Starting phenix.real_space_refine on Fri Feb 6 21:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d8h_46637/02_2026/9d8h_46637_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d8h_46637/02_2026/9d8h_46637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d8h_46637/02_2026/9d8h_46637_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d8h_46637/02_2026/9d8h_46637_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d8h_46637/02_2026/9d8h_46637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d8h_46637/02_2026/9d8h_46637.map" } resolution = 2.7 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= 0.001 sd= 0.046 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 120 5.16 5 C 17661 2.51 5 N 4497 2.21 5 O 5400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27678 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8936 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1112, 8727 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1112, 8727 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 bond proxies already assigned to first conformer: 8726 Chain: "B" Number of atoms: 8936 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1112, 8727 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1112, 8727 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 bond proxies already assigned to first conformer: 8726 Chain: "C" Number of atoms: 8936 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1112, 8727 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1112, 8727 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 54, 'TRANS': 1057} Chain breaks: 2 bond proxies already assigned to first conformer: 8726 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 72 residue: pdb=" N ATYR A1134 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A1134 " occ=0.49 residue: pdb=" N AASP A1135 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP A1135 " occ=0.49 residue: pdb=" N APRO A1136 " occ=0.51 ... (12 atoms not shown) pdb=" CD BPRO A1136 " occ=0.49 residue: pdb=" N ALEU A1137 " occ=0.51 ... (14 atoms not shown) pdb=" CD2BLEU A1137 " occ=0.49 residue: pdb=" N AGLN A1138 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN A1138 " occ=0.49 residue: pdb=" N ALEU A1139 " occ=0.51 ... (14 atoms not shown) pdb=" CD2BLEU A1139 " occ=0.49 residue: pdb=" N AGLU A1140 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU A1140 " occ=0.49 residue: pdb=" N ALEU A1141 " occ=0.51 ... (14 atoms not shown) pdb=" CD2BLEU A1141 " occ=0.49 residue: pdb=" N AASP A1142 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP A1142 " occ=0.49 residue: pdb=" N ASER A1143 " occ=0.51 ... (10 atoms not shown) pdb=" OG BSER A1143 " occ=0.49 residue: pdb=" N APHE A1144 " occ=0.51 ... (20 atoms not shown) pdb=" CZ BPHE A1144 " occ=0.49 residue: pdb=" N ALYS A1145 " occ=0.51 ... (16 atoms not shown) pdb=" NZ BLYS A1145 " occ=0.49 ... (remaining 60 not shown) Time building chain proxies: 10.11, per 1000 atoms: 0.37 Number of scatterers: 27678 At special positions: 0 Unit cell: (152.464, 157.595, 194.978, 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 120 16.00 O 5400 8.00 N 4497 7.00 C 17661 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 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 613 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 667 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.03 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 521 " distance=2.02 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 645 " distance=2.03 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 667 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.02 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.03 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG L 1 " - " FUC L 3 " " NAG Q 1 " - " FUC Q 3 " NAG-ASN " NAG A1401 " - " ASN A 328 " " NAG A1402 " - " ASN A 340 " " NAG A1403 " - " ASN A1070 " " NAG A1404 " - " ASN A1094 " " NAG A1405 " - " ASN A 231 " " NAG A1406 " - " ASN A 121 " " NAG A1407 " - " ASN A 163 " " NAG A1408 " - " ASN A 612 " " NAG A1409 " - " ASN A 62 " " NAG A1410 " - " ASN A 797 " " NAG B1401 " - " ASN B 328 " " NAG B1402 " - " ASN B 340 " " NAG B1403 " - " ASN B1070 " " NAG B1404 " - " ASN B1094 " " NAG B1405 " - " ASN B 231 " " NAG B1406 " - " ASN B 121 " " NAG B1407 " - " ASN B 163 " " NAG B1408 " - " ASN B 612 " " NAG B1409 " - " ASN B 62 " " NAG B1410 " - " ASN B 797 " " NAG C1401 " - " ASN C 328 " " NAG C1402 " - " ASN C 340 " " NAG C1403 " - " ASN C1070 " " NAG C1404 " - " ASN C1094 " " NAG C1405 " - " ASN C 231 " " NAG C1406 " - " ASN C 121 " " NAG C1407 " - " ASN C 163 " " NAG C1408 " - " ASN C 612 " " NAG C1409 " - " ASN C 62 " " NAG C1410 " - " ASN C 797 " " NAG D 1 " - " ASN A 279 " " NAG E 1 " - " ASN A 705 " " NAG F 1 " - " ASN A 713 " " NAG G 1 " - " ASN A1130 " " NAG H 1 " - " ASN A 351 " " NAG I 1 " - " ASN B 279 " " NAG J 1 " - " ASN B 705 " " NAG K 1 " - " ASN B 713 " " NAG L 1 " - " ASN B1130 " " NAG M 1 " - " ASN B 351 " " NAG N 1 " - " ASN C 279 " " NAG O 1 " - " ASN C 705 " " NAG P 1 " - " ASN C 713 " " NAG Q 1 " - " ASN C1130 " " NAG R 1 " - " ASN C 351 " Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 2.0 seconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6390 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 26.9% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.506A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.729A pdb=" N VAL A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.539A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 754 through 779 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.534A pdb=" N ASN A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 908 through 915 removed outlier: 4.057A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 937 removed outlier: 3.936A pdb=" N GLN A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 961 removed outlier: 4.081A pdb=" N GLN A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 4.191A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1157 removed outlier: 3.583A pdb=" N AGLU A1147 " --> pdb=" O ASER A1143 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N BHIS A1155 " --> pdb=" O BTYR A1151 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N BSER A1157 " --> pdb=" O BLYS A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.509A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.729A pdb=" N VAL B 364 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.525A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 742 through 750 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 754 through 779 Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 845 through 852 removed outlier: 3.526A pdb=" N ASN B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 908 through 915 removed outlier: 4.063A pdb=" N LEU B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 937 removed outlier: 3.948A pdb=" N GLN B 931 " --> pdb=" O ILE B 927 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 961 removed outlier: 4.019A pdb=" N GLN B 945 " --> pdb=" O LEU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 4.205A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1157 removed outlier: 3.589A pdb=" N AGLU B1147 " --> pdb=" O ASER B1143 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N BHIS B1155 " --> pdb=" O BTYR B1151 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N BSER B1157 " --> pdb=" O BLYS B1153 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.512A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 361 through 367 removed outlier: 3.734A pdb=" N VAL C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.539A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 742 through 750 Processing helix chain 'C' and resid 751 through 753 No H-bonds generated for 'chain 'C' and resid 751 through 753' Processing helix chain 'C' and resid 754 through 779 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 845 through 852 removed outlier: 3.714A pdb=" N ASN C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 908 through 915 removed outlier: 4.084A pdb=" N LEU C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 937 removed outlier: 3.948A pdb=" N GLN C 931 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 932 " --> pdb=" O GLY C 928 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C 935 " --> pdb=" O GLN C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 961 removed outlier: 4.079A pdb=" N GLN C 945 " --> pdb=" O LEU C 941 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 981 through 1029 removed outlier: 4.198A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1157 removed outlier: 3.589A pdb=" N AGLU C1147 " --> pdb=" O ASER C1143 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N BHIS C1155 " --> pdb=" O BTYR C1151 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N BSER C1157 " --> pdb=" O BLYS C1153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.323A pdb=" N ASN A 62 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR A 266 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER A 203 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.076A pdb=" N PHE A 44 " --> pdb=" O ARG C 563 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASP C 570 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU C 321 " --> pdb=" O CYS C 534 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 56 removed outlier: 7.453A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.646A pdb=" N LEU A 140 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.682A pdb=" N ARG A 234 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE A 105 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN A 236 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP A 103 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 238 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG A 101 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 166 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.693A pdb=" N VAL A 591 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN A 314 " --> pdb=" O GLY A 589 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY A 589 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 590 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 325 removed outlier: 5.442A pdb=" N ASP A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'A' and resid 650 through 656 removed outlier: 5.021A pdb=" N THR A 692 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN A 654 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 697 through 700 removed outlier: 6.463A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LYS B 786 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A 699 " --> pdb=" O LYS B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.779A pdb=" N ALA A1074 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A1091 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 714 through 724 removed outlier: 7.064A pdb=" N GLY A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER A1051 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1057 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A1059 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A1047 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A1061 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.340A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 783 through 786 Processing sheet with id=AC1, first strand: chain 'A' and resid 1116 through 1118 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.308A pdb=" N ASN B 62 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TYR B 266 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER B 203 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 56 removed outlier: 7.458A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.645A pdb=" N LEU B 140 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.687A pdb=" N ARG B 234 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B 105 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN B 236 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TRP B 103 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 238 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG B 101 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 166 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 308 through 316 removed outlier: 6.690A pdb=" N VAL B 591 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN B 314 " --> pdb=" O GLY B 589 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY B 589 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 590 " --> pdb=" O GLN B 609 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 321 through 325 removed outlier: 5.545A pdb=" N ASP B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AD1, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AD2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD4, first strand: chain 'B' and resid 650 through 656 removed outlier: 4.966A pdb=" N THR B 692 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 654 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA B 668 " --> pdb=" O PRO B 661 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 697 through 700 removed outlier: 6.480A pdb=" N ALA B 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LYS C 786 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 699 " --> pdb=" O LYS C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 707 through 711 removed outlier: 3.741A pdb=" N ALA B1074 " --> pdb=" O PHE B1091 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE B1091 " --> pdb=" O ALA B1074 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 714 through 724 removed outlier: 7.061A pdb=" N GLY B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER B1051 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B1057 " --> pdb=" O PRO B1049 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B1059 " --> pdb=" O SER B1047 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B1047 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B1061 " --> pdb=" O LEU B1045 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.341A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1116 through 1118 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.258A pdb=" N ASN C 62 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR C 266 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N SER C 203 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 56 removed outlier: 7.462A pdb=" N THR C 271 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASP C 287 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.646A pdb=" N LEU C 140 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 84 removed outlier: 6.687A pdb=" N ARG C 234 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C 105 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN C 236 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP C 103 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 238 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG C 101 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 166 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.684A pdb=" N VAL C 591 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN C 314 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY C 589 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY C 590 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE8, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF2, first strand: chain 'C' and resid 650 through 656 removed outlier: 5.010A pdb=" N THR C 692 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN C 654 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA C 668 " --> pdb=" O PRO C 661 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 707 through 711 removed outlier: 3.773A pdb=" N ALA C1074 " --> pdb=" O PHE C1091 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE C1091 " --> pdb=" O ALA C1074 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 714 through 724 removed outlier: 7.053A pdb=" N GLY C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C1051 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1057 " --> pdb=" O PRO C1049 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C1059 " --> pdb=" O SER C1047 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER C1047 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C1061 " --> pdb=" O LEU C1045 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.331A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1116 through 1118 1221 hydrogen bonds defined for protein. 3321 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: 7.17 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8631 1.34 - 1.46: 6014 1.46 - 1.58: 13540 1.58 - 1.70: 0 1.70 - 1.81: 153 Bond restraints: 28338 Sorted by residual: bond pdb=" N THR B 584 " pdb=" CA THR B 584 " ideal model delta sigma weight residual 1.462 1.448 0.014 1.00e-02 1.00e+04 2.04e+00 bond pdb=" CB CYS B 734 " pdb=" SG CYS B 734 " ideal model delta sigma weight residual 1.808 1.762 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB CYS A 734 " pdb=" SG CYS A 734 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CB CYS C 734 " pdb=" SG CYS C 734 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.67e+00 bond pdb=" N ASP B 741 " pdb=" CA ASP B 741 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.64e+00 ... (remaining 28333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 37906 1.87 - 3.75: 575 3.75 - 5.62: 51 5.62 - 7.50: 8 7.50 - 9.37: 4 Bond angle restraints: 38544 Sorted by residual: angle pdb=" C2 NAG A1406 " pdb=" N2 NAG A1406 " pdb=" C7 NAG A1406 " ideal model delta sigma weight residual 124.56 133.93 -9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" C2 NAG B1406 " pdb=" N2 NAG B1406 " pdb=" C7 NAG B1406 " ideal model delta sigma weight residual 124.56 133.90 -9.34 3.00e+00 1.11e-01 9.68e+00 angle pdb=" C2 NAG C1406 " pdb=" N2 NAG C1406 " pdb=" C7 NAG C1406 " ideal model delta sigma weight residual 124.56 133.88 -9.32 3.00e+00 1.11e-01 9.65e+00 angle pdb=" N ASN A1130 " pdb=" CA ASN A1130 " pdb=" CB ASN A1130 " ideal model delta sigma weight residual 109.85 114.36 -4.51 1.49e+00 4.50e-01 9.16e+00 angle pdb=" N GLY B 853 " pdb=" CA GLY B 853 " pdb=" C GLY B 853 " ideal model delta sigma weight residual 113.18 119.96 -6.78 2.37e+00 1.78e-01 8.18e+00 ... (remaining 38539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15504 17.97 - 35.94: 1552 35.94 - 53.91: 453 53.91 - 71.88: 108 71.88 - 89.85: 38 Dihedral angle restraints: 17655 sinusoidal: 7710 harmonic: 9945 Sorted by residual: dihedral pdb=" CA PRO B 585 " pdb=" C PRO B 585 " pdb=" N CYS B 586 " pdb=" CA CYS B 586 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CB CYS C 739 " pdb=" SG CYS C 739 " pdb=" SG CYS C 745 " pdb=" CB CYS C 745 " ideal model delta sinusoidal sigma weight residual -86.00 -47.00 -39.00 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS A 739 " pdb=" SG CYS A 739 " pdb=" SG CYS A 745 " pdb=" CB CYS A 745 " ideal model delta sinusoidal sigma weight residual -86.00 -47.57 -38.43 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 17652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4186 0.088 - 0.176: 307 0.176 - 0.265: 6 0.265 - 0.353: 1 0.353 - 0.441: 3 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1 NAG C1408 " pdb=" ND2 ASN C 612 " pdb=" C2 NAG C1408 " pdb=" O5 NAG C1408 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C1 NAG A1409 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG A1409 " pdb=" O5 NAG A1409 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG B1409 " pdb=" ND2 ASN B 62 " pdb=" C2 NAG B1409 " pdb=" O5 NAG B1409 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 4500 not shown) Planarity restraints: 4935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 705 " -0.036 2.00e-02 2.50e+03 3.44e-02 1.48e+01 pdb=" CG ASN A 705 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 705 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 705 " 0.040 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 713 " -0.037 2.00e-02 2.50e+03 3.37e-02 1.42e+01 pdb=" CG ASN B 713 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 713 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 713 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 705 " -0.034 2.00e-02 2.50e+03 3.12e-02 1.22e+01 pdb=" CG ASN B 705 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN B 705 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 705 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 4932 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 515 2.68 - 3.24: 25435 3.24 - 3.79: 43820 3.79 - 4.35: 60239 4.35 - 4.90: 99156 Nonbonded interactions: 229165 Sorted by model distance: nonbonded pdb=" OD1 ASP C 564 " pdb=" N ILE C 565 " model vdw 2.130 3.120 nonbonded pdb=" OD1 ASP B 564 " pdb=" N ILE B 565 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASP A 564 " pdb=" N ILE A 565 " model vdw 2.135 3.120 nonbonded pdb=" O ALA A 875 " pdb=" OG1 THR A 879 " model vdw 2.154 3.040 nonbonded pdb=" O ALA B 875 " pdb=" OG1 THR B 879 " model vdw 2.155 3.040 ... (remaining 229160 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 1133 or resid 1401 through 1410)) selection = (chain 'B' and (resid 15 through 1133 or resid 1401 through 1410)) selection = (chain 'C' and (resid 15 through 1133 or resid 1401 through 1410)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=0.98 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: 3.050 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: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 32.560 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.003 0.046 28443 Z= 0.123 Angle : 0.592 11.941 38817 Z= 0.295 Chirality : 0.045 0.441 4503 Planarity : 0.003 0.048 4890 Dihedral : 16.067 89.852 11139 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.90 % Allowed : 20.37 % Favored : 77.72 % 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: 0.24 (0.14), residues: 3390 helix: 1.98 (0.18), residues: 828 sheet: 0.17 (0.18), residues: 684 loop : -0.68 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.020 0.001 TYR B1063 PHE 0.044 0.001 PHE C 851 TRP 0.015 0.001 TRP C 629 HIS 0.003 0.000 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00263 (28338) covalent geometry : angle 0.54660 (38544) SS BOND : bond 0.00351 ( 42) SS BOND : angle 1.38719 ( 84) hydrogen bonds : bond 0.10217 ( 1203) hydrogen bonds : angle 6.69062 ( 3321) link_BETA1-4 : bond 0.00491 ( 15) link_BETA1-4 : angle 2.53601 ( 45) link_BETA1-6 : bond 0.00355 ( 3) link_BETA1-6 : angle 1.35859 ( 9) link_NAG-ASN : bond 0.00452 ( 45) link_NAG-ASN : angle 3.46131 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: -0.0873 (pp-130) cc_final: -0.1287 (ptm) REVERT: A 321 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 934 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7653 (tt) REVERT: B 33 PHE cc_start: 0.7746 (m-80) cc_final: 0.7539 (m-80) REVERT: B 512 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5506 (tm-30) REVERT: B 528 ASN cc_start: 0.8125 (m110) cc_final: 0.7913 (m110) REVERT: B 567 ASP cc_start: 0.7840 (m-30) cc_final: 0.7488 (m-30) REVERT: C 151 MET cc_start: 0.0570 (pp-130) cc_final: -0.0421 (ptm) REVERT: C 316 ARG cc_start: 0.8305 (ttt90) cc_final: 0.7676 (ttm110) REVERT: C 318 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8202 (mm110) REVERT: C 512 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5764 (tm-30) REVERT: C 528 ASN cc_start: 0.8240 (m110) cc_final: 0.7950 (m-40) REVERT: C 550 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6862 (tttt) REVERT: C 741 ASP cc_start: 0.7426 (p0) cc_final: 0.7143 (p0) REVERT: C 851 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6276 (OUTLIER) REVERT: C 934 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8101 (tt) REVERT: C 1109 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8531 (mt0) outliers start: 31 outliers final: 18 residues processed: 253 average time/residue: 0.5010 time to fit residues: 154.4408 Evaluate side-chains 236 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1001 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 318 GLN Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 734 CYS Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1109 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.6980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 385 ASN B 609 GLN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 609 GLN C 775 GLN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.231109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.192359 restraints weight = 47454.829| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.92 r_work: 0.3192 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28443 Z= 0.126 Angle : 0.558 9.330 38817 Z= 0.282 Chirality : 0.044 0.353 4503 Planarity : 0.004 0.049 4890 Dihedral : 6.046 57.578 5019 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.31 % Allowed : 18.70 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.14), residues: 3390 helix: 2.10 (0.18), residues: 813 sheet: 0.26 (0.18), residues: 699 loop : -0.64 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 316 TYR 0.020 0.001 TYR B1063 PHE 0.015 0.001 PHE B 190 TRP 0.015 0.001 TRP C 629 HIS 0.002 0.001 HIS B1060 Details of bonding type rmsd covalent geometry : bond 0.00287 (28338) covalent geometry : angle 0.52929 (38544) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.33807 ( 84) hydrogen bonds : bond 0.04119 ( 1203) hydrogen bonds : angle 5.50569 ( 3321) link_BETA1-4 : bond 0.00581 ( 15) link_BETA1-4 : angle 2.40561 ( 45) link_BETA1-6 : bond 0.00363 ( 3) link_BETA1-6 : angle 1.32637 ( 9) link_NAG-ASN : bond 0.00379 ( 45) link_NAG-ASN : angle 2.54354 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 1.017 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: A 53 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7922 (tp40) REVERT: A 151 MET cc_start: 0.1000 (pp-130) cc_final: -0.0567 (ptm) REVERT: A 512 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5763 (tm-30) REVERT: A 554 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6728 (mmtm) REVERT: A 560 GLN cc_start: 0.7222 (mm110) cc_final: 0.6991 (mm-40) REVERT: A 934 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7099 (tt) REVERT: A 1088 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: B 33 PHE cc_start: 0.7730 (m-80) cc_final: 0.7408 (m-80) REVERT: B 528 ASN cc_start: 0.8275 (m110) cc_final: 0.7917 (m110) REVERT: B 567 ASP cc_start: 0.7613 (m-30) cc_final: 0.7156 (m-30) REVERT: B 790 ILE cc_start: 0.7922 (mt) cc_final: 0.7630 (mt) REVERT: B 934 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7516 (tt) REVERT: B 1069 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (tttt) REVERT: C 151 MET cc_start: 0.0829 (pp-130) cc_final: -0.0296 (ptm) REVERT: C 316 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7419 (ttm110) REVERT: C 528 ASN cc_start: 0.8098 (m110) cc_final: 0.7749 (m-40) REVERT: C 576 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.4785 (mp10) REVERT: C 821 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6963 (tppt) REVERT: C 934 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7211 (tt) REVERT: C 1088 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7422 (pm20) outliers start: 75 outliers final: 24 residues processed: 276 average time/residue: 0.5268 time to fit residues: 176.8081 Evaluate side-chains 239 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1069 LYS Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Chi-restraints excluded: chain C residue 1115 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 217 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 304 optimal weight: 0.9980 chunk 187 optimal weight: 0.0980 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 118 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 318 GLN A 552 ASN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN C 775 GLN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.232186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.164267 restraints weight = 56658.006| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 6.23 r_work: 0.2893 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28443 Z= 0.103 Angle : 0.528 12.268 38817 Z= 0.266 Chirality : 0.043 0.327 4503 Planarity : 0.003 0.048 4890 Dihedral : 5.298 57.036 4987 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.84 % Allowed : 18.44 % Favored : 78.72 % 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: 0.38 (0.14), residues: 3390 helix: 2.16 (0.18), residues: 816 sheet: 0.40 (0.19), residues: 669 loop : -0.66 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 316 TYR 0.017 0.001 TYR B1063 PHE 0.012 0.001 PHE B 851 TRP 0.014 0.001 TRP C 629 HIS 0.002 0.000 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00226 (28338) covalent geometry : angle 0.50178 (38544) SS BOND : bond 0.00380 ( 42) SS BOND : angle 1.38618 ( 84) hydrogen bonds : bond 0.03700 ( 1203) hydrogen bonds : angle 5.25145 ( 3321) link_BETA1-4 : bond 0.00492 ( 15) link_BETA1-4 : angle 2.23164 ( 45) link_BETA1-6 : bond 0.00343 ( 3) link_BETA1-6 : angle 1.25323 ( 9) link_NAG-ASN : bond 0.00321 ( 45) link_NAG-ASN : angle 2.32098 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7784 (tp40) REVERT: A 151 MET cc_start: 0.1157 (pp-130) cc_final: -0.0389 (ptm) REVERT: A 316 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.6938 (ttp-170) REVERT: A 512 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5417 (tm-30) REVERT: A 552 ASN cc_start: 0.7709 (m-40) cc_final: 0.7494 (m-40) REVERT: A 554 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7174 (mptt) REVERT: A 934 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.6974 (tt) REVERT: A 1088 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: B 33 PHE cc_start: 0.7613 (m-80) cc_final: 0.7294 (m-80) REVERT: B 55 LEU cc_start: 0.8517 (mp) cc_final: 0.8293 (mm) REVERT: B 528 ASN cc_start: 0.8167 (m110) cc_final: 0.7802 (m110) REVERT: B 550 LYS cc_start: 0.7102 (tttt) cc_final: 0.6545 (ttpp) REVERT: B 560 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7048 (mm110) REVERT: B 567 ASP cc_start: 0.7392 (m-30) cc_final: 0.6899 (m-30) REVERT: B 790 ILE cc_start: 0.7692 (mt) cc_final: 0.7470 (mt) REVERT: B 821 LYS cc_start: 0.7510 (tmtt) cc_final: 0.6563 (mppt) REVERT: B 934 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7242 (tt) REVERT: B 1069 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8314 (tttt) REVERT: B 1088 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: C 55 LEU cc_start: 0.8575 (mp) cc_final: 0.8290 (mm) REVERT: C 151 MET cc_start: 0.1072 (pp-130) cc_final: -0.0144 (ptm) REVERT: C 268 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: C 316 ARG cc_start: 0.7938 (ttt90) cc_final: 0.7089 (ttm110) REVERT: C 528 ASN cc_start: 0.7981 (m110) cc_final: 0.7615 (m-40) REVERT: C 550 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6773 (tmtt) REVERT: C 689 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8183 (pp) REVERT: C 821 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6743 (tppt) REVERT: C 934 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7109 (tt) outliers start: 61 outliers final: 24 residues processed: 269 average time/residue: 0.5013 time to fit residues: 162.7764 Evaluate side-chains 238 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1069 LYS Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 308 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 287 optimal weight: 7.9990 chunk 140 optimal weight: 0.5980 chunk 296 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 318 GLN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.236455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.177917 restraints weight = 46799.188| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.76 r_work: 0.3645 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28443 Z= 0.186 Angle : 0.588 9.357 38817 Z= 0.301 Chirality : 0.045 0.244 4503 Planarity : 0.004 0.049 4890 Dihedral : 5.447 58.060 4985 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.14 % Allowed : 18.80 % Favored : 78.06 % 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: 0.26 (0.14), residues: 3390 helix: 1.95 (0.18), residues: 813 sheet: 0.43 (0.19), residues: 651 loop : -0.71 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.022 0.001 TYR B1063 PHE 0.018 0.002 PHE B 851 TRP 0.019 0.002 TRP B 150 HIS 0.004 0.001 HIS A1060 Details of bonding type rmsd covalent geometry : bond 0.00454 (28338) covalent geometry : angle 0.56437 (38544) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.89421 ( 84) hydrogen bonds : bond 0.04701 ( 1203) hydrogen bonds : angle 5.44860 ( 3321) link_BETA1-4 : bond 0.00544 ( 15) link_BETA1-4 : angle 2.20388 ( 45) link_BETA1-6 : bond 0.00286 ( 3) link_BETA1-6 : angle 1.22621 ( 9) link_NAG-ASN : bond 0.00457 ( 45) link_NAG-ASN : angle 2.14075 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 207 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7851 (tp40) REVERT: A 151 MET cc_start: -0.0398 (pp-130) cc_final: -0.1426 (ptm) REVERT: A 316 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7682 (ttm-80) REVERT: A 321 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7888 (mt-10) REVERT: A 512 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6273 (tm-30) REVERT: A 554 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7188 (mmtm) REVERT: A 821 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7395 (tppt) REVERT: A 934 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7401 (tt) REVERT: A 1088 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: B 53 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7811 (tp40) REVERT: B 151 MET cc_start: 0.0482 (pmm) cc_final: 0.0098 (ptm) REVERT: B 528 ASN cc_start: 0.8318 (m110) cc_final: 0.8017 (m110) REVERT: B 567 ASP cc_start: 0.7744 (m-30) cc_final: 0.7334 (m-30) REVERT: B 821 LYS cc_start: 0.7858 (tmtt) cc_final: 0.7379 (mppt) REVERT: B 934 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7770 (tt) REVERT: B 1088 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: B 1109 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: C 151 MET cc_start: -0.0633 (pp-130) cc_final: -0.1261 (ptm) REVERT: C 316 ARG cc_start: 0.8309 (ttt90) cc_final: 0.7848 (ttm110) REVERT: C 528 ASN cc_start: 0.8165 (m110) cc_final: 0.7903 (m-40) REVERT: C 550 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6916 (ttpp) REVERT: C 576 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.5560 (mp10) REVERT: C 821 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7353 (tppt) REVERT: C 934 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7485 (tt) REVERT: C 1088 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7537 (pm20) outliers start: 68 outliers final: 28 residues processed: 260 average time/residue: 0.5613 time to fit residues: 179.8962 Evaluate side-chains 250 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 256 optimal weight: 10.0000 chunk 285 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 48 optimal weight: 40.0000 chunk 172 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 chunk 4 optimal weight: 0.0050 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.231459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.160429 restraints weight = 47355.487| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 6.94 r_work: 0.2877 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28443 Z= 0.104 Angle : 0.522 9.334 38817 Z= 0.265 Chirality : 0.043 0.249 4503 Planarity : 0.004 0.049 4890 Dihedral : 5.155 56.965 4984 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.74 % Allowed : 19.21 % Favored : 78.06 % 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: 0.35 (0.14), residues: 3390 helix: 2.13 (0.18), residues: 816 sheet: 0.44 (0.19), residues: 648 loop : -0.69 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 316 TYR 0.016 0.001 TYR A1063 PHE 0.021 0.001 PHE A 798 TRP 0.013 0.001 TRP B 629 HIS 0.002 0.000 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00233 (28338) covalent geometry : angle 0.49852 (38544) SS BOND : bond 0.00324 ( 42) SS BOND : angle 1.54534 ( 84) hydrogen bonds : bond 0.03711 ( 1203) hydrogen bonds : angle 5.18342 ( 3321) link_BETA1-4 : bond 0.00495 ( 15) link_BETA1-4 : angle 2.09293 ( 45) link_BETA1-6 : bond 0.00279 ( 3) link_BETA1-6 : angle 1.19262 ( 9) link_NAG-ASN : bond 0.00260 ( 45) link_NAG-ASN : angle 2.06593 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7850 (tp40) REVERT: A 151 MET cc_start: 0.0994 (pp-130) cc_final: -0.0571 (ptm) REVERT: A 270 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7214 (mmt90) REVERT: A 316 ARG cc_start: 0.7485 (mtp-110) cc_final: 0.7059 (ttp-170) REVERT: A 321 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 512 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5555 (tm-30) REVERT: A 552 ASN cc_start: 0.7721 (m-40) cc_final: 0.7520 (m-40) REVERT: A 554 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7273 (mptt) REVERT: A 821 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7011 (tppt) REVERT: A 934 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7008 (tt) REVERT: A 1088 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: B 55 LEU cc_start: 0.8591 (mp) cc_final: 0.8389 (mm) REVERT: B 151 MET cc_start: 0.1514 (pmm) cc_final: 0.0553 (ptm) REVERT: B 316 ARG cc_start: 0.7638 (mtp-110) cc_final: 0.6927 (ttp-170) REVERT: B 528 ASN cc_start: 0.8197 (m110) cc_final: 0.7844 (m110) REVERT: B 560 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7126 (mm110) REVERT: B 567 ASP cc_start: 0.7442 (m-30) cc_final: 0.6969 (m-30) REVERT: B 790 ILE cc_start: 0.7788 (mt) cc_final: 0.7584 (mt) REVERT: B 821 LYS cc_start: 0.7562 (tmtt) cc_final: 0.6699 (mppt) REVERT: B 934 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7241 (tt) REVERT: B 1088 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: B 1109 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: C 53 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7218 (tp-100) REVERT: C 55 LEU cc_start: 0.8670 (mp) cc_final: 0.8398 (mm) REVERT: C 151 MET cc_start: 0.1159 (pp-130) cc_final: -0.0232 (ptm) REVERT: C 316 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7051 (ttm110) REVERT: C 528 ASN cc_start: 0.8046 (m110) cc_final: 0.7666 (m-40) REVERT: C 550 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6629 (ttpp) REVERT: C 576 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.4522 (mp10) REVERT: C 821 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6828 (tppt) REVERT: C 934 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7127 (tt) REVERT: C 1088 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7302 (pm20) outliers start: 59 outliers final: 28 residues processed: 267 average time/residue: 0.5480 time to fit residues: 176.6775 Evaluate side-chains 259 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 956 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 6 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 45 optimal weight: 50.0000 chunk 126 optimal weight: 9.9990 chunk 292 optimal weight: 3.9990 chunk 297 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** C 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.227580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.141876 restraints weight = 38568.677| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 10.65 r_work: 0.2776 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 28443 Z= 0.226 Angle : 0.617 9.366 38817 Z= 0.317 Chirality : 0.047 0.243 4503 Planarity : 0.004 0.050 4890 Dihedral : 5.516 58.108 4984 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.24 % Allowed : 18.77 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.14), residues: 3390 helix: 1.83 (0.18), residues: 813 sheet: 0.28 (0.18), residues: 681 loop : -0.75 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 316 TYR 0.023 0.002 TYR B1063 PHE 0.017 0.002 PHE A 66 TRP 0.014 0.002 TRP C 629 HIS 0.003 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00555 (28338) covalent geometry : angle 0.59333 (38544) SS BOND : bond 0.00434 ( 42) SS BOND : angle 2.11302 ( 84) hydrogen bonds : bond 0.05036 ( 1203) hydrogen bonds : angle 5.49998 ( 3321) link_BETA1-4 : bond 0.00447 ( 15) link_BETA1-4 : angle 2.14160 ( 45) link_BETA1-6 : bond 0.00204 ( 3) link_BETA1-6 : angle 1.25142 ( 9) link_NAG-ASN : bond 0.00275 ( 45) link_NAG-ASN : angle 2.13074 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 206 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7807 (tp40) REVERT: A 151 MET cc_start: 0.1348 (pp-130) cc_final: -0.0156 (ptm) REVERT: A 316 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.7135 (ttp-170) REVERT: A 321 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 512 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5570 (tm-30) REVERT: A 554 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6570 (mmtm) REVERT: A 821 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7012 (tppt) REVERT: A 934 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.6805 (tt) REVERT: A 1088 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: B 53 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7735 (tp40) REVERT: B 316 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7119 (ttp-170) REVERT: B 528 ASN cc_start: 0.8114 (m110) cc_final: 0.7734 (m110) REVERT: B 554 LYS cc_start: 0.7303 (mtmm) cc_final: 0.6297 (mmtm) REVERT: B 564 ASP cc_start: 0.7342 (t0) cc_final: 0.6737 (t0) REVERT: B 567 ASP cc_start: 0.7600 (m-30) cc_final: 0.7095 (m-30) REVERT: B 821 LYS cc_start: 0.7553 (tmtt) cc_final: 0.6690 (mppt) REVERT: B 934 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7384 (tt) REVERT: B 1088 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: B 1109 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: C 316 ARG cc_start: 0.7938 (ttt90) cc_final: 0.7044 (ttm110) REVERT: C 528 ASN cc_start: 0.8026 (m110) cc_final: 0.7633 (m-40) REVERT: C 550 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (ttpp) REVERT: C 576 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.4563 (mp10) REVERT: C 821 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6876 (tppt) REVERT: C 934 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7074 (tt) REVERT: C 1088 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7281 (pm20) outliers start: 72 outliers final: 34 residues processed: 261 average time/residue: 0.5422 time to fit residues: 171.7720 Evaluate side-chains 249 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 956 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 231 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 552 ASN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 318 GLN B 536 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 183 ASN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.225192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.189807 restraints weight = 38827.242| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.78 r_work: 0.3568 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28443 Z= 0.219 Angle : 0.616 12.940 38817 Z= 0.315 Chirality : 0.046 0.248 4503 Planarity : 0.004 0.051 4890 Dihedral : 5.641 57.217 4982 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.17 % Allowed : 18.94 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.06 (0.14), residues: 3390 helix: 1.52 (0.18), residues: 834 sheet: 0.27 (0.18), residues: 681 loop : -0.90 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 234 TYR 0.021 0.002 TYR B1063 PHE 0.016 0.002 PHE A 66 TRP 0.014 0.002 TRP C 629 HIS 0.006 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00542 (28338) covalent geometry : angle 0.59335 (38544) SS BOND : bond 0.00554 ( 42) SS BOND : angle 2.03320 ( 84) hydrogen bonds : bond 0.04873 ( 1203) hydrogen bonds : angle 5.50114 ( 3321) link_BETA1-4 : bond 0.00431 ( 15) link_BETA1-4 : angle 2.04083 ( 45) link_BETA1-6 : bond 0.00302 ( 3) link_BETA1-6 : angle 1.24714 ( 9) link_NAG-ASN : bond 0.00262 ( 45) link_NAG-ASN : angle 2.13608 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7874 (tp40) REVERT: A 151 MET cc_start: -0.0506 (pp-130) cc_final: -0.1418 (ptm) REVERT: A 316 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7668 (ttm-80) REVERT: A 321 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7900 (mt-10) REVERT: A 554 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7284 (mmtm) REVERT: A 576 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.5897 (mp10) REVERT: A 821 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7313 (tppt) REVERT: A 934 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 1069 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8218 (ttmt) REVERT: A 1088 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: B 53 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7861 (tp40) REVERT: B 151 MET cc_start: 0.0101 (pmt) cc_final: -0.0694 (ptm) REVERT: B 316 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7698 (ttm-80) REVERT: B 528 ASN cc_start: 0.8296 (m110) cc_final: 0.7993 (m110) REVERT: B 554 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7160 (mmtm) REVERT: B 567 ASP cc_start: 0.7786 (m-30) cc_final: 0.7412 (m-30) REVERT: B 821 LYS cc_start: 0.7746 (tmtt) cc_final: 0.7349 (mppt) REVERT: B 934 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7962 (tt) REVERT: B 1088 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: B 1109 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: C 53 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7399 (tp-100) REVERT: C 151 MET cc_start: 0.0288 (pmm) cc_final: -0.0567 (ptm) REVERT: C 316 ARG cc_start: 0.8253 (ttt90) cc_final: 0.7806 (ttm110) REVERT: C 528 ASN cc_start: 0.8172 (m110) cc_final: 0.7917 (m-40) REVERT: C 550 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7051 (ttpp) REVERT: C 576 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.5713 (mp10) REVERT: C 821 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7216 (tppt) REVERT: C 934 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7795 (tt) REVERT: C 1088 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7507 (pm20) outliers start: 68 outliers final: 37 residues processed: 253 average time/residue: 0.5481 time to fit residues: 167.5855 Evaluate side-chains 248 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1069 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 144 HIS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 956 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 250 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 265 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 142 optimal weight: 0.0170 chunk 297 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN A 775 GLN A 783 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.227119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.191611 restraints weight = 36503.115| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.78 r_work: 0.3627 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28443 Z= 0.137 Angle : 0.557 9.342 38817 Z= 0.286 Chirality : 0.044 0.245 4503 Planarity : 0.004 0.050 4890 Dihedral : 5.419 57.223 4982 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.11 % Allowed : 19.04 % Favored : 77.86 % 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: 0.06 (0.14), residues: 3390 helix: 1.74 (0.18), residues: 834 sheet: 0.26 (0.18), residues: 681 loop : -0.84 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 316 TYR 0.018 0.001 TYR B1063 PHE 0.026 0.001 PHE B 851 TRP 0.014 0.001 TRP C 629 HIS 0.007 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00323 (28338) covalent geometry : angle 0.53553 (38544) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.77698 ( 84) hydrogen bonds : bond 0.04207 ( 1203) hydrogen bonds : angle 5.32614 ( 3321) link_BETA1-4 : bond 0.00446 ( 15) link_BETA1-4 : angle 2.00464 ( 45) link_BETA1-6 : bond 0.00306 ( 3) link_BETA1-6 : angle 1.18944 ( 9) link_NAG-ASN : bond 0.00230 ( 45) link_NAG-ASN : angle 1.99125 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7908 (tp40) REVERT: A 151 MET cc_start: -0.0578 (pp-130) cc_final: -0.1487 (ptm) REVERT: A 316 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7735 (ttp-170) REVERT: A 321 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 554 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7304 (mmtm) REVERT: A 576 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.5877 (mp10) REVERT: A 821 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7280 (tppt) REVERT: A 934 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7345 (tt) REVERT: A 1069 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8151 (ttmt) REVERT: A 1088 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: B 55 LEU cc_start: 0.9136 (mp) cc_final: 0.8932 (mm) REVERT: B 151 MET cc_start: 0.0299 (pmt) cc_final: -0.0844 (ptm) REVERT: B 316 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7786 (ttp-170) REVERT: B 512 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6077 (tm-30) REVERT: B 528 ASN cc_start: 0.8297 (m110) cc_final: 0.8000 (m110) REVERT: B 554 LYS cc_start: 0.7670 (mtmm) cc_final: 0.7130 (mmtm) REVERT: B 567 ASP cc_start: 0.7741 (m-30) cc_final: 0.7368 (m-30) REVERT: B 821 LYS cc_start: 0.7706 (tmtt) cc_final: 0.7345 (mppt) REVERT: B 934 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7849 (tt) REVERT: B 1088 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: B 1109 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: C 53 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7434 (tp-100) REVERT: C 55 LEU cc_start: 0.9179 (mp) cc_final: 0.8955 (mm) REVERT: C 151 MET cc_start: 0.0465 (pmm) cc_final: -0.0907 (ptm) REVERT: C 316 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7825 (ttm110) REVERT: C 528 ASN cc_start: 0.8168 (m110) cc_final: 0.7925 (m-40) REVERT: C 550 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6985 (ttpp) REVERT: C 576 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.5694 (mp10) REVERT: C 821 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7205 (tppt) REVERT: C 934 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7570 (tt) REVERT: C 1088 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7508 (pm20) outliers start: 64 outliers final: 35 residues processed: 257 average time/residue: 0.5385 time to fit residues: 168.0488 Evaluate side-chains 250 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1069 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 956 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 131 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 244 optimal weight: 10.0000 chunk 53 optimal weight: 0.1980 chunk 117 optimal weight: 0.4980 chunk 147 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1155 HIS B ** 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 = 0.4370 r_free = 0.4370 target = 0.225631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.181193 restraints weight = 39844.466| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.93 r_work: 0.3450 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28443 Z= 0.149 Angle : 0.567 9.336 38817 Z= 0.291 Chirality : 0.044 0.244 4503 Planarity : 0.004 0.050 4890 Dihedral : 5.367 57.268 4980 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.84 % Allowed : 19.21 % Favored : 77.96 % 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: 0.07 (0.14), residues: 3390 helix: 1.76 (0.18), residues: 834 sheet: 0.28 (0.18), residues: 681 loop : -0.85 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 316 TYR 0.020 0.001 TYR B1063 PHE 0.019 0.001 PHE C 368 TRP 0.014 0.001 TRP C 629 HIS 0.010 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00357 (28338) covalent geometry : angle 0.54585 (38544) SS BOND : bond 0.00372 ( 42) SS BOND : angle 1.83659 ( 84) hydrogen bonds : bond 0.04284 ( 1203) hydrogen bonds : angle 5.32741 ( 3321) link_BETA1-4 : bond 0.00432 ( 15) link_BETA1-4 : angle 1.99865 ( 45) link_BETA1-6 : bond 0.00281 ( 3) link_BETA1-6 : angle 1.20857 ( 9) link_NAG-ASN : bond 0.00230 ( 45) link_NAG-ASN : angle 1.99227 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8104 (tp40) REVERT: A 151 MET cc_start: -0.0375 (pp-130) cc_final: -0.1448 (ptm) REVERT: A 316 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7706 (ttm-80) REVERT: A 321 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 554 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7272 (mmtm) REVERT: A 576 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.5784 (mp10) REVERT: A 821 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7357 (tppt) REVERT: A 934 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7372 (tt) REVERT: A 1069 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8350 (ttmt) REVERT: A 1088 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: B 55 LEU cc_start: 0.9110 (mp) cc_final: 0.8896 (mm) REVERT: B 151 MET cc_start: 0.0387 (pmt) cc_final: -0.0826 (ptm) REVERT: B 316 ARG cc_start: 0.8098 (mtp-110) cc_final: 0.7806 (ttp-170) REVERT: B 512 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6089 (tm-30) REVERT: B 528 ASN cc_start: 0.8408 (m110) cc_final: 0.8073 (m110) REVERT: B 554 LYS cc_start: 0.7734 (mtmm) cc_final: 0.7058 (mmtm) REVERT: B 567 ASP cc_start: 0.7899 (m-30) cc_final: 0.7454 (m-30) REVERT: B 821 LYS cc_start: 0.7839 (tmtt) cc_final: 0.7346 (mppt) REVERT: B 934 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7808 (tt) REVERT: B 1088 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: B 1109 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8376 (mt0) REVERT: C 55 LEU cc_start: 0.9171 (mp) cc_final: 0.8922 (mm) REVERT: C 151 MET cc_start: 0.0650 (pmm) cc_final: -0.0972 (ptm) REVERT: C 316 ARG cc_start: 0.8327 (ttt90) cc_final: 0.7831 (ttm110) REVERT: C 528 ASN cc_start: 0.8314 (m110) cc_final: 0.8031 (m-40) REVERT: C 550 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6991 (ttpp) REVERT: C 576 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.5597 (mp10) REVERT: C 821 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7245 (tppt) REVERT: C 934 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7529 (tt) REVERT: C 1088 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7544 (pm20) outliers start: 56 outliers final: 37 residues processed: 250 average time/residue: 0.5383 time to fit residues: 163.0144 Evaluate side-chains 255 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1069 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 956 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 306 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 271 optimal weight: 9.9990 chunk 283 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C1155 HIS B ** 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 = 0.4372 r_free = 0.4372 target = 0.225721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.183037 restraints weight = 42464.527| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.98 r_work: 0.3589 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 28443 Z= 0.191 Angle : 0.598 9.365 38817 Z= 0.308 Chirality : 0.045 0.241 4503 Planarity : 0.004 0.051 4890 Dihedral : 5.529 57.239 4980 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.94 % Allowed : 19.21 % Favored : 77.86 % 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: -0.02 (0.14), residues: 3390 helix: 1.61 (0.18), residues: 834 sheet: 0.26 (0.18), residues: 681 loop : -0.89 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 316 TYR 0.021 0.001 TYR B1063 PHE 0.015 0.002 PHE A 66 TRP 0.014 0.001 TRP C 629 HIS 0.007 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00467 (28338) covalent geometry : angle 0.57519 (38544) SS BOND : bond 0.00399 ( 42) SS BOND : angle 2.06290 ( 84) hydrogen bonds : bond 0.04732 ( 1203) hydrogen bonds : angle 5.43524 ( 3321) link_BETA1-4 : bond 0.00368 ( 15) link_BETA1-4 : angle 2.00905 ( 45) link_BETA1-6 : bond 0.00230 ( 3) link_BETA1-6 : angle 1.18040 ( 9) link_NAG-ASN : bond 0.00236 ( 45) link_NAG-ASN : angle 2.06849 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7884 (tp40) REVERT: A 151 MET cc_start: -0.0603 (pp-130) cc_final: -0.1466 (ptm) REVERT: A 316 ARG cc_start: 0.7947 (mtp-110) cc_final: 0.7733 (ttp-170) REVERT: A 321 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 554 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7343 (mmtm) REVERT: A 564 ASP cc_start: 0.7167 (t0) cc_final: 0.6484 (t0) REVERT: A 576 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.5921 (mp10) REVERT: A 821 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7266 (tppt) REVERT: A 934 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7372 (tt) REVERT: A 1069 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8168 (ttmt) REVERT: A 1088 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: B 53 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7848 (tp40) REVERT: B 151 MET cc_start: 0.0238 (pmt) cc_final: -0.0897 (ptm) REVERT: B 316 ARG cc_start: 0.8085 (mtp-110) cc_final: 0.7821 (ttp-170) REVERT: B 512 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.6073 (tm-30) REVERT: B 528 ASN cc_start: 0.8247 (m110) cc_final: 0.7957 (m110) REVERT: B 554 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7212 (mmtm) REVERT: B 564 ASP cc_start: 0.7149 (t0) cc_final: 0.6409 (t70) REVERT: B 567 ASP cc_start: 0.7681 (m-30) cc_final: 0.7294 (m-30) REVERT: B 821 LYS cc_start: 0.7678 (tmtt) cc_final: 0.7345 (mppt) REVERT: B 934 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7915 (tt) REVERT: B 1088 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: B 1109 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: C 53 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7390 (tp-100) REVERT: C 316 ARG cc_start: 0.8214 (ttt90) cc_final: 0.7836 (ttm110) REVERT: C 528 ASN cc_start: 0.8131 (m110) cc_final: 0.7896 (m-40) REVERT: C 550 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7033 (ttpp) REVERT: C 576 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.5812 (mp10) REVERT: C 821 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7170 (tppt) REVERT: C 934 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7558 (tt) REVERT: C 1088 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7437 (pm20) outliers start: 58 outliers final: 39 residues processed: 247 average time/residue: 0.5510 time to fit residues: 164.3430 Evaluate side-chains 250 residues out of total 2850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain A residue 698 GLU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1069 LYS Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 821 LYS Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 956 ASN Chi-restraints excluded: chain C residue 987 VAL Chi-restraints excluded: chain C residue 1088 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 317 optimal weight: 0.9990 chunk 122 optimal weight: 30.0000 chunk 311 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 298 optimal weight: 0.0870 chunk 289 optimal weight: 0.8980 chunk 287 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 ASN A 775 GLN ** A1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN ** C1155 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.227006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.160222 restraints weight = 44572.523| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 5.83 r_work: 0.2823 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 28443 Z= 0.160 Angle : 0.732 59.193 38817 Z= 0.397 Chirality : 0.049 1.468 4503 Planarity : 0.004 0.050 4890 Dihedral : 5.540 57.245 4980 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.91 % Allowed : 19.31 % Favored : 77.79 % Cbeta Deviations : 0.03 % 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: -0.03 (0.14), residues: 3390 helix: 1.62 (0.18), residues: 834 sheet: 0.23 (0.18), residues: 681 loop : -0.89 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 316 TYR 0.021 0.001 TYR B1063 PHE 0.016 0.001 PHE C 91 TRP 0.014 0.001 TRP C 629 HIS 0.006 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00377 (28338) covalent geometry : angle 0.71475 (38544) SS BOND : bond 0.00374 ( 42) SS BOND : angle 2.01200 ( 84) hydrogen bonds : bond 0.04620 ( 1203) hydrogen bonds : angle 5.43432 ( 3321) link_BETA1-4 : bond 0.00388 ( 15) link_BETA1-4 : angle 2.00513 ( 45) link_BETA1-6 : bond 0.00272 ( 3) link_BETA1-6 : angle 1.21743 ( 9) link_NAG-ASN : bond 0.00230 ( 45) link_NAG-ASN : angle 2.08323 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12016.08 seconds wall clock time: 205 minutes 7.90 seconds (12307.90 seconds total)