0010 (OUTLIER) cc_final: -0.1078 (tt0) REVERT: B 266 TYR cc_start: 0.2797 (OUTLIER) cc_final: 0.2378 (m-80) REVERT: B 297 SER cc_start: 0.7429 (m) cc_final: 0.7065 (p) REVERT: B 558 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6915 (mmmm) REVERT: B 580 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6708 (mm110) REVERT: B 779 GLN cc_start: 0.8275 (tp40) cc_final: 0.8002 (mm-40) REVERT: B 814 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7822 (mmmt) REVERT: B 983 ARG cc_start: 0.8693 (ttm110) cc_final: 0.8274 (mtm-85) REVERT: B 988 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8147 (mp0) REVERT: B 990 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7762 (mm-30) REVERT: B 994 ASP cc_start: 0.8346 (t70) cc_final: 0.8127 (t0) REVERT: C 41 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7204 (mmtm) REVERT: C 153 MET cc_start: 0.9254 (ppp) cc_final: 0.9013 (pmm) REVERT: C 177 MET cc_start: 0.2470 (ttt) cc_final: 0.0161 (mpt) REVERT: C 349 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7631 (t) REVERT: C 365 TYR cc_start: 0.7461 (m-80) cc_final: 0.7186 (m-80) REVERT: C 508 TYR cc_start: 0.7332 (m-80) cc_final: 0.7010 (m-80) REVERT: C 586 ASP cc_start: 0.7983 (m-30) cc_final: 0.7777 (m-30) REVERT: C 786 LYS cc_start: 0.7861 (pttm) cc_final: 0.7520 (mmmt) REVERT: R 48 MET cc_start: 0.8194 (ptp) cc_final: 0.7581 (mpp) REVERT: R 81 MET cc_start: 0.0022 (mmm) cc_final: -0.0517 (mmm) REVERT: T 23 LYS cc_start: 0.9340 (tptt) cc_final: 0.9049 (tppt) REVERT: T 30 ASN cc_start: 0.9369 (OUTLIER) cc_final: 0.9081 (p0) REVERT: T 39 GLN cc_start: 0.7573 (mt0) cc_final: 0.7254 (mt0) REVERT: T 52 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8439 (pp) REVERT: T 54 MET cc_start: 0.9067 (mmp) cc_final: 0.8578 (mpm) REVERT: Q 24 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8043 (mmp80) REVERT: Q 88 TYR cc_start: 0.8816 (m-80) cc_final: 0.8580 (m-80) REVERT: K 48 MET cc_start: 0.6126 (pmm) cc_final: 0.5857 (pmm) REVERT: K 54 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8134 (pmm) outliers start: 99 outliers final: 74 residues processed: 305 average time/residue: 0.5094 time to fit residues: 193.1413 Evaluate side-chains 303 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 218 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR 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 976 VAL 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 141 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 317 ASN 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 553 THR 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 703 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN 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 208 THR 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 478 THR Chi-restraints excluded: chain C residue 489 TYR 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 735 SER Chi-restraints excluded: chain C residue 754 LEU 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 976 VAL Chi-restraints excluded: chain C residue 1077 THR 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 71 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 269 optimal weight: 0.1980 chunk 227 optimal weight: 0.8980 chunk 340 optimal weight: 10.0000 chunk 369 optimal weight: 50.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 703 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 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 = 0.4778 r_free = 0.4778 target = 0.195947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.128257 restraints weight = 54193.471| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.36 r_work: 0.3589 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.6416 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= 0.179 Angle : 0.718 13.774 43175 Z= 0.362 Chirality : 0.050 0.448 4983 Planarity : 0.005 0.097 5487 Dihedral : 6.472 59.810 5369 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.02 % Rotamer: Outliers : 2.92 % Allowed : 20.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 3814 helix: 1.44 (0.19), residues: 701 sheet: -0.49 (0.16), residues: 938 loop : -1.46 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 346 TYR 0.034 0.002 TYR C 200 PHE 0.036 0.002 PHE Q 63 TRP 0.036 0.002 TRP T 47 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00404 (31558) covalent geometry : angle 0.69604 (42932) SS BOND : bond 0.00708 ( 42) SS BOND : angle 1.64894 ( 84) hydrogen bonds : bond 0.04429 ( 1123) hydrogen bonds : angle 6.06375 ( 3177) link_BETA1-4 : bond 0.00531 ( 7) link_BETA1-4 : angle 1.69592 ( 21) link_NAG-ASN : bond 0.00623 ( 46) link_NAG-ASN : angle 2.94924 ( 138) ********************** 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 314 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 217 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8005 (m-80) cc_final: 0.7480 (t80) REVERT: A 396 TYR cc_start: 0.7376 (m-80) cc_final: 0.6209 (m-10) REVERT: A 451 TYR cc_start: 0.7319 (m-80) cc_final: 0.6522 (m-10) REVERT: A 537 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6785 (tptp) REVERT: A 565 PHE cc_start: 0.6642 (p90) cc_final: 0.6244 (p90) REVERT: A 646 ARG cc_start: 0.7569 (ptm-80) cc_final: 0.7227 (ptp90) REVERT: A 900 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7157 (mtp) REVERT: B 91 TYR cc_start: 0.5370 (t80) cc_final: 0.5143 (t80) REVERT: B 177 MET cc_start: 0.2940 (mmt) cc_final: -0.0330 (ttt) REVERT: B 180 GLU cc_start: 0.0005 (OUTLIER) cc_final: -0.1132 (tt0) REVERT: B 218 GLN cc_start: 0.0390 (OUTLIER) cc_final: -0.1141 (pm20) REVERT: B 266 TYR cc_start: 0.2959 (OUTLIER) cc_final: 0.2585 (m-80) REVERT: B 558 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6960 (mmmm) REVERT: B 580 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6724 (mm110) REVERT: B 779 GLN cc_start: 0.8257 (tp40) cc_final: 0.7990 (mm-40) REVERT: B 814 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7810 (mmmt) REVERT: B 983 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8286 (mtm-85) REVERT: B 988 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8159 (mp0) REVERT: B 990 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7794 (mm-30) REVERT: B 994 ASP cc_start: 0.8407 (t70) cc_final: 0.8168 (t0) REVERT: C 153 MET cc_start: 0.9220 (ppp) cc_final: 0.8992 (pmm) REVERT: C 177 MET cc_start: 0.2454 (ttt) cc_final: 0.0243 (mpt) REVERT: C 349 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7564 (t) REVERT: C 365 TYR cc_start: 0.7499 (m-80) cc_final: 0.7230 (m-80) REVERT: C 508 TYR cc_start: 0.7317 (m-80) cc_final: 0.6996 (m-80) REVERT: C 586 ASP cc_start: 0.7990 (m-30) cc_final: 0.7781 (m-30) REVERT: C 786 LYS cc_start: 0.7955 (pttm) cc_final: 0.7546 (mmmt) REVERT: R 48 MET cc_start: 0.8177 (ptp) cc_final: 0.7565 (mpp) REVERT: T 23 LYS cc_start: 0.9304 (tptt) cc_final: 0.8992 (tppt) REVERT: T 30 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.9071 (p0) REVERT: T 52 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8449 (pp) REVERT: T 54 MET cc_start: 0.9069 (mmp) cc_final: 0.8608 (mpm) REVERT: T 82 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8677 (mp0) REVERT: Q 88 TYR cc_start: 0.8799 (m-80) cc_final: 0.8535 (m-80) REVERT: K 48 MET cc_start: 0.6134 (pmm) cc_final: 0.5767 (pmm) REVERT: K 54 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7973 (pmm) outliers start: 97 outliers final: 72 residues processed: 294 average time/residue: 0.5089 time to fit residues: 185.2754 Evaluate side-chains 293 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 210 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 602 THR 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 976 VAL 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 141 LEU Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR 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 735 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 208 THR 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 495 TYR 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 735 SER Chi-restraints excluded: chain C residue 754 LEU 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 976 VAL Chi-restraints excluded: chain C residue 1077 THR 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 120 THR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 21 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 168 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 308 optimal weight: 0.9980 chunk 151 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 292 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 314 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 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 = 0.4795 r_free = 0.4795 target = 0.202716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.135138 restraints weight = 54177.436| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.11 r_work: 0.3599 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31653 Z= 0.176 Angle : 0.715 14.665 43175 Z= 0.359 Chirality : 0.049 0.432 4983 Planarity : 0.005 0.095 5487 Dihedral : 6.426 59.990 5369 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 2.71 % Allowed : 20.35 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3814 helix: 1.40 (0.19), residues: 701 sheet: -0.62 (0.16), residues: 954 loop : -1.45 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 346 TYR 0.024 0.002 TYR O 50 PHE 0.037 0.002 PHE C 486 TRP 0.037 0.002 TRP T 47 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00400 (31558) covalent geometry : angle 0.69302 (42932) SS BOND : bond 0.00691 ( 42) SS BOND : angle 1.57885 ( 84) hydrogen bonds : bond 0.04393 ( 1123) hydrogen bonds : angle 6.03775 ( 3177) link_BETA1-4 : bond 0.00420 ( 7) link_BETA1-4 : angle 1.71002 ( 21) link_NAG-ASN : bond 0.00620 ( 46) link_NAG-ASN : angle 2.93318 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24105.26 seconds wall clock time: 407 minutes 15.21 seconds (24435.21 seconds total)