Starting phenix.real_space_refine on Fri Mar 6 02:04:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sy3_25515/03_2026/7sy3_25515.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sy3_25515/03_2026/7sy3_25515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sy3_25515/03_2026/7sy3_25515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sy3_25515/03_2026/7sy3_25515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sy3_25515/03_2026/7sy3_25515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sy3_25515/03_2026/7sy3_25515.map" } resolution = 2.95 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= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 17186 2.51 5 N 4412 2.21 5 O 5279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27001 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6555 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 45, 'TRANS': 795} Chain breaks: 8 Chain: "B" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 6580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 6580 Classifications: {'peptide': 844} Link IDs: {'PTRANS': 45, 'TRANS': 798} Chain breaks: 8 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} 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: "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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "U" 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: "V" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.36, per 1000 atoms: 0.24 Number of scatterers: 27001 At special positions: 0 Unit cell: (140, 158, 237, 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 124 16.00 O 5279 8.00 N 4412 7.00 C 17186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6242 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 46 sheets defined 34.0% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.911A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 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: 3.623A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.934A 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 945 through 965 removed outlier: 3.554A 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 removed outlier: 3.507A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.234A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.501A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.725A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.093A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.597A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.923A 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 945 through 965 removed outlier: 3.503A 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: 4.073A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.583A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 744 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: 3.579A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.542A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.875A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.111A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.079A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.571A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.797A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.080A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.979A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.705A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.700A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.779A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.523A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.577A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.666A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.259A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.593A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.390A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.777A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.555A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.894A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.274A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.244A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.156A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.869A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.489A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.170A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.204A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.606A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.579A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.579A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.024A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.235A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.532A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.204A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.532A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.730A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.238A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.103A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.070A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.829A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.639A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.639A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.295A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.374A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.114A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.689A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 154 through 163 removed outlier: 5.444A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.295A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.600A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.600A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.379A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'E' and resid 131 through 132 removed outlier: 3.553A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.001A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.325A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1307 hydrogen bonds defined for protein. 3678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8513 1.34 - 1.47: 6883 1.47 - 1.59: 12046 1.59 - 1.72: 0 1.72 - 1.84: 172 Bond restraints: 27614 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.75e+00 ... (remaining 27609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 36177 1.98 - 3.96: 1232 3.96 - 5.94: 119 5.94 - 7.92: 29 7.92 - 9.90: 14 Bond angle restraints: 37571 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.23 -5.53 1.22e+00 6.72e-01 2.05e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.82 129.24 -6.42 1.42e+00 4.96e-01 2.05e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.21 -5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.09 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" CA GLY B 89 " pdb=" C GLY B 89 " pdb=" N VAL B 90 " ideal model delta sigma weight residual 114.58 118.21 -3.63 8.60e-01 1.35e+00 1.78e+01 ... (remaining 37566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15891 17.93 - 35.86: 1097 35.86 - 53.78: 183 53.78 - 71.71: 57 71.71 - 89.64: 36 Dihedral angle restraints: 17264 sinusoidal: 7591 harmonic: 9673 Sorted by residual: dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -46.53 -39.47 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual 79.00 14.26 64.74 1 2.00e+01 2.50e-03 1.38e+01 dihedral pdb=" CA ALA E 396 " pdb=" C ALA E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3536 0.069 - 0.139: 778 0.139 - 0.208: 95 0.208 - 0.277: 6 0.277 - 0.346: 2 Chirality restraints: 4417 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 4414 not shown) Planarity restraints: 4822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 169 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ARG E 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG E 169 " 0.019 2.00e-02 2.50e+03 pdb=" N SER E 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 902 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C MET A 902 " 0.050 2.00e-02 2.50e+03 pdb=" O MET A 902 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 903 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 589 " -0.042 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO E 590 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 590 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 590 " -0.035 5.00e-02 4.00e+02 ... (remaining 4819 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6915 2.80 - 3.33: 23123 3.33 - 3.85: 46036 3.85 - 4.38: 52709 4.38 - 4.90: 91079 Nonbonded interactions: 219862 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.305 3.040 ... (remaining 219857 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' selection = (chain 'C' and (resid 14 through 330 or resid 530 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.240 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.005 0.072 27712 Z= 0.238 Angle : 0.856 15.256 37829 Z= 0.452 Chirality : 0.056 0.346 4417 Planarity : 0.006 0.063 4778 Dihedral : 13.038 89.642 10914 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 3267 helix: 0.78 (0.15), residues: 980 sheet: 0.55 (0.19), residues: 632 loop : -0.76 (0.13), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 460 TYR 0.026 0.002 TYR E 385 PHE 0.034 0.002 PHE C 238 TRP 0.021 0.002 TRP E 69 HIS 0.008 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00482 (27614) covalent geometry : angle 0.81940 (37571) SS BOND : bond 0.00279 ( 36) SS BOND : angle 1.59703 ( 72) hydrogen bonds : bond 0.11644 ( 1243) hydrogen bonds : angle 6.97336 ( 3678) link_BETA1-4 : bond 0.00534 ( 18) link_BETA1-4 : angle 1.75483 ( 54) link_NAG-ASN : bond 0.00636 ( 44) link_NAG-ASN : angle 4.00268 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6720 (ptp) cc_final: 0.6386 (pmm) REVERT: A 189 LEU cc_start: 0.9269 (tp) cc_final: 0.9067 (tp) REVERT: A 245 HIS cc_start: 0.7454 (m-70) cc_final: 0.6220 (t-90) REVERT: B 950 ASP cc_start: 0.8394 (t0) cc_final: 0.8050 (t0) REVERT: B 1002 GLN cc_start: 0.8508 (tt0) cc_final: 0.8079 (tm-30) REVERT: C 79 PHE cc_start: 0.6123 (t80) cc_final: 0.5437 (t80) REVERT: C 85 PRO cc_start: 0.8630 (Cg_exo) cc_final: 0.8399 (Cg_endo) REVERT: C 565 PHE cc_start: 0.8301 (p90) cc_final: 0.8100 (p90) REVERT: C 582 LEU cc_start: 0.9192 (mp) cc_final: 0.8990 (tt) REVERT: E 123 MET cc_start: 0.2932 (mtt) cc_final: 0.2210 (tmm) REVERT: E 202 TYR cc_start: 0.8407 (t80) cc_final: 0.8153 (t80) REVERT: E 367 ASP cc_start: 0.8749 (m-30) cc_final: 0.8533 (p0) outliers start: 0 outliers final: 2 residues processed: 269 average time/residue: 0.7149 time to fit residues: 221.5454 Evaluate side-chains 124 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 121 ASN A1011 GLN B 115 GLN B 354 ASN ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN C 218 GLN C 331 ASN C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.089518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.053639 restraints weight = 106720.398| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.00 r_work: 0.2983 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27712 Z= 0.223 Angle : 0.655 11.422 37829 Z= 0.327 Chirality : 0.045 0.252 4417 Planarity : 0.005 0.062 4778 Dihedral : 5.752 54.156 4845 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.30 % Allowed : 7.75 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.56 (0.14), residues: 3267 helix: 1.77 (0.16), residues: 989 sheet: 0.55 (0.20), residues: 642 loop : -0.55 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 995 TYR 0.019 0.002 TYR B1067 PHE 0.018 0.002 PHE A 32 TRP 0.018 0.002 TRP E 165 HIS 0.007 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00493 (27614) covalent geometry : angle 0.63025 (37571) SS BOND : bond 0.00565 ( 36) SS BOND : angle 1.13190 ( 72) hydrogen bonds : bond 0.04442 ( 1243) hydrogen bonds : angle 5.52987 ( 3678) link_BETA1-4 : bond 0.00157 ( 18) link_BETA1-4 : angle 1.17778 ( 54) link_NAG-ASN : bond 0.00640 ( 44) link_NAG-ASN : angle 2.94979 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6689 (ptp) cc_final: 0.6302 (pmm) REVERT: A 189 LEU cc_start: 0.9370 (tp) cc_final: 0.9138 (tp) REVERT: A 245 HIS cc_start: 0.7669 (m-70) cc_final: 0.6718 (m-70) REVERT: A 762 GLN cc_start: 0.9461 (mt0) cc_final: 0.8983 (mt0) REVERT: A 779 GLN cc_start: 0.9300 (tp-100) cc_final: 0.8821 (tm-30) REVERT: B 200 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8425 (t80) REVERT: B 552 LEU cc_start: 0.9561 (mt) cc_final: 0.9356 (mm) REVERT: B 780 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8453 (mm-30) REVERT: B 950 ASP cc_start: 0.9221 (t0) cc_final: 0.8904 (t0) REVERT: B 1010 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8758 (tp-100) REVERT: C 565 PHE cc_start: 0.8512 (p90) cc_final: 0.8157 (p90) REVERT: C 582 LEU cc_start: 0.9359 (mp) cc_final: 0.9103 (tt) REVERT: C 1145 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8091 (pt) REVERT: E 123 MET cc_start: 0.2890 (mtt) cc_final: 0.2184 (tmm) REVERT: E 455 MET cc_start: 0.4512 (pp-130) cc_final: 0.3582 (pp-130) REVERT: E 579 MET cc_start: 0.4245 (mtp) cc_final: 0.3722 (mtm) outliers start: 38 outliers final: 10 residues processed: 147 average time/residue: 0.6514 time to fit residues: 112.8928 Evaluate side-chains 112 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 299 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 259 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 314 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 214 optimal weight: 0.0370 chunk 94 optimal weight: 9.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN E 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.090553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.055325 restraints weight = 106999.566| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.06 r_work: 0.3018 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27712 Z= 0.107 Angle : 0.552 10.755 37829 Z= 0.276 Chirality : 0.043 0.276 4417 Planarity : 0.004 0.063 4778 Dihedral : 5.202 54.350 4841 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.41 % Allowed : 8.43 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.86 (0.14), residues: 3267 helix: 2.17 (0.16), residues: 989 sheet: 0.56 (0.20), residues: 624 loop : -0.40 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.020 0.001 TYR B1067 PHE 0.015 0.001 PHE A 220 TRP 0.013 0.001 TRP E 165 HIS 0.006 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00226 (27614) covalent geometry : angle 0.52849 (37571) SS BOND : bond 0.00251 ( 36) SS BOND : angle 0.88834 ( 72) hydrogen bonds : bond 0.03894 ( 1243) hydrogen bonds : angle 5.22186 ( 3678) link_BETA1-4 : bond 0.00331 ( 18) link_BETA1-4 : angle 0.95982 ( 54) link_NAG-ASN : bond 0.00534 ( 44) link_NAG-ASN : angle 2.65445 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: A 153 MET cc_start: 0.6735 (ptp) cc_final: 0.6328 (pmm) REVERT: A 245 HIS cc_start: 0.7641 (m-70) cc_final: 0.6627 (m-70) REVERT: A 762 GLN cc_start: 0.9390 (mt0) cc_final: 0.8971 (mt0) REVERT: A 779 GLN cc_start: 0.9309 (tp-100) cc_final: 0.8787 (tm-30) REVERT: B 200 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 498 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7821 (mp-120) REVERT: B 780 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8496 (mm-30) REVERT: B 950 ASP cc_start: 0.9162 (t0) cc_final: 0.8836 (t0) REVERT: C 88 ASP cc_start: 0.7680 (p0) cc_final: 0.7457 (p0) REVERT: C 565 PHE cc_start: 0.8542 (p90) cc_final: 0.8172 (p90) REVERT: C 582 LEU cc_start: 0.9322 (mp) cc_final: 0.9046 (tt) REVERT: C 779 GLN cc_start: 0.9284 (tp40) cc_final: 0.9081 (tp40) REVERT: C 990 GLU cc_start: 0.9148 (pp20) cc_final: 0.8931 (pp20) REVERT: C 1029 MET cc_start: 0.9459 (tpp) cc_final: 0.9205 (tpp) REVERT: C 1145 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8232 (pt) REVERT: E 123 MET cc_start: 0.2788 (mtt) cc_final: 0.2219 (tmm) REVERT: E 190 MET cc_start: 0.3778 (pp-130) cc_final: 0.3428 (ptm) REVERT: E 366 MET cc_start: 0.3979 (tpt) cc_final: 0.2810 (mmm) outliers start: 41 outliers final: 9 residues processed: 132 average time/residue: 0.6043 time to fit residues: 94.9425 Evaluate side-chains 109 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 299 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 11 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 299 optimal weight: 0.4980 chunk 180 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN E 96 GLN E 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.088718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053324 restraints weight = 106255.022| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.09 r_work: 0.2962 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27712 Z= 0.183 Angle : 0.581 10.836 37829 Z= 0.287 Chirality : 0.044 0.274 4417 Planarity : 0.004 0.061 4778 Dihedral : 5.012 54.599 4841 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.41 % Allowed : 9.18 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.95 (0.14), residues: 3267 helix: 2.31 (0.16), residues: 995 sheet: 0.43 (0.20), residues: 637 loop : -0.31 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.019 0.001 TYR C 170 PHE 0.017 0.001 PHE B 106 TRP 0.021 0.001 TRP C 258 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00402 (27614) covalent geometry : angle 0.56114 (37571) SS BOND : bond 0.00184 ( 36) SS BOND : angle 0.75785 ( 72) hydrogen bonds : bond 0.04003 ( 1243) hydrogen bonds : angle 5.11350 ( 3678) link_BETA1-4 : bond 0.00171 ( 18) link_BETA1-4 : angle 1.15775 ( 54) link_NAG-ASN : bond 0.00594 ( 44) link_NAG-ASN : angle 2.51478 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: A 153 MET cc_start: 0.6972 (ptp) cc_final: 0.6553 (pmm) REVERT: A 245 HIS cc_start: 0.7700 (m-70) cc_final: 0.6763 (m-70) REVERT: A 762 GLN cc_start: 0.9447 (mt0) cc_final: 0.8984 (mt0) REVERT: A 779 GLN cc_start: 0.9326 (tp-100) cc_final: 0.8843 (tm-30) REVERT: B 200 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8507 (t80) REVERT: B 458 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7619 (mptt) REVERT: B 780 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 950 ASP cc_start: 0.9205 (t0) cc_final: 0.8885 (t0) REVERT: B 1010 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8492 (tp-100) REVERT: C 565 PHE cc_start: 0.8603 (p90) cc_final: 0.8237 (p90) REVERT: C 582 LEU cc_start: 0.9345 (mp) cc_final: 0.9082 (tt) REVERT: C 740 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8848 (tpp) REVERT: C 779 GLN cc_start: 0.9315 (tp40) cc_final: 0.9060 (tp40) REVERT: C 1145 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8387 (pt) REVERT: E 123 MET cc_start: 0.2831 (mtt) cc_final: 0.2206 (tmm) REVERT: E 190 MET cc_start: 0.3650 (pp-130) cc_final: 0.3313 (ptm) REVERT: E 366 MET cc_start: 0.3905 (tpt) cc_final: 0.2696 (mmm) outliers start: 41 outliers final: 14 residues processed: 138 average time/residue: 0.5881 time to fit residues: 97.1974 Evaluate side-chains 114 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 299 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 216 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN B 388 ASN B 824 ASN E 524 GLN ** E 535 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 = 0.4005 r_free = 0.4005 target = 0.087669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052439 restraints weight = 104966.980| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.97 r_work: 0.2944 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27712 Z= 0.201 Angle : 0.586 10.329 37829 Z= 0.292 Chirality : 0.044 0.280 4417 Planarity : 0.004 0.059 4778 Dihedral : 4.977 54.192 4841 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.64 % Allowed : 9.70 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.91 (0.14), residues: 3267 helix: 2.32 (0.16), residues: 1002 sheet: 0.19 (0.20), residues: 621 loop : -0.28 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.019 0.001 TYR B1067 PHE 0.026 0.001 PHE A 135 TRP 0.011 0.001 TRP E 328 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00445 (27614) covalent geometry : angle 0.56790 (37571) SS BOND : bond 0.00145 ( 36) SS BOND : angle 0.64553 ( 72) hydrogen bonds : bond 0.04007 ( 1243) hydrogen bonds : angle 5.10301 ( 3678) link_BETA1-4 : bond 0.00156 ( 18) link_BETA1-4 : angle 1.10765 ( 54) link_NAG-ASN : bond 0.00551 ( 44) link_NAG-ASN : angle 2.45086 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: A 153 MET cc_start: 0.7048 (ptp) cc_final: 0.6626 (pmm) REVERT: A 189 LEU cc_start: 0.9278 (tp) cc_final: 0.9062 (tp) REVERT: A 245 HIS cc_start: 0.7662 (m-70) cc_final: 0.6711 (m-70) REVERT: A 740 MET cc_start: 0.9223 (tpt) cc_final: 0.8724 (tmm) REVERT: A 762 GLN cc_start: 0.9439 (mt0) cc_final: 0.8958 (mt0) REVERT: A 786 LYS cc_start: 0.9068 (pmtt) cc_final: 0.8806 (pmmt) REVERT: B 200 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8544 (t80) REVERT: B 458 LYS cc_start: 0.8577 (mmtt) cc_final: 0.7696 (mppt) REVERT: B 780 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 950 ASP cc_start: 0.9207 (t0) cc_final: 0.8872 (t0) REVERT: B 1010 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8635 (tm-30) REVERT: C 153 MET cc_start: 0.3520 (pmm) cc_final: 0.3318 (pmm) REVERT: C 565 PHE cc_start: 0.8668 (p90) cc_final: 0.8459 (p90) REVERT: C 740 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8764 (tpp) REVERT: C 779 GLN cc_start: 0.9329 (tp40) cc_final: 0.9076 (tp40) REVERT: C 1145 LEU cc_start: 0.8749 (tm) cc_final: 0.8387 (pp) REVERT: E 190 MET cc_start: 0.3810 (pp-130) cc_final: 0.3575 (ptm) REVERT: E 365 THR cc_start: 0.7076 (OUTLIER) cc_final: 0.6756 (t) REVERT: E 366 MET cc_start: 0.3809 (tpt) cc_final: 0.2498 (mmm) REVERT: E 474 MET cc_start: 0.1942 (tpp) cc_final: 0.1019 (tpp) outliers start: 48 outliers final: 20 residues processed: 137 average time/residue: 0.5451 time to fit residues: 90.3009 Evaluate side-chains 112 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 568 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 277 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 323 optimal weight: 50.0000 chunk 114 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 360 ASN C 824 ASN C 907 ASN ** E 535 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 = 0.3954 r_free = 0.3954 target = 0.085059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.049278 restraints weight = 106800.490| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.00 r_work: 0.2869 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 27712 Z= 0.388 Angle : 0.756 19.254 37829 Z= 0.375 Chirality : 0.047 0.252 4417 Planarity : 0.004 0.058 4778 Dihedral : 5.626 55.526 4841 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.95 % Allowed : 9.87 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.51 (0.14), residues: 3267 helix: 1.96 (0.16), residues: 1008 sheet: -0.18 (0.20), residues: 611 loop : -0.43 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 214 TYR 0.021 0.002 TYR C1067 PHE 0.024 0.002 PHE C 106 TRP 0.012 0.002 TRP E 461 HIS 0.008 0.002 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00864 (27614) covalent geometry : angle 0.73908 (37571) SS BOND : bond 0.00200 ( 36) SS BOND : angle 0.72739 ( 72) hydrogen bonds : bond 0.04786 ( 1243) hydrogen bonds : angle 5.44198 ( 3678) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 1.52998 ( 54) link_NAG-ASN : bond 0.00777 ( 44) link_NAG-ASN : angle 2.61799 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 87 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6905 (ptp) cc_final: 0.6522 (pmm) REVERT: A 189 LEU cc_start: 0.9297 (tp) cc_final: 0.9072 (tp) REVERT: A 245 HIS cc_start: 0.7653 (m-70) cc_final: 0.6760 (m-70) REVERT: A 740 MET cc_start: 0.9305 (tpt) cc_final: 0.8776 (tmm) REVERT: A 762 GLN cc_start: 0.9470 (mt0) cc_final: 0.8916 (mt0) REVERT: A 786 LYS cc_start: 0.9156 (pmtt) cc_final: 0.8926 (pmmt) REVERT: A 1029 MET cc_start: 0.9551 (OUTLIER) cc_final: 0.9259 (tpp) REVERT: B 780 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8649 (mm-30) REVERT: B 950 ASP cc_start: 0.9343 (t0) cc_final: 0.8964 (t0) REVERT: B 1010 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8758 (tm-30) REVERT: C 1145 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8436 (pp) REVERT: E 62 MET cc_start: 0.8208 (ptt) cc_final: 0.8006 (mtm) REVERT: E 190 MET cc_start: 0.4135 (pp-130) cc_final: 0.3865 (ptm) REVERT: E 366 MET cc_start: 0.3941 (tpt) cc_final: 0.2791 (mmm) outliers start: 57 outliers final: 22 residues processed: 128 average time/residue: 0.5397 time to fit residues: 83.5116 Evaluate side-chains 108 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 568 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 159 optimal weight: 0.6980 chunk 255 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 307 optimal weight: 20.0000 chunk 262 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 907 ASN E 417 HIS ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.086984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052546 restraints weight = 104298.424| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.80 r_work: 0.2944 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27712 Z= 0.121 Angle : 0.572 12.250 37829 Z= 0.283 Chirality : 0.043 0.296 4417 Planarity : 0.004 0.056 4778 Dihedral : 5.145 53.803 4841 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.27 % Allowed : 10.59 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.87 (0.15), residues: 3267 helix: 2.38 (0.16), residues: 990 sheet: -0.04 (0.20), residues: 652 loop : -0.25 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.019 0.001 TYR C1067 PHE 0.017 0.001 PHE C 238 TRP 0.010 0.001 TRP E 165 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00260 (27614) covalent geometry : angle 0.55436 (37571) SS BOND : bond 0.00118 ( 36) SS BOND : angle 0.48145 ( 72) hydrogen bonds : bond 0.03901 ( 1243) hydrogen bonds : angle 5.11932 ( 3678) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 1.06508 ( 54) link_NAG-ASN : bond 0.00506 ( 44) link_NAG-ASN : angle 2.38514 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6921 (ptp) cc_final: 0.6553 (pmm) REVERT: A 189 LEU cc_start: 0.9317 (tp) cc_final: 0.9086 (tp) REVERT: A 245 HIS cc_start: 0.7633 (m-70) cc_final: 0.6730 (m-70) REVERT: A 740 MET cc_start: 0.9230 (tpt) cc_final: 0.8721 (tmm) REVERT: A 762 GLN cc_start: 0.9432 (mt0) cc_final: 0.8880 (mt0) REVERT: A 786 LYS cc_start: 0.9121 (pmtt) cc_final: 0.8917 (pmmt) REVERT: B 458 LYS cc_start: 0.8515 (mmpt) cc_final: 0.7481 (mppt) REVERT: B 780 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8683 (mm-30) REVERT: B 950 ASP cc_start: 0.9190 (t0) cc_final: 0.8792 (t0) REVERT: B 1010 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8600 (tm-30) REVERT: C 779 GLN cc_start: 0.9315 (tp40) cc_final: 0.8895 (tm-30) REVERT: C 869 MET cc_start: 0.9137 (mtm) cc_final: 0.8873 (ptp) REVERT: C 1145 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8462 (pp) REVERT: E 152 MET cc_start: 0.3384 (OUTLIER) cc_final: 0.2536 (tpp) REVERT: E 190 MET cc_start: 0.3943 (OUTLIER) cc_final: 0.3703 (ptm) REVERT: E 231 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7049 (pt0) REVERT: E 365 THR cc_start: 0.7069 (OUTLIER) cc_final: 0.6722 (t) REVERT: E 366 MET cc_start: 0.3928 (tpt) cc_final: 0.2581 (mmm) REVERT: E 557 MET cc_start: 0.7658 (tmt) cc_final: 0.6867 (ptm) outliers start: 37 outliers final: 14 residues processed: 115 average time/residue: 0.5366 time to fit residues: 73.9378 Evaluate side-chains 108 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 365 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 233 optimal weight: 2.9990 chunk 326 optimal weight: 0.0370 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 0.4980 chunk 313 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.087020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.052194 restraints weight = 105881.161| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.94 r_work: 0.2947 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27712 Z= 0.131 Angle : 0.561 11.646 37829 Z= 0.276 Chirality : 0.043 0.290 4417 Planarity : 0.004 0.055 4778 Dihedral : 4.858 54.435 4841 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.20 % Allowed : 10.97 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.94 (0.15), residues: 3267 helix: 2.40 (0.16), residues: 996 sheet: -0.07 (0.20), residues: 625 loop : -0.17 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 245 TYR 0.019 0.001 TYR C1067 PHE 0.016 0.001 PHE C 238 TRP 0.011 0.001 TRP E 165 HIS 0.008 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00289 (27614) covalent geometry : angle 0.54346 (37571) SS BOND : bond 0.00109 ( 36) SS BOND : angle 0.47033 ( 72) hydrogen bonds : bond 0.03723 ( 1243) hydrogen bonds : angle 4.97943 ( 3678) link_BETA1-4 : bond 0.00223 ( 18) link_BETA1-4 : angle 1.08856 ( 54) link_NAG-ASN : bond 0.00497 ( 44) link_NAG-ASN : angle 2.32515 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6890 (ptp) cc_final: 0.6527 (pmm) REVERT: A 189 LEU cc_start: 0.9322 (tp) cc_final: 0.9095 (tp) REVERT: A 245 HIS cc_start: 0.7642 (m-70) cc_final: 0.6738 (m-70) REVERT: A 598 ILE cc_start: 0.9387 (mp) cc_final: 0.9127 (pp) REVERT: A 740 MET cc_start: 0.9218 (tpt) cc_final: 0.8737 (tmm) REVERT: A 762 GLN cc_start: 0.9422 (mt0) cc_final: 0.8937 (mt0) REVERT: B 200 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8538 (t80) REVERT: B 212 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5390 (tt) REVERT: B 458 LYS cc_start: 0.8506 (mmpt) cc_final: 0.7522 (mptt) REVERT: B 498 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7993 (mm110) REVERT: B 780 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8705 (mm-30) REVERT: B 950 ASP cc_start: 0.9191 (t0) cc_final: 0.8876 (t0) REVERT: B 1010 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8610 (tm-30) REVERT: C 779 GLN cc_start: 0.9321 (tp40) cc_final: 0.8906 (tm-30) REVERT: C 1145 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8409 (pp) REVERT: E 62 MET cc_start: 0.8058 (ptt) cc_final: 0.7832 (mtm) REVERT: E 152 MET cc_start: 0.3431 (OUTLIER) cc_final: 0.2546 (tpp) REVERT: E 231 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7113 (pt0) REVERT: E 323 MET cc_start: 0.5692 (tpp) cc_final: 0.5070 (tmm) REVERT: E 365 THR cc_start: 0.7090 (OUTLIER) cc_final: 0.6707 (t) REVERT: E 366 MET cc_start: 0.4037 (tpt) cc_final: 0.2644 (mmm) REVERT: E 557 MET cc_start: 0.7625 (tmt) cc_final: 0.6936 (ptm) outliers start: 35 outliers final: 15 residues processed: 119 average time/residue: 0.5848 time to fit residues: 83.8424 Evaluate side-chains 108 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 96 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.087098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.052596 restraints weight = 105283.249| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.93 r_work: 0.2954 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27712 Z= 0.119 Angle : 0.558 11.267 37829 Z= 0.275 Chirality : 0.043 0.295 4417 Planarity : 0.004 0.054 4778 Dihedral : 4.720 54.755 4841 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.99 % Allowed : 11.24 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.99 (0.15), residues: 3267 helix: 2.43 (0.16), residues: 1000 sheet: -0.03 (0.20), residues: 631 loop : -0.14 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 567 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE B 106 TRP 0.010 0.001 TRP E 165 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00262 (27614) covalent geometry : angle 0.54108 (37571) SS BOND : bond 0.00104 ( 36) SS BOND : angle 0.45619 ( 72) hydrogen bonds : bond 0.03621 ( 1243) hydrogen bonds : angle 4.91263 ( 3678) link_BETA1-4 : bond 0.00265 ( 18) link_BETA1-4 : angle 1.03673 ( 54) link_NAG-ASN : bond 0.00469 ( 44) link_NAG-ASN : angle 2.28211 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6967 (ptp) cc_final: 0.6623 (pmm) REVERT: A 189 LEU cc_start: 0.9316 (tp) cc_final: 0.9086 (tp) REVERT: A 245 HIS cc_start: 0.7807 (m-70) cc_final: 0.6828 (m-70) REVERT: A 598 ILE cc_start: 0.9370 (mp) cc_final: 0.9143 (pp) REVERT: A 740 MET cc_start: 0.9216 (tpt) cc_final: 0.8625 (tmm) REVERT: A 762 GLN cc_start: 0.9409 (mt0) cc_final: 0.8939 (mt0) REVERT: B 212 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5490 (tt) REVERT: B 458 LYS cc_start: 0.8510 (mmpt) cc_final: 0.7439 (mptt) REVERT: B 498 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8004 (mm110) REVERT: B 780 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8716 (mm-30) REVERT: B 1010 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8576 (tm-30) REVERT: C 779 GLN cc_start: 0.9318 (tp40) cc_final: 0.8920 (tm-30) REVERT: C 869 MET cc_start: 0.9092 (mtm) cc_final: 0.8846 (ptp) REVERT: C 983 ARG cc_start: 0.9073 (mtm110) cc_final: 0.8867 (mtm110) REVERT: C 1145 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8419 (pp) REVERT: E 62 MET cc_start: 0.8139 (ptt) cc_final: 0.7922 (mtm) REVERT: E 152 MET cc_start: 0.3393 (OUTLIER) cc_final: 0.2440 (tpp) REVERT: E 231 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7126 (pt0) REVERT: E 323 MET cc_start: 0.5661 (tpp) cc_final: 0.5143 (tmm) REVERT: E 365 THR cc_start: 0.7104 (OUTLIER) cc_final: 0.6721 (t) REVERT: E 366 MET cc_start: 0.4062 (tpt) cc_final: 0.2684 (mmm) REVERT: E 472 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6981 (pp30) REVERT: E 557 MET cc_start: 0.7584 (tmt) cc_final: 0.6908 (ptm) outliers start: 29 outliers final: 16 residues processed: 117 average time/residue: 0.6017 time to fit residues: 84.5415 Evaluate side-chains 111 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 35 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 295 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.085985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051572 restraints weight = 105419.919| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.82 r_work: 0.2923 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27712 Z= 0.202 Angle : 0.610 14.106 37829 Z= 0.300 Chirality : 0.044 0.282 4417 Planarity : 0.004 0.054 4778 Dihedral : 4.829 54.167 4841 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.96 % Allowed : 11.41 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: 0.89 (0.15), residues: 3267 helix: 2.35 (0.16), residues: 999 sheet: -0.14 (0.20), residues: 634 loop : -0.17 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.039 0.001 TYR C 904 PHE 0.018 0.001 PHE C 238 TRP 0.043 0.001 TRP A 258 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00447 (27614) covalent geometry : angle 0.59433 (37571) SS BOND : bond 0.00127 ( 36) SS BOND : angle 0.49065 ( 72) hydrogen bonds : bond 0.03882 ( 1243) hydrogen bonds : angle 5.03183 ( 3678) link_BETA1-4 : bond 0.00178 ( 18) link_BETA1-4 : angle 1.18462 ( 54) link_NAG-ASN : bond 0.00537 ( 44) link_NAG-ASN : angle 2.33165 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6942 (ptp) cc_final: 0.6581 (pmm) REVERT: A 189 LEU cc_start: 0.9332 (tp) cc_final: 0.9101 (tp) REVERT: A 245 HIS cc_start: 0.7776 (m-70) cc_final: 0.6866 (m-70) REVERT: A 598 ILE cc_start: 0.9412 (mp) cc_final: 0.9118 (pp) REVERT: A 740 MET cc_start: 0.9239 (tpt) cc_final: 0.8648 (tmm) REVERT: A 762 GLN cc_start: 0.9429 (mt0) cc_final: 0.8950 (mt0) REVERT: B 212 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5611 (tt) REVERT: B 458 LYS cc_start: 0.8480 (mmpt) cc_final: 0.7387 (mppt) REVERT: B 780 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8743 (mm-30) REVERT: B 1010 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8642 (tm-30) REVERT: C 779 GLN cc_start: 0.9340 (tp40) cc_final: 0.8946 (tm-30) REVERT: C 983 ARG cc_start: 0.9030 (mtm110) cc_final: 0.8825 (mtm110) REVERT: C 1145 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8426 (pp) REVERT: E 152 MET cc_start: 0.2886 (OUTLIER) cc_final: 0.1916 (tpp) REVERT: E 231 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7148 (pt0) REVERT: E 323 MET cc_start: 0.5544 (tpp) cc_final: 0.5103 (tmm) REVERT: E 365 THR cc_start: 0.7010 (OUTLIER) cc_final: 0.6624 (t) REVERT: E 366 MET cc_start: 0.3995 (tpt) cc_final: 0.2602 (mmm) REVERT: E 557 MET cc_start: 0.7613 (tmt) cc_final: 0.6839 (ptm) outliers start: 28 outliers final: 19 residues processed: 112 average time/residue: 0.5960 time to fit residues: 80.2376 Evaluate side-chains 106 residues out of total 2918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 408 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 276 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 157 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 16 optimal weight: 0.0010 chunk 198 optimal weight: 7.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.086978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.052566 restraints weight = 105495.285| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.79 r_work: 0.2956 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 27712 Z= 0.114 Angle : 0.575 13.614 37829 Z= 0.283 Chirality : 0.044 0.302 4417 Planarity : 0.004 0.054 4778 Dihedral : 4.648 54.968 4841 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.89 % Allowed : 11.55 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.15), residues: 3267 helix: 2.47 (0.16), residues: 991 sheet: -0.06 (0.20), residues: 630 loop : -0.09 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 567 TYR 0.025 0.001 TYR C 904 PHE 0.017 0.001 PHE A 140 TRP 0.023 0.001 TRP A 258 HIS 0.007 0.001 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00249 (27614) covalent geometry : angle 0.55956 (37571) SS BOND : bond 0.00117 ( 36) SS BOND : angle 0.42900 ( 72) hydrogen bonds : bond 0.03569 ( 1243) hydrogen bonds : angle 4.92668 ( 3678) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 1.00941 ( 54) link_NAG-ASN : bond 0.00453 ( 44) link_NAG-ASN : angle 2.24519 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10950.70 seconds wall clock time: 186 minutes 49.37 seconds (11209.37 seconds total)