Starting phenix.real_space_refine on Thu Mar 5 23:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkl_23898/03_2026/7mkl_23898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkl_23898/03_2026/7mkl_23898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mkl_23898/03_2026/7mkl_23898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkl_23898/03_2026/7mkl_23898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mkl_23898/03_2026/7mkl_23898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkl_23898/03_2026/7mkl_23898.map" } resolution = 3.2 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 111 5.16 5 C 16288 2.51 5 N 4164 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25597 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 948} Chain breaks: 7 Chain: "B" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "C" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.16, per 1000 atoms: 0.24 Number of scatterers: 25597 At special positions: 0 Unit cell: (135.72, 131.08, 214.6, 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 111 16.00 O 5034 8.00 N 4164 7.00 C 16288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 282 " " NAG A1205 " - " ASN A 331 " " NAG A1206 " - " ASN A 343 " " NAG A1207 " - " ASN A 603 " " NAG A1208 " - " ASN A 616 " " NAG A1209 " - " ASN A 657 " " NAG A1210 " - " ASN A 709 " " NAG A1211 " - " ASN A1074 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 282 " " NAG B1205 " - " ASN B 331 " " NAG B1206 " - " ASN B 343 " " NAG B1207 " - " ASN B 603 " " NAG B1208 " - " ASN B 616 " " NAG B1209 " - " ASN B 657 " " NAG B1210 " - " ASN B 709 " " NAG B1211 " - " ASN B1074 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 331 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 603 " " NAG C1208 " - " ASN C 616 " " NAG C1209 " - " ASN C 657 " " NAG C1210 " - " ASN C 709 " " NAG C1211 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5930 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 44 sheets defined 24.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.777A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.246A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.180A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.049A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.125A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.544A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.871A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.085A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.018A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.030A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.892A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.388A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.662A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.126A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.201A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.945A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.707A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.852A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.793A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.535A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.372A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.523A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.119A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.547A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.689A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.283A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.245A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 7.049A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.304A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.770A pdb=" N ARG C 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.555A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.870A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.099A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.693A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.747A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 378 through 379 removed outlier: 4.593A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.738A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.529A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.752A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.785A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.269A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.718A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.395A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.046A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.777A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.660A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.622A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.303A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.702A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.591A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.979A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.519A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2511 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: 6.07 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8082 1.35 - 1.47: 6865 1.47 - 1.60: 11073 1.60 - 1.73: 0 1.73 - 1.86: 140 Bond restraints: 26160 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.74e+00 ... (remaining 26155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 35428 3.89 - 7.79: 152 7.79 - 11.68: 16 11.68 - 15.57: 3 15.57 - 19.46: 1 Bond angle restraints: 35600 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 133.86 -19.46 2.30e+00 1.89e-01 7.16e+01 angle pdb=" CA CYS B 738 " pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " ideal model delta sigma weight residual 114.40 126.86 -12.46 2.30e+00 1.89e-01 2.93e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 125.98 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 124.90 -10.50 2.30e+00 1.89e-01 2.09e+01 angle pdb=" C LYS A 386 " pdb=" N LEU A 387 " pdb=" CA LEU A 387 " ideal model delta sigma weight residual 122.58 113.22 9.36 2.07e+00 2.33e-01 2.05e+01 ... (remaining 35595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 15558 22.74 - 45.47: 649 45.47 - 68.21: 145 68.21 - 90.94: 40 90.94 - 113.68: 14 Dihedral angle restraints: 16406 sinusoidal: 7204 harmonic: 9202 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 173.33 -80.33 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.64 70.64 1 1.00e+01 1.00e-02 6.42e+01 ... (remaining 16403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 4217 0.211 - 0.422: 17 0.422 - 0.633: 1 0.633 - 0.844: 0 0.844 - 1.055: 1 Chirality restraints: 4236 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.34 -1.06 2.00e-01 2.50e+01 2.79e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" C1 NAG A1203 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1203 " pdb=" O5 NAG A1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 4233 not shown) Planarity restraints: 4562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " 0.085 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 899 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " -0.007 2.00e-02 2.50e+03 3.67e-02 1.69e+01 pdb=" CG ASN B1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 816 " 0.065 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO A 817 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 817 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 817 " 0.054 5.00e-02 4.00e+02 ... (remaining 4559 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 86 2.47 - 3.08: 17186 3.08 - 3.68: 35944 3.68 - 4.29: 51071 4.29 - 4.90: 85344 Nonbonded interactions: 189631 Sorted by model distance: nonbonded pdb=" O PRO B 85 " pdb=" OH TYR B 269 " model vdw 1.862 3.040 nonbonded pdb=" O PHE B 329 " pdb=" NE2 GLN B 580 " model vdw 2.150 3.120 nonbonded pdb=" OD1 ASN A 360 " pdb=" OG1 THR A 523 " model vdw 2.170 3.040 nonbonded pdb=" OE2 GLU B 96 " pdb=" N ILE B 100 " model vdw 2.176 3.120 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.177 3.040 ... (remaining 189626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 444 or resid 447 through 454 or resid 462 throu \ gh 468 or resid 489 through 501 or resid 503 through 1211)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.340 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 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 : 0.004 0.107 26262 Z= 0.204 Angle : 0.896 22.084 35867 Z= 0.449 Chirality : 0.056 1.055 4236 Planarity : 0.006 0.128 4514 Dihedral : 13.439 113.679 10359 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.37 (0.14), residues: 3096 helix: 0.76 (0.19), residues: 696 sheet: 1.21 (0.19), residues: 629 loop : -0.29 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 328 TYR 0.034 0.002 TYR B 423 PHE 0.026 0.002 PHE C 92 TRP 0.015 0.001 TRP B 353 HIS 0.011 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00437 (26160) covalent geometry : angle 0.81960 (35600) SS BOND : bond 0.00788 ( 39) SS BOND : angle 2.45333 ( 78) hydrogen bonds : bond 0.22153 ( 891) hydrogen bonds : angle 8.18452 ( 2511) link_BETA1-4 : bond 0.00880 ( 15) link_BETA1-4 : angle 2.86221 ( 45) link_NAG-ASN : bond 0.00845 ( 48) link_NAG-ASN : angle 5.28369 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.6632 (p0) cc_final: 0.5886 (p0) REVERT: A 568 ASP cc_start: 0.7320 (t0) cc_final: 0.7082 (t0) REVERT: B 265 TYR cc_start: 0.5243 (p90) cc_final: 0.4593 (p90) REVERT: B 558 LYS cc_start: 0.5761 (tmtt) cc_final: 0.5508 (tptp) REVERT: B 781 VAL cc_start: 0.4733 (t) cc_final: 0.4448 (t) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1716 time to fit residues: 93.9461 Evaluate side-chains 297 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 334 ASN A 506 GLN A 613 GLN A 779 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 450 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 824 ASN C 613 GLN C 787 GLN H 35 HIS L 91 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.218577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.181494 restraints weight = 43146.767| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 3.29 r_work: 0.4256 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 26262 Z= 0.195 Angle : 0.793 20.655 35867 Z= 0.393 Chirality : 0.058 1.731 4236 Planarity : 0.005 0.077 4514 Dihedral : 9.836 93.142 4697 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.23 % Allowed : 4.79 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.29 (0.14), residues: 3096 helix: 1.50 (0.20), residues: 684 sheet: 0.64 (0.19), residues: 653 loop : -0.49 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.028 0.002 TYR A 279 PHE 0.029 0.002 PHE B 400 TRP 0.020 0.002 TRP A 436 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00437 (26160) covalent geometry : angle 0.72659 (35600) SS BOND : bond 0.00766 ( 39) SS BOND : angle 1.81487 ( 78) hydrogen bonds : bond 0.06501 ( 891) hydrogen bonds : angle 6.56028 ( 2511) link_BETA1-4 : bond 0.00864 ( 15) link_BETA1-4 : angle 2.48631 ( 45) link_NAG-ASN : bond 0.00842 ( 48) link_NAG-ASN : angle 4.71712 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 VAL cc_start: 0.7189 (t) cc_final: 0.6922 (p) REVERT: A 568 ASP cc_start: 0.7916 (t0) cc_final: 0.7531 (t0) REVERT: B 265 TYR cc_start: 0.5202 (p90) cc_final: 0.4577 (p90) REVERT: B 298 GLU cc_start: 0.5587 (pp20) cc_final: 0.5357 (pp20) REVERT: B 465 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 781 VAL cc_start: 0.5421 (t) cc_final: 0.5045 (t) REVERT: B 964 LYS cc_start: 0.8389 (tppp) cc_final: 0.8110 (tppp) REVERT: C 578 ASP cc_start: 0.7374 (m-30) cc_final: 0.7159 (m-30) REVERT: C 825 LYS cc_start: 0.7665 (tppp) cc_final: 0.7380 (tptt) REVERT: C 869 MET cc_start: 0.7287 (mtp) cc_final: 0.6965 (mtp) REVERT: C 902 MET cc_start: 0.4055 (tpp) cc_final: 0.3837 (tpt) REVERT: C 957 GLN cc_start: 0.8077 (tt0) cc_final: 0.7812 (tt0) outliers start: 34 outliers final: 20 residues processed: 347 average time/residue: 0.1683 time to fit residues: 94.1359 Evaluate side-chains 315 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 295 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 36 optimal weight: 2.9990 chunk 206 optimal weight: 0.1980 chunk 291 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 278 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 chunk 110 optimal weight: 0.0040 chunk 286 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1101 HIS B 824 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.219238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.182140 restraints weight = 43121.110| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.30 r_work: 0.4273 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26262 Z= 0.134 Angle : 0.694 20.400 35867 Z= 0.335 Chirality : 0.050 0.874 4236 Planarity : 0.005 0.066 4514 Dihedral : 9.138 91.088 4697 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.12 % Allowed : 7.71 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.28 (0.14), residues: 3096 helix: 1.64 (0.20), residues: 682 sheet: 0.58 (0.19), residues: 659 loop : -0.54 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.025 0.001 TYR A 423 PHE 0.020 0.001 PHE C 400 TRP 0.016 0.001 TRP H 36 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00286 (26160) covalent geometry : angle 0.62318 (35600) SS BOND : bond 0.00599 ( 39) SS BOND : angle 1.52449 ( 78) hydrogen bonds : bond 0.05592 ( 891) hydrogen bonds : angle 6.01441 ( 2511) link_BETA1-4 : bond 0.00670 ( 15) link_BETA1-4 : angle 2.61418 ( 45) link_NAG-ASN : bond 0.00837 ( 48) link_NAG-ASN : angle 4.53351 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 317 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6333 (pp) REVERT: A 510 VAL cc_start: 0.7318 (t) cc_final: 0.7025 (p) REVERT: A 976 VAL cc_start: 0.8365 (t) cc_final: 0.8004 (p) REVERT: B 265 TYR cc_start: 0.5179 (p90) cc_final: 0.4614 (p90) REVERT: B 465 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7479 (mm-30) REVERT: B 781 VAL cc_start: 0.5213 (t) cc_final: 0.4860 (t) REVERT: C 289 VAL cc_start: 0.8084 (t) cc_final: 0.7793 (p) REVERT: C 614 ASP cc_start: 0.6213 (t0) cc_final: 0.5993 (t0) REVERT: C 825 LYS cc_start: 0.7569 (tppp) cc_final: 0.7293 (tptt) REVERT: C 902 MET cc_start: 0.4328 (tpp) cc_final: 0.4057 (tpt) REVERT: C 988 GLU cc_start: 0.6412 (mp0) cc_final: 0.6078 (mp0) REVERT: H 103 ASP cc_start: 0.8132 (m-30) cc_final: 0.7848 (m-30) outliers start: 31 outliers final: 17 residues processed: 334 average time/residue: 0.1621 time to fit residues: 87.5878 Evaluate side-chains 314 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 296 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 223 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 295 optimal weight: 30.0000 chunk 290 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 221 optimal weight: 0.0670 chunk 155 optimal weight: 5.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 784 GLN A 926 GLN A 935 GLN B1088 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.214004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.176096 restraints weight = 42346.870| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 3.84 r_work: 0.4186 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 26262 Z= 0.193 Angle : 0.776 24.890 35867 Z= 0.378 Chirality : 0.051 0.685 4236 Planarity : 0.005 0.062 4514 Dihedral : 8.830 87.220 4697 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.80 % Allowed : 9.01 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.21 (0.14), residues: 3096 helix: 1.40 (0.20), residues: 670 sheet: 0.18 (0.19), residues: 653 loop : -0.88 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 190 TYR 0.026 0.002 TYR A 423 PHE 0.026 0.002 PHE A 543 TRP 0.038 0.002 TRP H 47 HIS 0.010 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00441 (26160) covalent geometry : angle 0.70332 (35600) SS BOND : bond 0.00704 ( 39) SS BOND : angle 1.83768 ( 78) hydrogen bonds : bond 0.06719 ( 891) hydrogen bonds : angle 6.01184 ( 2511) link_BETA1-4 : bond 0.00629 ( 15) link_BETA1-4 : angle 2.68092 ( 45) link_NAG-ASN : bond 0.00882 ( 48) link_NAG-ASN : angle 4.84883 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.7895 (t0) cc_final: 0.7552 (t0) REVERT: A 750 SER cc_start: 0.7433 (t) cc_final: 0.7087 (p) REVERT: B 265 TYR cc_start: 0.5438 (p90) cc_final: 0.4728 (p90) REVERT: B 423 TYR cc_start: 0.4324 (m-10) cc_final: 0.3942 (m-10) REVERT: B 465 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 523 THR cc_start: 0.7796 (m) cc_final: 0.7573 (m) REVERT: B 781 VAL cc_start: 0.5642 (t) cc_final: 0.5288 (t) REVERT: B 964 LYS cc_start: 0.8515 (tppp) cc_final: 0.8196 (tppp) REVERT: B 988 GLU cc_start: 0.6349 (mp0) cc_final: 0.6148 (mp0) REVERT: B 1106 GLN cc_start: 0.8020 (pt0) cc_final: 0.7587 (mp-120) REVERT: C 266 TYR cc_start: 0.5484 (OUTLIER) cc_final: 0.5097 (m-80) REVERT: C 289 VAL cc_start: 0.8206 (t) cc_final: 0.7894 (p) REVERT: C 614 ASP cc_start: 0.6731 (t0) cc_final: 0.6413 (t0) REVERT: C 825 LYS cc_start: 0.7677 (tppp) cc_final: 0.7397 (tptt) REVERT: C 869 MET cc_start: 0.7591 (mtp) cc_final: 0.7363 (mtp) REVERT: H 103 ASP cc_start: 0.8158 (m-30) cc_final: 0.7885 (m-30) outliers start: 50 outliers final: 31 residues processed: 345 average time/residue: 0.1651 time to fit residues: 91.0600 Evaluate side-chains 328 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 0.4980 chunk 263 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 193 optimal weight: 0.0670 chunk 248 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 256 optimal weight: 0.4980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 935 GLN B 239 GLN B 536 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.215442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.178209 restraints weight = 42790.829| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 3.49 r_work: 0.4206 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26262 Z= 0.137 Angle : 0.700 19.976 35867 Z= 0.338 Chirality : 0.049 0.613 4236 Planarity : 0.005 0.055 4514 Dihedral : 8.337 85.157 4697 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 11.25 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.11 (0.14), residues: 3096 helix: 1.60 (0.20), residues: 677 sheet: 0.18 (0.20), residues: 633 loop : -0.84 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.022 0.001 TYR C 674 PHE 0.021 0.001 PHE C 201 TRP 0.017 0.001 TRP H 47 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00296 (26160) covalent geometry : angle 0.62745 (35600) SS BOND : bond 0.00572 ( 39) SS BOND : angle 2.07724 ( 78) hydrogen bonds : bond 0.05760 ( 891) hydrogen bonds : angle 5.75360 ( 2511) link_BETA1-4 : bond 0.00605 ( 15) link_BETA1-4 : angle 2.59559 ( 45) link_NAG-ASN : bond 0.00845 ( 48) link_NAG-ASN : angle 4.49277 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.7778 (t0) cc_final: 0.7403 (t0) REVERT: B 47 VAL cc_start: 0.8379 (p) cc_final: 0.8142 (m) REVERT: B 265 TYR cc_start: 0.5373 (p90) cc_final: 0.4696 (p90) REVERT: B 287 ASP cc_start: 0.6814 (t0) cc_final: 0.6406 (m-30) REVERT: B 423 TYR cc_start: 0.4175 (m-10) cc_final: 0.3846 (m-10) REVERT: B 450 ASN cc_start: 0.8016 (m-40) cc_final: 0.7646 (m110) REVERT: B 523 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7435 (m) REVERT: B 781 VAL cc_start: 0.5288 (t) cc_final: 0.4913 (t) REVERT: B 964 LYS cc_start: 0.8413 (tppp) cc_final: 0.8065 (tppp) REVERT: B 1106 GLN cc_start: 0.7940 (pt0) cc_final: 0.7574 (mp-120) REVERT: C 289 VAL cc_start: 0.8233 (t) cc_final: 0.7904 (p) REVERT: C 465 GLU cc_start: 0.7002 (mp0) cc_final: 0.6629 (mt-10) REVERT: C 614 ASP cc_start: 0.6601 (t0) cc_final: 0.6271 (t0) REVERT: C 825 LYS cc_start: 0.7602 (tppp) cc_final: 0.7303 (tttt) REVERT: C 988 GLU cc_start: 0.6586 (mp0) cc_final: 0.6158 (mp0) REVERT: H 103 ASP cc_start: 0.8132 (m-30) cc_final: 0.7850 (m-30) outliers start: 48 outliers final: 31 residues processed: 338 average time/residue: 0.1683 time to fit residues: 91.0912 Evaluate side-chains 331 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 156 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 chunk 306 optimal weight: 0.0770 chunk 116 optimal weight: 0.0670 chunk 91 optimal weight: 0.0570 chunk 265 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.216745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.179784 restraints weight = 43000.439| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 3.33 r_work: 0.4230 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26262 Z= 0.121 Angle : 0.702 23.571 35867 Z= 0.332 Chirality : 0.048 0.554 4236 Planarity : 0.005 0.055 4514 Dihedral : 8.087 83.329 4697 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.48 % Allowed : 11.75 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.03 (0.15), residues: 3096 helix: 1.75 (0.21), residues: 673 sheet: 0.22 (0.20), residues: 625 loop : -0.81 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.018 0.001 TYR A 674 PHE 0.032 0.001 PHE A 201 TRP 0.016 0.001 TRP H 36 HIS 0.004 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00259 (26160) covalent geometry : angle 0.61904 (35600) SS BOND : bond 0.00459 ( 39) SS BOND : angle 1.96137 ( 78) hydrogen bonds : bond 0.05178 ( 891) hydrogen bonds : angle 5.50923 ( 2511) link_BETA1-4 : bond 0.00550 ( 15) link_BETA1-4 : angle 2.73962 ( 45) link_NAG-ASN : bond 0.00746 ( 48) link_NAG-ASN : angle 4.85133 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 309 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.7821 (t0) cc_final: 0.7422 (t0) REVERT: B 47 VAL cc_start: 0.8371 (p) cc_final: 0.8156 (m) REVERT: B 265 TYR cc_start: 0.5288 (p90) cc_final: 0.4606 (p90) REVERT: B 287 ASP cc_start: 0.6802 (t0) cc_final: 0.6390 (m-30) REVERT: B 423 TYR cc_start: 0.4158 (m-10) cc_final: 0.3864 (m-10) REVERT: B 523 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7366 (m) REVERT: B 781 VAL cc_start: 0.4950 (t) cc_final: 0.4604 (t) REVERT: B 902 MET cc_start: 0.6433 (tpp) cc_final: 0.6186 (tpp) REVERT: B 948 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5904 (mp) REVERT: B 988 GLU cc_start: 0.6244 (mp0) cc_final: 0.5911 (mp0) REVERT: B 1106 GLN cc_start: 0.7884 (pt0) cc_final: 0.7515 (mp-120) REVERT: C 289 VAL cc_start: 0.8195 (t) cc_final: 0.7886 (p) REVERT: C 396 TYR cc_start: 0.6420 (m-80) cc_final: 0.6115 (m-80) REVERT: C 614 ASP cc_start: 0.6542 (t0) cc_final: 0.6197 (t0) REVERT: C 702 GLU cc_start: 0.7787 (tt0) cc_final: 0.7579 (tm-30) REVERT: C 825 LYS cc_start: 0.7546 (tppp) cc_final: 0.7260 (tptt) REVERT: H 103 ASP cc_start: 0.8142 (m-30) cc_final: 0.7844 (m-30) REVERT: L 21 MET cc_start: 0.1202 (pmm) cc_final: -0.1646 (ptt) outliers start: 41 outliers final: 31 residues processed: 333 average time/residue: 0.1667 time to fit residues: 89.1221 Evaluate side-chains 330 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 414 GLN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 255 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN A 655 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 779 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.213334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.175784 restraints weight = 42283.516| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 3.87 r_work: 0.4176 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26262 Z= 0.161 Angle : 0.755 22.862 35867 Z= 0.358 Chirality : 0.049 0.508 4236 Planarity : 0.005 0.056 4514 Dihedral : 8.066 81.857 4697 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.95 % Allowed : 12.04 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.27 (0.15), residues: 3096 helix: 1.53 (0.20), residues: 682 sheet: -0.00 (0.20), residues: 645 loop : -0.95 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.018 0.002 TYR C 204 PHE 0.023 0.002 PHE A 201 TRP 0.015 0.001 TRP H 36 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00361 (26160) covalent geometry : angle 0.65928 (35600) SS BOND : bond 0.00533 ( 39) SS BOND : angle 2.37501 ( 78) hydrogen bonds : bond 0.05933 ( 891) hydrogen bonds : angle 5.61490 ( 2511) link_BETA1-4 : bond 0.00657 ( 15) link_BETA1-4 : angle 2.73362 ( 45) link_NAG-ASN : bond 0.00967 ( 48) link_NAG-ASN : angle 5.40808 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8249 (mttp) cc_final: 0.7796 (mmmt) REVERT: A 568 ASP cc_start: 0.7891 (t0) cc_final: 0.7443 (t0) REVERT: A 750 SER cc_start: 0.7580 (t) cc_final: 0.7216 (p) REVERT: B 47 VAL cc_start: 0.8369 (p) cc_final: 0.8133 (m) REVERT: B 238 PHE cc_start: 0.1866 (OUTLIER) cc_final: 0.1572 (p90) REVERT: B 287 ASP cc_start: 0.6846 (t0) cc_final: 0.6419 (t0) REVERT: B 423 TYR cc_start: 0.4262 (m-10) cc_final: 0.3988 (m-10) REVERT: B 450 ASN cc_start: 0.8059 (m-40) cc_final: 0.7692 (m110) REVERT: B 655 HIS cc_start: 0.8163 (t70) cc_final: 0.7924 (t-170) REVERT: B 781 VAL cc_start: 0.5365 (t) cc_final: 0.5013 (t) REVERT: B 948 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5891 (mt) REVERT: B 964 LYS cc_start: 0.8546 (tppp) cc_final: 0.8128 (tppp) REVERT: B 988 GLU cc_start: 0.6192 (mp0) cc_final: 0.5878 (mp0) REVERT: B 1106 GLN cc_start: 0.8011 (pt0) cc_final: 0.7593 (mp-120) REVERT: C 266 TYR cc_start: 0.5707 (OUTLIER) cc_final: 0.5395 (m-80) REVERT: C 289 VAL cc_start: 0.8291 (t) cc_final: 0.7955 (p) REVERT: C 465 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: C 614 ASP cc_start: 0.6590 (t0) cc_final: 0.6242 (t0) REVERT: C 702 GLU cc_start: 0.7849 (tt0) cc_final: 0.7646 (tm-30) REVERT: C 825 LYS cc_start: 0.7670 (tppp) cc_final: 0.7385 (tptt) REVERT: C 918 GLU cc_start: 0.5351 (OUTLIER) cc_final: 0.3114 (mm-30) REVERT: C 988 GLU cc_start: 0.6610 (mp0) cc_final: 0.6227 (mp0) REVERT: H 103 ASP cc_start: 0.8189 (m-30) cc_final: 0.7884 (m-30) outliers start: 54 outliers final: 38 residues processed: 340 average time/residue: 0.1644 time to fit residues: 89.2342 Evaluate side-chains 339 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 305 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.212644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.175873 restraints weight = 42365.153| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 3.77 r_work: 0.4184 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26262 Z= 0.157 Angle : 0.753 21.430 35867 Z= 0.359 Chirality : 0.050 0.497 4236 Planarity : 0.005 0.055 4514 Dihedral : 7.735 80.528 4697 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.69 % Allowed : 12.94 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.34 (0.15), residues: 3096 helix: 1.57 (0.20), residues: 676 sheet: -0.05 (0.20), residues: 664 loop : -1.03 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.021 0.001 TYR C 204 PHE 0.023 0.002 PHE A 201 TRP 0.015 0.001 TRP H 36 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00354 (26160) covalent geometry : angle 0.66478 (35600) SS BOND : bond 0.00546 ( 39) SS BOND : angle 2.07961 ( 78) hydrogen bonds : bond 0.05977 ( 891) hydrogen bonds : angle 5.55822 ( 2511) link_BETA1-4 : bond 0.00566 ( 15) link_BETA1-4 : angle 2.76955 ( 45) link_NAG-ASN : bond 0.00912 ( 48) link_NAG-ASN : angle 5.21169 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.738 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 41 LYS cc_start: 0.8319 (mttp) cc_final: 0.7863 (mmmt) REVERT: A 568 ASP cc_start: 0.7881 (t0) cc_final: 0.7566 (t0) REVERT: A 595 VAL cc_start: 0.8569 (t) cc_final: 0.8333 (p) REVERT: A 750 SER cc_start: 0.7646 (t) cc_final: 0.7268 (p) REVERT: B 47 VAL cc_start: 0.8435 (p) cc_final: 0.8204 (m) REVERT: B 238 PHE cc_start: 0.1852 (OUTLIER) cc_final: 0.1590 (p90) REVERT: B 265 TYR cc_start: 0.5608 (p90) cc_final: 0.5194 (p90) REVERT: B 287 ASP cc_start: 0.6785 (t0) cc_final: 0.6380 (t0) REVERT: B 423 TYR cc_start: 0.4520 (m-10) cc_final: 0.4242 (m-10) REVERT: B 655 HIS cc_start: 0.7995 (t70) cc_final: 0.7790 (t-170) REVERT: B 781 VAL cc_start: 0.5468 (t) cc_final: 0.5100 (t) REVERT: B 824 ASN cc_start: 0.8131 (t0) cc_final: 0.7899 (t0) REVERT: B 948 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5954 (mt) REVERT: B 964 LYS cc_start: 0.8514 (tppp) cc_final: 0.8132 (tppp) REVERT: B 1106 GLN cc_start: 0.8000 (pt0) cc_final: 0.7642 (mp-120) REVERT: C 52 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 289 VAL cc_start: 0.8332 (t) cc_final: 0.8010 (p) REVERT: C 537 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8040 (ttpt) REVERT: C 614 ASP cc_start: 0.6613 (t0) cc_final: 0.6252 (t0) REVERT: C 675 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 730 SER cc_start: 0.8383 (m) cc_final: 0.8109 (p) REVERT: C 825 LYS cc_start: 0.7649 (tppp) cc_final: 0.7335 (tttt) REVERT: C 918 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.3340 (tp30) REVERT: C 988 GLU cc_start: 0.6874 (mp0) cc_final: 0.6448 (mp0) REVERT: H 103 ASP cc_start: 0.8138 (m-30) cc_final: 0.7820 (m-30) outliers start: 47 outliers final: 41 residues processed: 343 average time/residue: 0.1667 time to fit residues: 90.1650 Evaluate side-chains 349 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 282 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN B 125 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.208990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.173107 restraints weight = 42442.086| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 3.61 r_work: 0.4139 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 26262 Z= 0.200 Angle : 0.793 21.706 35867 Z= 0.385 Chirality : 0.051 0.459 4236 Planarity : 0.005 0.061 4514 Dihedral : 7.747 79.280 4697 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.98 % Allowed : 13.27 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.59 (0.15), residues: 3096 helix: 1.41 (0.20), residues: 666 sheet: -0.11 (0.20), residues: 651 loop : -1.24 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1091 TYR 0.026 0.002 TYR C 204 PHE 0.026 0.002 PHE B 888 TRP 0.014 0.002 TRP H 52 HIS 0.030 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00460 (26160) covalent geometry : angle 0.70734 (35600) SS BOND : bond 0.00705 ( 39) SS BOND : angle 2.24328 ( 78) hydrogen bonds : bond 0.06949 ( 891) hydrogen bonds : angle 5.79842 ( 2511) link_BETA1-4 : bond 0.00536 ( 15) link_BETA1-4 : angle 2.66716 ( 45) link_NAG-ASN : bond 0.00876 ( 48) link_NAG-ASN : angle 5.30658 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 325 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8451 (mttp) cc_final: 0.7947 (mmmt) REVERT: A 568 ASP cc_start: 0.7863 (t0) cc_final: 0.7662 (t0) REVERT: A 740 MET cc_start: 0.8268 (ttm) cc_final: 0.8058 (ttm) REVERT: A 750 SER cc_start: 0.7733 (t) cc_final: 0.7354 (p) REVERT: A 950 ASP cc_start: 0.7314 (p0) cc_final: 0.6965 (m-30) REVERT: B 47 VAL cc_start: 0.8562 (p) cc_final: 0.8310 (m) REVERT: B 238 PHE cc_start: 0.1852 (OUTLIER) cc_final: 0.1613 (p90) REVERT: B 265 TYR cc_start: 0.5937 (p90) cc_final: 0.5489 (p90) REVERT: B 287 ASP cc_start: 0.6722 (t0) cc_final: 0.6185 (t0) REVERT: B 423 TYR cc_start: 0.4963 (m-10) cc_final: 0.4689 (m-10) REVERT: B 450 ASN cc_start: 0.8130 (m-40) cc_final: 0.7722 (m110) REVERT: B 465 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 781 VAL cc_start: 0.5694 (t) cc_final: 0.5313 (t) REVERT: B 902 MET cc_start: 0.6353 (tpp) cc_final: 0.6118 (tpp) REVERT: B 964 LYS cc_start: 0.8652 (tppp) cc_final: 0.8274 (tppp) REVERT: B 994 ASP cc_start: 0.5789 (p0) cc_final: 0.5574 (p0) REVERT: B 1106 GLN cc_start: 0.8041 (pt0) cc_final: 0.7684 (mp10) REVERT: C 52 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 266 TYR cc_start: 0.6014 (OUTLIER) cc_final: 0.5683 (m-80) REVERT: C 289 VAL cc_start: 0.8407 (t) cc_final: 0.8072 (p) REVERT: C 465 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: C 537 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8086 (ttpt) REVERT: C 614 ASP cc_start: 0.6739 (t0) cc_final: 0.6397 (t0) REVERT: C 675 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 730 SER cc_start: 0.8398 (m) cc_final: 0.8161 (p) REVERT: C 825 LYS cc_start: 0.7836 (tppp) cc_final: 0.7567 (tptt) REVERT: C 918 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.3609 (mm-30) REVERT: C 968 SER cc_start: 0.8440 (t) cc_final: 0.7959 (p) REVERT: C 988 GLU cc_start: 0.6653 (mp0) cc_final: 0.6313 (mp0) REVERT: H 103 ASP cc_start: 0.8133 (m-30) cc_final: 0.7785 (m-30) outliers start: 55 outliers final: 44 residues processed: 360 average time/residue: 0.1746 time to fit residues: 99.8264 Evaluate side-chains 357 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 309 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 212 optimal weight: 0.2980 chunk 314 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 269 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 125 ASN B 655 HIS B 777 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** 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 = 0.4671 r_free = 0.4671 target = 0.210522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.174784 restraints weight = 42344.598| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 3.63 r_work: 0.4177 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26262 Z= 0.152 Angle : 0.751 21.291 35867 Z= 0.361 Chirality : 0.049 0.464 4236 Planarity : 0.005 0.057 4514 Dihedral : 7.491 80.461 4697 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.73 % Allowed : 13.73 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.47 (0.15), residues: 3096 helix: 1.54 (0.20), residues: 671 sheet: -0.21 (0.21), residues: 640 loop : -1.11 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.021 0.001 TYR B 396 PHE 0.030 0.002 PHE B 888 TRP 0.016 0.001 TRP H 36 HIS 0.025 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00339 (26160) covalent geometry : angle 0.66495 (35600) SS BOND : bond 0.00519 ( 39) SS BOND : angle 1.96263 ( 78) hydrogen bonds : bond 0.06154 ( 891) hydrogen bonds : angle 5.62855 ( 2511) link_BETA1-4 : bond 0.00516 ( 15) link_BETA1-4 : angle 2.64781 ( 45) link_NAG-ASN : bond 0.00861 ( 48) link_NAG-ASN : angle 5.19599 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8421 (mttp) cc_final: 0.7883 (mmmt) REVERT: A 568 ASP cc_start: 0.7839 (t0) cc_final: 0.7625 (t0) REVERT: A 750 SER cc_start: 0.7672 (t) cc_final: 0.7210 (p) REVERT: A 790 LYS cc_start: 0.7271 (mmmt) cc_final: 0.7004 (mmmt) REVERT: B 47 VAL cc_start: 0.8541 (p) cc_final: 0.8305 (m) REVERT: B 238 PHE cc_start: 0.1787 (OUTLIER) cc_final: 0.1549 (p90) REVERT: B 265 TYR cc_start: 0.5762 (p90) cc_final: 0.5296 (p90) REVERT: B 275 PHE cc_start: 0.2535 (OUTLIER) cc_final: 0.1653 (m-80) REVERT: B 287 ASP cc_start: 0.6661 (t0) cc_final: 0.6130 (t0) REVERT: B 423 TYR cc_start: 0.4722 (m-10) cc_final: 0.4468 (m-10) REVERT: B 450 ASN cc_start: 0.8056 (m-40) cc_final: 0.7644 (m110) REVERT: B 781 VAL cc_start: 0.5454 (t) cc_final: 0.5094 (t) REVERT: B 964 LYS cc_start: 0.8527 (tppp) cc_final: 0.8160 (tppp) REVERT: B 1106 GLN cc_start: 0.7959 (pt0) cc_final: 0.7625 (mp10) REVERT: C 52 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7606 (tm-30) REVERT: C 266 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: C 289 VAL cc_start: 0.8365 (t) cc_final: 0.8047 (p) REVERT: C 465 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: C 537 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7922 (ttpt) REVERT: C 614 ASP cc_start: 0.6648 (t0) cc_final: 0.6299 (t0) REVERT: C 675 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7386 (tm-30) REVERT: C 730 SER cc_start: 0.8362 (m) cc_final: 0.8110 (p) REVERT: C 825 LYS cc_start: 0.7695 (tppp) cc_final: 0.7433 (tptt) REVERT: C 918 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.4005 (mm-30) REVERT: C 988 GLU cc_start: 0.6889 (mp0) cc_final: 0.6462 (mp0) REVERT: H 103 ASP cc_start: 0.8202 (m-30) cc_final: 0.7913 (m-30) outliers start: 48 outliers final: 39 residues processed: 339 average time/residue: 0.1751 time to fit residues: 93.8634 Evaluate side-chains 348 residues out of total 2774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 211 optimal weight: 0.2980 chunk 236 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 291 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 824 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.208026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.172093 restraints weight = 41972.619| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 3.62 r_work: 0.4142 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 26262 Z= 0.196 Angle : 0.800 21.369 35867 Z= 0.387 Chirality : 0.051 0.444 4236 Planarity : 0.005 0.059 4514 Dihedral : 7.577 79.491 4697 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.77 % Allowed : 13.84 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.68 (0.15), residues: 3096 helix: 1.43 (0.20), residues: 663 sheet: -0.27 (0.21), residues: 616 loop : -1.28 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 355 TYR 0.026 0.002 TYR C 204 PHE 0.033 0.002 PHE B 888 TRP 0.015 0.001 TRP H 52 HIS 0.023 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00451 (26160) covalent geometry : angle 0.70860 (35600) SS BOND : bond 0.00597 ( 39) SS BOND : angle 2.27209 ( 78) hydrogen bonds : bond 0.06907 ( 891) hydrogen bonds : angle 5.78234 ( 2511) link_BETA1-4 : bond 0.00598 ( 15) link_BETA1-4 : angle 2.65782 ( 45) link_NAG-ASN : bond 0.00911 ( 48) link_NAG-ASN : angle 5.51749 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6542.12 seconds wall clock time: 112 minutes 39.67 seconds (6759.67 seconds total)