Starting phenix.real_space_refine on Fri Mar 6 04:57:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjh_23873/03_2026/7mjh_23873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjh_23873/03_2026/7mjh_23873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjh_23873/03_2026/7mjh_23873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjh_23873/03_2026/7mjh_23873.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjh_23873/03_2026/7mjh_23873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjh_23873/03_2026/7mjh_23873.cif" } resolution = 2.66 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= 0.030 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 129 5.16 5 C 17865 2.51 5 N 4629 2.21 5 O 5520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 28143 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "F" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} 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: "W" 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: "X" 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: 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: "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: 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 Time building chain proxies: 6.46, per 1000 atoms: 0.23 Number of scatterers: 28143 At special positions: 0 Unit cell: (143, 143, 215, 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 129 16.00 O 5520 8.00 N 4629 7.00 C 17865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 D 43 " - pdb=" SG CYS D 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 116 " 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 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 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 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " 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 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG G 1 " - " ASN A 17 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 17 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 17 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1074 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6516 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 60 sheets defined 23.5% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.658A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.834A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.117A 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: 3.647A 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: 3.925A 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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.009A 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: 3.762A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.822A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.551A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.048A 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: 3.631A 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 removed outlier: 3.545A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.883A 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: 3.571A 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 1032 removed outlier: 4.120A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (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 337 through 343 removed outlier: 4.000A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.731A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.819A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.571A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.945A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) 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: 3.662A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.992A 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 removed outlier: 3.587A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.542A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.252A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.661A pdb=" N LEU D 87 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.650A pdb=" N LEU E 87 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL E 88 " --> pdb=" O LYS E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.649A pdb=" N LEU F 87 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL F 88 " --> pdb=" O LYS F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 88' Processing helix chain 'F' and resid 107 through 111 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: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.019A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.514A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 163 removed outlier: 9.440A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.661A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.079A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.964A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.964A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.048A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.745A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.583A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.583A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.686A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.326A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.164A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.738A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.396A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.261A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 13.157A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.399A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.987A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.523A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.664A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.693A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.849A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.849A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.628A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.539A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.539A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.328A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.128A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.155A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.907A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.400A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.390A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.219A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.237A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.738A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.738A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.180A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.567A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.357A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'D' and resid 24 through 28 removed outlier: 3.608A pdb=" N VAL D 26 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.296A pdb=" N GLY D 31 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET D 55 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG D 71 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP D 57 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.296A pdb=" N GLY D 31 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 134 " --> pdb=" O ARG D 118 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 24 through 28 removed outlier: 3.637A pdb=" N VAL E 26 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.238A pdb=" N GLY E 31 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET E 55 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG E 71 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP E 57 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.238A pdb=" N GLY E 31 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL E 134 " --> pdb=" O ARG E 118 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 24 through 28 removed outlier: 3.684A pdb=" N VAL F 26 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.266A pdb=" N GLY F 31 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET F 55 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG F 71 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP F 57 " --> pdb=" O ILE F 69 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.266A pdb=" N GLY F 31 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL F 134 " --> pdb=" O ARG F 118 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.76 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8406 1.34 - 1.46: 6644 1.46 - 1.58: 13552 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 28770 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 28765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 37965 2.03 - 4.06: 1081 4.06 - 6.09: 63 6.09 - 8.11: 25 8.11 - 10.14: 13 Bond angle restraints: 39147 Sorted by residual: angle pdb=" C LYS D 96 " pdb=" N ASN D 97 " pdb=" CA ASN D 97 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C LYS E 96 " pdb=" N ASN E 97 " pdb=" CA ASN E 97 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C LYS F 96 " pdb=" N ASN F 97 " pdb=" CA ASN F 97 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.45 -5.75 1.22e+00 6.72e-01 2.22e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.10 -5.40 1.22e+00 6.72e-01 1.96e+01 ... (remaining 39142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16521 17.99 - 35.98: 1076 35.98 - 53.97: 217 53.97 - 71.96: 77 71.96 - 89.95: 31 Dihedral angle restraints: 17922 sinusoidal: 7773 harmonic: 10149 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -47.89 -38.11 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA LEU A 517 " pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 17919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3791 0.072 - 0.143: 740 0.143 - 0.215: 44 0.215 - 0.286: 9 0.286 - 0.358: 3 Chirality restraints: 4587 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4584 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 43 " 0.026 2.00e-02 2.50e+03 5.23e-02 2.74e+01 pdb=" C CYS E 43 " -0.091 2.00e-02 2.50e+03 pdb=" O CYS E 43 " 0.034 2.00e-02 2.50e+03 pdb=" N ALA E 44 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 43 " -0.026 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C CYS F 43 " 0.089 2.00e-02 2.50e+03 pdb=" O CYS F 43 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA F 44 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 43 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C CYS D 43 " -0.087 2.00e-02 2.50e+03 pdb=" O CYS D 43 " 0.033 2.00e-02 2.50e+03 pdb=" N ALA D 44 " 0.029 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6453 2.79 - 3.32: 23465 3.32 - 3.85: 47847 3.85 - 4.37: 55766 4.37 - 4.90: 96314 Nonbonded interactions: 229845 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR B 415 " pdb=" OH TYR C 369 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.306 3.040 nonbonded pdb=" OG SER B 366 " pdb=" OD1 ASN B 388 " model vdw 2.306 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.316 3.040 ... (remaining 229840 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = 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' selection = chain 'W' selection = chain 'X' } 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: 3.980 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.760 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 0.057 28875 Z= 0.220 Angle : 0.795 15.024 39417 Z= 0.414 Chirality : 0.054 0.358 4587 Planarity : 0.007 0.067 4998 Dihedral : 13.182 89.948 11271 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.13), residues: 3441 helix: -0.04 (0.18), residues: 678 sheet: 0.01 (0.17), residues: 834 loop : -0.69 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 40 TYR 0.029 0.002 TYR C1067 PHE 0.033 0.002 PHE B 135 TRP 0.020 0.002 TRP A 886 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00458 (28770) covalent geometry : angle 0.76876 (39147) SS BOND : bond 0.00226 ( 45) SS BOND : angle 1.27242 ( 90) hydrogen bonds : bond 0.13542 ( 1155) hydrogen bonds : angle 7.87207 ( 3321) link_BETA1-4 : bond 0.00702 ( 18) link_BETA1-4 : angle 1.36947 ( 54) link_NAG-ASN : bond 0.00744 ( 42) link_NAG-ASN : angle 3.45487 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8331 (tp40) REVERT: A 54 LEU cc_start: 0.9449 (mp) cc_final: 0.9229 (mp) REVERT: B 55 PHE cc_start: 0.8628 (m-80) cc_final: 0.7718 (m-80) REVERT: B 168 PHE cc_start: 0.8311 (t80) cc_final: 0.7990 (t80) REVERT: B 367 VAL cc_start: 0.9399 (m) cc_final: 0.9199 (p) REVERT: B 380 TYR cc_start: 0.8600 (m-80) cc_final: 0.7796 (m-80) REVERT: C 200 TYR cc_start: 0.8005 (m-80) cc_final: 0.7795 (m-80) REVERT: C 244 LEU cc_start: 0.4405 (mt) cc_final: 0.4076 (mp) REVERT: C 453 TYR cc_start: 0.8116 (p90) cc_final: 0.7676 (p90) REVERT: C 456 PHE cc_start: 0.7478 (m-80) cc_final: 0.7274 (m-80) REVERT: C 904 TYR cc_start: 0.7682 (m-10) cc_final: 0.7401 (m-10) REVERT: E 53 TYR cc_start: 0.8337 (m-80) cc_final: 0.7527 (m-10) REVERT: E 69 ILE cc_start: 0.8205 (mt) cc_final: 0.7888 (mm) REVERT: F 53 TYR cc_start: 0.7592 (m-80) cc_final: 0.7301 (m-10) REVERT: F 100 TYR cc_start: 0.9002 (m-80) cc_final: 0.8481 (m-80) REVERT: F 132 MET cc_start: 0.6725 (mmt) cc_final: 0.5348 (mmp) outliers start: 0 outliers final: 1 residues processed: 400 average time/residue: 0.6957 time to fit residues: 324.4888 Evaluate side-chains 207 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1084 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 196 ASN A 218 GLN A 317 ASN A 388 ASN A 762 GLN A 926 GLN A 955 ASN A 957 GLN A1010 GLN B 388 ASN B 460 ASN B 872 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1005 GLN C 52 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 606 ASN C 907 ASN C 960 ASN C1002 GLN C1005 GLN E 120 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.138961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.084877 restraints weight = 63201.263| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.67 r_work: 0.3142 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 28875 Z= 0.234 Angle : 0.666 16.980 39417 Z= 0.335 Chirality : 0.046 0.297 4587 Planarity : 0.005 0.066 4998 Dihedral : 6.531 55.665 5027 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.57 % Allowed : 7.58 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3441 helix: 1.23 (0.20), residues: 679 sheet: 0.17 (0.16), residues: 988 loop : -0.41 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 319 TYR 0.026 0.002 TYR C 265 PHE 0.019 0.002 PHE C 898 TRP 0.014 0.002 TRP B 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00530 (28770) covalent geometry : angle 0.64281 (39147) SS BOND : bond 0.00390 ( 45) SS BOND : angle 1.53498 ( 90) hydrogen bonds : bond 0.04689 ( 1155) hydrogen bonds : angle 6.33177 ( 3321) link_BETA1-4 : bond 0.00221 ( 18) link_BETA1-4 : angle 1.24964 ( 54) link_NAG-ASN : bond 0.00577 ( 42) link_NAG-ASN : angle 2.82965 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8491 (tp40) REVERT: A 53 ASP cc_start: 0.8452 (t0) cc_final: 0.8114 (t0) REVERT: A 66 HIS cc_start: 0.6434 (OUTLIER) cc_final: 0.5876 (t70) REVERT: A 132 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: A 200 TYR cc_start: 0.8256 (m-80) cc_final: 0.7985 (m-80) REVERT: A 237 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7798 (ttp-110) REVERT: B 55 PHE cc_start: 0.8601 (m-80) cc_final: 0.7831 (m-80) REVERT: B 104 TRP cc_start: 0.6266 (OUTLIER) cc_final: 0.5923 (p90) REVERT: B 189 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7426 (tm) REVERT: B 239 GLN cc_start: 0.8062 (tt0) cc_final: 0.7580 (tp40) REVERT: B 357 ARG cc_start: 0.9205 (ttt90) cc_final: 0.8545 (tmt-80) REVERT: B 378 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8234 (ttpt) REVERT: B 516 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 740 MET cc_start: 0.8717 (ttt) cc_final: 0.8028 (ttp) REVERT: C 52 GLN cc_start: 0.9063 (tt0) cc_final: 0.8231 (tm-30) REVERT: C 102 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6352 (mmp-170) REVERT: C 137 ASN cc_start: 0.8010 (t0) cc_final: 0.7390 (m110) REVERT: C 489 TYR cc_start: 0.7474 (m-10) cc_final: 0.7237 (m-10) REVERT: C 495 TYR cc_start: 0.6279 (m-80) cc_final: 0.5942 (m-80) REVERT: C 907 ASN cc_start: 0.9341 (OUTLIER) cc_final: 0.8811 (m110) REVERT: C 988 GLU cc_start: 0.8800 (mp0) cc_final: 0.8521 (mp0) REVERT: E 50 PHE cc_start: 0.6700 (m-10) cc_final: 0.6271 (m-10) REVERT: E 53 TYR cc_start: 0.8296 (m-80) cc_final: 0.7639 (m-80) REVERT: E 69 ILE cc_start: 0.7733 (mt) cc_final: 0.7510 (mm) REVERT: E 77 ARG cc_start: 0.9231 (ttm-80) cc_final: 0.9017 (ptm160) REVERT: E 87 LEU cc_start: 0.8332 (pp) cc_final: 0.7904 (pp) REVERT: E 103 MET cc_start: 0.6871 (mtm) cc_final: 0.6114 (tmm) REVERT: F 53 TYR cc_start: 0.7745 (m-80) cc_final: 0.6874 (m-10) REVERT: F 100 TYR cc_start: 0.9020 (m-80) cc_final: 0.8681 (m-80) outliers start: 48 outliers final: 15 residues processed: 251 average time/residue: 0.6223 time to fit residues: 185.6832 Evaluate side-chains 202 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 265 optimal weight: 0.8980 chunk 206 optimal weight: 0.3980 chunk 180 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 613 GLN A 779 GLN A 955 ASN B 196 ASN B 901 GLN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1010 GLN C1011 GLN C1142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.140016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086669 restraints weight = 63953.803| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.61 r_work: 0.3150 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28875 Z= 0.124 Angle : 0.577 10.980 39417 Z= 0.288 Chirality : 0.044 0.243 4587 Planarity : 0.004 0.059 4998 Dihedral : 5.805 53.965 5025 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.28 % Allowed : 9.45 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3441 helix: 1.72 (0.20), residues: 678 sheet: 0.22 (0.16), residues: 962 loop : -0.31 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 118 TYR 0.021 0.001 TYR C 265 PHE 0.020 0.001 PHE B 168 TRP 0.021 0.001 TRP F 57 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00271 (28770) covalent geometry : angle 0.55453 (39147) SS BOND : bond 0.00315 ( 45) SS BOND : angle 1.27175 ( 90) hydrogen bonds : bond 0.04057 ( 1155) hydrogen bonds : angle 5.94083 ( 3321) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 1.03576 ( 54) link_NAG-ASN : bond 0.00531 ( 42) link_NAG-ASN : angle 2.62929 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8391 (tp40) REVERT: A 53 ASP cc_start: 0.8602 (t0) cc_final: 0.8239 (t0) REVERT: A 81 ASN cc_start: 0.8601 (m-40) cc_final: 0.7813 (t0) REVERT: A 237 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8030 (ttt90) REVERT: A 740 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8062 (tmm) REVERT: B 55 PHE cc_start: 0.8511 (m-80) cc_final: 0.7905 (m-80) REVERT: B 104 TRP cc_start: 0.6239 (p90) cc_final: 0.5860 (p90) REVERT: B 189 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7484 (tm) REVERT: B 357 ARG cc_start: 0.9186 (ttt90) cc_final: 0.8243 (tpt170) REVERT: B 378 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8162 (ttpt) REVERT: B 380 TYR cc_start: 0.8484 (m-80) cc_final: 0.7961 (m-80) REVERT: B 516 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 740 MET cc_start: 0.8691 (ttt) cc_final: 0.8013 (ttp) REVERT: C 52 GLN cc_start: 0.9118 (tt0) cc_final: 0.8298 (tm-30) REVERT: C 102 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6220 (mmp-170) REVERT: C 189 LEU cc_start: 0.8759 (tp) cc_final: 0.8511 (tm) REVERT: C 495 TYR cc_start: 0.6279 (m-80) cc_final: 0.5895 (m-80) REVERT: C 780 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: C 904 TYR cc_start: 0.8516 (m-10) cc_final: 0.8092 (m-10) REVERT: C 985 ASP cc_start: 0.8644 (p0) cc_final: 0.8014 (p0) REVERT: E 53 TYR cc_start: 0.8374 (m-80) cc_final: 0.7674 (m-80) REVERT: E 77 ARG cc_start: 0.9238 (ttm-80) cc_final: 0.9030 (ptm160) REVERT: E 87 LEU cc_start: 0.8214 (pp) cc_final: 0.7700 (pp) REVERT: E 103 MET cc_start: 0.6853 (mtm) cc_final: 0.5968 (tmm) REVERT: F 100 TYR cc_start: 0.9065 (m-80) cc_final: 0.8794 (m-80) outliers start: 39 outliers final: 12 residues processed: 236 average time/residue: 0.5981 time to fit residues: 169.2288 Evaluate side-chains 193 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain E residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 148 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 125 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B 125 ASN B 196 ASN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083138 restraints weight = 63506.239| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.66 r_work: 0.3096 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28875 Z= 0.242 Angle : 0.634 11.552 39417 Z= 0.316 Chirality : 0.046 0.230 4587 Planarity : 0.004 0.055 4998 Dihedral : 5.619 54.974 5025 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.64 % Allowed : 10.14 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3441 helix: 1.80 (0.20), residues: 679 sheet: 0.14 (0.17), residues: 915 loop : -0.29 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 77 TYR 0.025 0.002 TYR B 756 PHE 0.021 0.002 PHE A 543 TRP 0.018 0.002 TRP A 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00547 (28770) covalent geometry : angle 0.61175 (39147) SS BOND : bond 0.00194 ( 45) SS BOND : angle 1.19642 ( 90) hydrogen bonds : bond 0.04527 ( 1155) hydrogen bonds : angle 5.89799 ( 3321) link_BETA1-4 : bond 0.00228 ( 18) link_BETA1-4 : angle 1.26848 ( 54) link_NAG-ASN : bond 0.00632 ( 42) link_NAG-ASN : angle 2.75692 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8453 (tp40) REVERT: A 81 ASN cc_start: 0.8687 (m-40) cc_final: 0.8002 (t0) REVERT: A 138 ASP cc_start: 0.7911 (t0) cc_final: 0.7400 (m-30) REVERT: A 237 ARG cc_start: 0.8427 (ttm110) cc_final: 0.7982 (ttp-110) REVERT: A 661 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 740 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8081 (tmm) REVERT: A 918 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8356 (mt-10) REVERT: B 55 PHE cc_start: 0.8551 (m-80) cc_final: 0.8310 (m-80) REVERT: B 104 TRP cc_start: 0.6311 (p90) cc_final: 0.5982 (p90) REVERT: B 168 PHE cc_start: 0.8860 (t80) cc_final: 0.8545 (t80) REVERT: B 239 GLN cc_start: 0.8139 (tt0) cc_final: 0.7683 (tp40) REVERT: B 357 ARG cc_start: 0.9198 (ttt90) cc_final: 0.8594 (ttt90) REVERT: B 378 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8082 (ttpp) REVERT: B 380 TYR cc_start: 0.8634 (m-80) cc_final: 0.8158 (m-80) REVERT: B 516 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 740 MET cc_start: 0.8703 (ttt) cc_final: 0.7987 (ttp) REVERT: B 934 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8583 (tp) REVERT: B 985 ASP cc_start: 0.8618 (p0) cc_final: 0.8334 (p0) REVERT: B 1145 LEU cc_start: 0.8032 (tm) cc_final: 0.7781 (pt) REVERT: C 52 GLN cc_start: 0.9104 (tt0) cc_final: 0.8331 (tm-30) REVERT: C 102 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6425 (mmp-170) REVERT: C 904 TYR cc_start: 0.8498 (m-10) cc_final: 0.7946 (m-10) REVERT: E 49 THR cc_start: 0.7938 (m) cc_final: 0.7639 (p) REVERT: E 50 PHE cc_start: 0.6142 (m-10) cc_final: 0.5879 (m-10) REVERT: E 53 TYR cc_start: 0.8316 (m-80) cc_final: 0.7573 (m-80) REVERT: E 77 ARG cc_start: 0.9292 (ttm-80) cc_final: 0.9031 (ptm160) REVERT: E 81 ASN cc_start: 0.7654 (t0) cc_final: 0.7417 (t0) REVERT: E 87 LEU cc_start: 0.8245 (pp) cc_final: 0.7800 (pp) REVERT: E 103 MET cc_start: 0.6768 (mtm) cc_final: 0.5932 (tmm) REVERT: E 129 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7763 (pt) REVERT: F 100 TYR cc_start: 0.9076 (m-80) cc_final: 0.8788 (m-80) REVERT: F 132 MET cc_start: 0.5783 (mmp) cc_final: 0.5527 (mmp) outliers start: 50 outliers final: 19 residues processed: 222 average time/residue: 0.6417 time to fit residues: 169.6911 Evaluate side-chains 190 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 129 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 78 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 326 optimal weight: 7.9990 chunk 39 optimal weight: 30.0000 chunk 125 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 315 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 907 ASN B 196 ASN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 120 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.139111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086111 restraints weight = 63140.751| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.54 r_work: 0.3146 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28875 Z= 0.116 Angle : 0.559 11.277 39417 Z= 0.278 Chirality : 0.044 0.238 4587 Planarity : 0.004 0.055 4998 Dihedral : 5.204 53.164 5025 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.48 % Allowed : 10.96 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3441 helix: 2.15 (0.20), residues: 677 sheet: 0.20 (0.17), residues: 879 loop : -0.26 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 214 TYR 0.019 0.001 TYR C 265 PHE 0.019 0.001 PHE A 65 TRP 0.019 0.001 TRP A 104 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00254 (28770) covalent geometry : angle 0.53871 (39147) SS BOND : bond 0.00110 ( 45) SS BOND : angle 0.91141 ( 90) hydrogen bonds : bond 0.03838 ( 1155) hydrogen bonds : angle 5.62944 ( 3321) link_BETA1-4 : bond 0.00337 ( 18) link_BETA1-4 : angle 1.01135 ( 54) link_NAG-ASN : bond 0.00530 ( 42) link_NAG-ASN : angle 2.57501 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8386 (tp40) REVERT: A 81 ASN cc_start: 0.8555 (m-40) cc_final: 0.8283 (t0) REVERT: A 138 ASP cc_start: 0.8136 (t0) cc_final: 0.7471 (m-30) REVERT: A 661 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7985 (tp30) REVERT: A 740 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8066 (tmm) REVERT: A 918 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 55 PHE cc_start: 0.8475 (m-80) cc_final: 0.8208 (m-80) REVERT: B 104 TRP cc_start: 0.6393 (p90) cc_final: 0.6027 (p90) REVERT: B 206 LYS cc_start: 0.8526 (tppt) cc_final: 0.7799 (ttpp) REVERT: B 357 ARG cc_start: 0.9145 (ttt90) cc_final: 0.8537 (ttt90) REVERT: B 378 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8056 (ttpp) REVERT: B 380 TYR cc_start: 0.8581 (m-80) cc_final: 0.8113 (m-80) REVERT: B 516 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7822 (tm-30) REVERT: B 740 MET cc_start: 0.8609 (ttt) cc_final: 0.7923 (ttp) REVERT: B 745 ASP cc_start: 0.8841 (p0) cc_final: 0.8626 (t0) REVERT: B 934 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8455 (tp) REVERT: B 985 ASP cc_start: 0.8545 (p0) cc_final: 0.8329 (p0) REVERT: C 52 GLN cc_start: 0.9029 (tt0) cc_final: 0.8229 (tm-30) REVERT: C 102 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.6377 (mmp-170) REVERT: C 237 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7800 (mtp-110) REVERT: C 269 TYR cc_start: 0.8291 (m-80) cc_final: 0.7891 (m-10) REVERT: C 370 ASN cc_start: 0.9088 (m-40) cc_final: 0.8813 (m110) REVERT: C 780 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: C 904 TYR cc_start: 0.8481 (m-10) cc_final: 0.7972 (m-10) REVERT: E 53 TYR cc_start: 0.8172 (m-80) cc_final: 0.7437 (m-80) REVERT: E 87 LEU cc_start: 0.8328 (pp) cc_final: 0.7920 (pp) REVERT: E 103 MET cc_start: 0.6797 (mtm) cc_final: 0.5878 (tmm) REVERT: E 129 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7867 (pt) REVERT: F 58 VAL cc_start: 0.2869 (m) cc_final: 0.2657 (t) REVERT: F 100 TYR cc_start: 0.8952 (m-80) cc_final: 0.8586 (m-80) REVERT: F 132 MET cc_start: 0.5729 (mmp) cc_final: 0.5468 (mmp) outliers start: 45 outliers final: 15 residues processed: 222 average time/residue: 0.6238 time to fit residues: 164.6576 Evaluate side-chains 194 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 129 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 234 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 321 optimal weight: 50.0000 chunk 313 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 338 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 115 GLN B 196 ASN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083082 restraints weight = 63716.746| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.60 r_work: 0.3100 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28875 Z= 0.230 Angle : 0.615 11.894 39417 Z= 0.304 Chirality : 0.045 0.233 4587 Planarity : 0.004 0.055 4998 Dihedral : 5.315 53.834 5025 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.48 % Allowed : 11.68 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3441 helix: 1.99 (0.20), residues: 684 sheet: 0.15 (0.17), residues: 898 loop : -0.30 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 77 TYR 0.020 0.001 TYR B 756 PHE 0.019 0.001 PHE A 65 TRP 0.022 0.002 TRP A 104 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00518 (28770) covalent geometry : angle 0.59500 (39147) SS BOND : bond 0.00134 ( 45) SS BOND : angle 0.89216 ( 90) hydrogen bonds : bond 0.04331 ( 1155) hydrogen bonds : angle 5.71330 ( 3321) link_BETA1-4 : bond 0.00190 ( 18) link_BETA1-4 : angle 1.19749 ( 54) link_NAG-ASN : bond 0.00594 ( 42) link_NAG-ASN : angle 2.70305 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8504 (m-40) cc_final: 0.8301 (t0) REVERT: A 138 ASP cc_start: 0.8163 (t0) cc_final: 0.7437 (m-30) REVERT: A 237 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7675 (ttp-110) REVERT: A 543 PHE cc_start: 0.4361 (m-80) cc_final: 0.4059 (m-10) REVERT: A 661 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 740 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8100 (tmm) REVERT: B 104 TRP cc_start: 0.6446 (p90) cc_final: 0.6233 (p90) REVERT: B 206 LYS cc_start: 0.8567 (tppt) cc_final: 0.8023 (tptm) REVERT: B 239 GLN cc_start: 0.8167 (tt0) cc_final: 0.7803 (tp40) REVERT: B 357 ARG cc_start: 0.9131 (ttt90) cc_final: 0.8420 (ttt90) REVERT: B 378 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8037 (ttpp) REVERT: B 380 TYR cc_start: 0.8581 (m-80) cc_final: 0.8204 (m-80) REVERT: B 516 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 740 MET cc_start: 0.8656 (ttt) cc_final: 0.7992 (ttp) REVERT: B 934 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8533 (tp) REVERT: C 52 GLN cc_start: 0.9112 (tt0) cc_final: 0.8343 (tm-30) REVERT: C 102 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6543 (mmp-170) REVERT: C 200 TYR cc_start: 0.8328 (m-80) cc_final: 0.7900 (m-80) REVERT: C 237 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7946 (mtp-110) REVERT: C 269 TYR cc_start: 0.8359 (m-80) cc_final: 0.7983 (m-80) REVERT: C 370 ASN cc_start: 0.9065 (m-40) cc_final: 0.8566 (p0) REVERT: C 780 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: C 904 TYR cc_start: 0.8428 (m-10) cc_final: 0.7945 (m-10) REVERT: C 934 ILE cc_start: 0.9214 (tp) cc_final: 0.9013 (tp) REVERT: E 49 THR cc_start: 0.7636 (m) cc_final: 0.7386 (p) REVERT: E 53 TYR cc_start: 0.8137 (m-80) cc_final: 0.7339 (m-80) REVERT: E 74 ASN cc_start: 0.8493 (p0) cc_final: 0.8202 (p0) REVERT: E 87 LEU cc_start: 0.8164 (pp) cc_final: 0.7818 (pp) REVERT: E 103 MET cc_start: 0.6871 (mtm) cc_final: 0.5892 (tmm) REVERT: F 58 VAL cc_start: 0.2894 (m) cc_final: 0.2652 (t) REVERT: F 71 ARG cc_start: 0.5202 (OUTLIER) cc_final: 0.4880 (ptp-110) REVERT: F 100 TYR cc_start: 0.9019 (m-80) cc_final: 0.8638 (m-80) outliers start: 45 outliers final: 19 residues processed: 220 average time/residue: 0.6271 time to fit residues: 164.2382 Evaluate side-chains 197 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 71 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 315 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 196 ASN B 239 GLN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.138045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.084884 restraints weight = 63419.241| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.50 r_work: 0.3144 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28875 Z= 0.142 Angle : 0.572 11.498 39417 Z= 0.283 Chirality : 0.044 0.243 4587 Planarity : 0.004 0.056 4998 Dihedral : 5.082 52.870 5025 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.38 % Allowed : 12.66 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3441 helix: 2.22 (0.20), residues: 675 sheet: 0.13 (0.17), residues: 898 loop : -0.26 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 77 TYR 0.019 0.001 TYR A 904 PHE 0.021 0.001 PHE B 168 TRP 0.027 0.001 TRP A 104 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00319 (28770) covalent geometry : angle 0.55285 (39147) SS BOND : bond 0.00108 ( 45) SS BOND : angle 0.73634 ( 90) hydrogen bonds : bond 0.03850 ( 1155) hydrogen bonds : angle 5.54695 ( 3321) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 0.97838 ( 54) link_NAG-ASN : bond 0.00520 ( 42) link_NAG-ASN : angle 2.58722 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8147 (t0) cc_final: 0.7491 (m-30) REVERT: A 543 PHE cc_start: 0.4399 (m-80) cc_final: 0.4121 (m-10) REVERT: A 661 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8000 (tp30) REVERT: A 740 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8085 (tmm) REVERT: A 918 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8350 (mt-10) REVERT: B 206 LYS cc_start: 0.8494 (tppt) cc_final: 0.7936 (tptm) REVERT: B 238 PHE cc_start: 0.6324 (p90) cc_final: 0.6048 (p90) REVERT: B 357 ARG cc_start: 0.9150 (ttt90) cc_final: 0.8745 (ttm-80) REVERT: B 378 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8071 (ttpp) REVERT: B 380 TYR cc_start: 0.8583 (m-80) cc_final: 0.8214 (m-80) REVERT: B 415 THR cc_start: 0.8783 (p) cc_final: 0.8456 (t) REVERT: B 516 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 740 MET cc_start: 0.8635 (ttt) cc_final: 0.7974 (ttp) REVERT: C 52 GLN cc_start: 0.9094 (tt0) cc_final: 0.8336 (tm-30) REVERT: C 102 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6611 (mmp-170) REVERT: C 237 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8021 (mtp-110) REVERT: C 269 TYR cc_start: 0.8314 (m-80) cc_final: 0.7879 (m-10) REVERT: C 370 ASN cc_start: 0.9050 (m-40) cc_final: 0.8606 (p0) REVERT: C 780 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: C 904 TYR cc_start: 0.8424 (m-10) cc_final: 0.7931 (m-10) REVERT: E 49 THR cc_start: 0.7405 (m) cc_final: 0.7197 (p) REVERT: E 53 TYR cc_start: 0.8106 (m-80) cc_final: 0.7337 (m-80) REVERT: E 74 ASN cc_start: 0.8506 (p0) cc_final: 0.8216 (p0) REVERT: E 87 LEU cc_start: 0.8161 (pp) cc_final: 0.7691 (pp) REVERT: E 103 MET cc_start: 0.6821 (mtm) cc_final: 0.5904 (tmm) REVERT: F 58 VAL cc_start: 0.2924 (m) cc_final: 0.2637 (t) REVERT: F 71 ARG cc_start: 0.5146 (OUTLIER) cc_final: 0.4686 (ptp-110) REVERT: F 77 ARG cc_start: 0.6475 (mtm110) cc_final: 0.6142 (mtm110) REVERT: F 100 TYR cc_start: 0.9050 (m-80) cc_final: 0.8666 (m-80) REVERT: F 132 MET cc_start: 0.5612 (mmp) cc_final: 0.5329 (mmp) outliers start: 42 outliers final: 22 residues processed: 212 average time/residue: 0.6533 time to fit residues: 164.7296 Evaluate side-chains 196 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 71 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 226 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 360 ASN B 907 ASN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.136327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082927 restraints weight = 63813.390| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.50 r_work: 0.3087 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 28875 Z= 0.228 Angle : 0.620 12.055 39417 Z= 0.306 Chirality : 0.045 0.236 4587 Planarity : 0.004 0.057 4998 Dihedral : 5.243 53.629 5025 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.44 % Allowed : 12.83 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3441 helix: 2.15 (0.20), residues: 675 sheet: 0.08 (0.17), residues: 892 loop : -0.30 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 77 TYR 0.024 0.001 TYR B 904 PHE 0.023 0.001 PHE B 55 TRP 0.028 0.002 TRP A 104 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00516 (28770) covalent geometry : angle 0.59999 (39147) SS BOND : bond 0.00163 ( 45) SS BOND : angle 0.80595 ( 90) hydrogen bonds : bond 0.04263 ( 1155) hydrogen bonds : angle 5.64600 ( 3321) link_BETA1-4 : bond 0.00168 ( 18) link_BETA1-4 : angle 1.17012 ( 54) link_NAG-ASN : bond 0.00592 ( 42) link_NAG-ASN : angle 2.69158 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8112 (t0) cc_final: 0.7535 (m-30) REVERT: A 237 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7764 (ttp-110) REVERT: A 661 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 740 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8085 (tmm) REVERT: A 904 TYR cc_start: 0.8492 (m-10) cc_final: 0.8252 (m-10) REVERT: B 160 TYR cc_start: 0.6439 (p90) cc_final: 0.6196 (p90) REVERT: B 206 LYS cc_start: 0.8464 (tppt) cc_final: 0.7814 (ttpp) REVERT: B 357 ARG cc_start: 0.9075 (ttt90) cc_final: 0.8629 (ttm-80) REVERT: B 378 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8024 (ttpp) REVERT: B 380 TYR cc_start: 0.8521 (m-80) cc_final: 0.8150 (m-80) REVERT: B 516 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 740 MET cc_start: 0.8652 (ttt) cc_final: 0.8011 (ttp) REVERT: C 52 GLN cc_start: 0.9144 (tt0) cc_final: 0.8419 (tm-30) REVERT: C 102 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6454 (mmp-170) REVERT: C 200 TYR cc_start: 0.8448 (m-80) cc_final: 0.8080 (m-80) REVERT: C 269 TYR cc_start: 0.8361 (m-80) cc_final: 0.8072 (m-80) REVERT: C 366 SER cc_start: 0.9065 (m) cc_final: 0.8850 (p) REVERT: C 370 ASN cc_start: 0.9089 (m-40) cc_final: 0.8629 (p0) REVERT: C 780 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: C 904 TYR cc_start: 0.8452 (m-10) cc_final: 0.7958 (m-10) REVERT: E 53 TYR cc_start: 0.8147 (m-80) cc_final: 0.7578 (m-80) REVERT: E 74 ASN cc_start: 0.8547 (p0) cc_final: 0.8274 (p0) REVERT: E 87 LEU cc_start: 0.8141 (pp) cc_final: 0.7644 (pp) REVERT: E 103 MET cc_start: 0.6869 (mtm) cc_final: 0.5908 (tmm) REVERT: F 58 VAL cc_start: 0.2768 (m) cc_final: 0.2522 (t) REVERT: F 100 TYR cc_start: 0.9046 (m-80) cc_final: 0.8671 (m-80) REVERT: F 132 MET cc_start: 0.5720 (mmp) cc_final: 0.5464 (mmp) outliers start: 44 outliers final: 20 residues processed: 203 average time/residue: 0.6335 time to fit residues: 153.4381 Evaluate side-chains 187 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 263 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 907 ASN B 824 ASN B 907 ASN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C1010 GLN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.134233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080498 restraints weight = 64176.037| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.55 r_work: 0.3042 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 28875 Z= 0.380 Angle : 0.731 13.296 39417 Z= 0.364 Chirality : 0.049 0.238 4587 Planarity : 0.005 0.061 4998 Dihedral : 5.866 54.800 5025 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.61 % Allowed : 12.96 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3441 helix: 1.67 (0.20), residues: 694 sheet: -0.18 (0.16), residues: 899 loop : -0.46 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 408 TYR 0.023 0.002 TYR B 756 PHE 0.034 0.002 PHE A 220 TRP 0.034 0.002 TRP B 104 HIS 0.007 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00862 (28770) covalent geometry : angle 0.71058 (39147) SS BOND : bond 0.00252 ( 45) SS BOND : angle 1.05227 ( 90) hydrogen bonds : bond 0.04909 ( 1155) hydrogen bonds : angle 5.95169 ( 3321) link_BETA1-4 : bond 0.00207 ( 18) link_BETA1-4 : angle 1.29710 ( 54) link_NAG-ASN : bond 0.00756 ( 42) link_NAG-ASN : angle 2.94465 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8208 (m-80) cc_final: 0.8002 (m-10) REVERT: A 138 ASP cc_start: 0.8136 (t0) cc_final: 0.7902 (t0) REVERT: A 237 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7869 (ttp-110) REVERT: A 661 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 740 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8005 (tmm) REVERT: B 160 TYR cc_start: 0.6292 (p90) cc_final: 0.6084 (p90) REVERT: B 357 ARG cc_start: 0.9125 (ttt90) cc_final: 0.8682 (ttm-80) REVERT: B 378 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7994 (ttpp) REVERT: B 516 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 740 MET cc_start: 0.8768 (ttt) cc_final: 0.8110 (ttp) REVERT: B 934 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8739 (tp) REVERT: C 52 GLN cc_start: 0.9153 (tt0) cc_final: 0.8467 (tm-30) REVERT: C 102 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6719 (mmp-170) REVERT: C 200 TYR cc_start: 0.8600 (m-80) cc_final: 0.8254 (m-80) REVERT: C 366 SER cc_start: 0.9103 (m) cc_final: 0.8900 (p) REVERT: C 370 ASN cc_start: 0.9078 (m-40) cc_final: 0.8673 (p0) REVERT: C 495 TYR cc_start: 0.6626 (m-80) cc_final: 0.6411 (m-80) REVERT: C 904 TYR cc_start: 0.8462 (m-10) cc_final: 0.7949 (m-10) REVERT: E 74 ASN cc_start: 0.8697 (p0) cc_final: 0.8482 (p0) REVERT: E 87 LEU cc_start: 0.8110 (pp) cc_final: 0.7597 (pp) REVERT: E 103 MET cc_start: 0.6827 (mtm) cc_final: 0.5904 (tmm) REVERT: F 58 VAL cc_start: 0.2809 (m) cc_final: 0.2560 (t) REVERT: F 75 ASN cc_start: 0.8946 (t0) cc_final: 0.8464 (p0) outliers start: 49 outliers final: 19 residues processed: 211 average time/residue: 0.6237 time to fit residues: 156.5919 Evaluate side-chains 189 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 301 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 240 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 907 ASN B 907 ASN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN C1010 GLN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.136800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083695 restraints weight = 63479.218| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.52 r_work: 0.3123 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28875 Z= 0.140 Angle : 0.608 11.773 39417 Z= 0.300 Chirality : 0.045 0.237 4587 Planarity : 0.004 0.055 4998 Dihedral : 5.426 52.407 5025 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.92 % Allowed : 14.21 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3441 helix: 2.17 (0.20), residues: 675 sheet: -0.04 (0.17), residues: 888 loop : -0.35 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1107 TYR 0.023 0.001 TYR A 904 PHE 0.026 0.001 PHE A 220 TRP 0.045 0.002 TRP B 104 HIS 0.002 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00310 (28770) covalent geometry : angle 0.58868 (39147) SS BOND : bond 0.00157 ( 45) SS BOND : angle 0.78859 ( 90) hydrogen bonds : bond 0.04016 ( 1155) hydrogen bonds : angle 5.66197 ( 3321) link_BETA1-4 : bond 0.00330 ( 18) link_BETA1-4 : angle 1.05998 ( 54) link_NAG-ASN : bond 0.00529 ( 42) link_NAG-ASN : angle 2.67054 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8065 (m-80) cc_final: 0.7862 (m-10) REVERT: A 138 ASP cc_start: 0.8178 (t0) cc_final: 0.7874 (t0) REVERT: A 237 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7640 (ttp-110) REVERT: A 661 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8016 (tp30) REVERT: A 740 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.7979 (tmm) REVERT: B 160 TYR cc_start: 0.6458 (p90) cc_final: 0.6182 (p90) REVERT: B 206 LYS cc_start: 0.7913 (tppt) cc_final: 0.7676 (tppt) REVERT: B 357 ARG cc_start: 0.9051 (ttt90) cc_final: 0.8554 (ttt-90) REVERT: B 516 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 740 MET cc_start: 0.8613 (ttt) cc_final: 0.7992 (ttp) REVERT: B 934 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8558 (tp) REVERT: C 52 GLN cc_start: 0.9132 (tt0) cc_final: 0.8392 (tm-30) REVERT: C 102 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6542 (mmp-170) REVERT: C 200 TYR cc_start: 0.8519 (m-80) cc_final: 0.8314 (m-80) REVERT: C 269 TYR cc_start: 0.8000 (m-80) cc_final: 0.7375 (m-10) REVERT: C 370 ASN cc_start: 0.9081 (m-40) cc_final: 0.8652 (p0) REVERT: C 780 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: C 904 TYR cc_start: 0.8453 (m-10) cc_final: 0.7954 (m-10) REVERT: E 53 TYR cc_start: 0.8104 (m-80) cc_final: 0.7273 (m-80) REVERT: E 74 ASN cc_start: 0.8603 (p0) cc_final: 0.8321 (p0) REVERT: E 87 LEU cc_start: 0.8183 (pp) cc_final: 0.7733 (pp) REVERT: E 103 MET cc_start: 0.6770 (mtm) cc_final: 0.5861 (tmm) REVERT: F 58 VAL cc_start: 0.2937 (m) cc_final: 0.2652 (t) REVERT: F 75 ASN cc_start: 0.8954 (t0) cc_final: 0.8404 (p0) outliers start: 28 outliers final: 11 residues processed: 190 average time/residue: 0.6535 time to fit residues: 147.2715 Evaluate side-chains 175 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain F residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 96 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 287 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 907 ASN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.136475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.083330 restraints weight = 63843.935| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.53 r_work: 0.3109 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28875 Z= 0.175 Angle : 0.617 11.770 39417 Z= 0.304 Chirality : 0.045 0.241 4587 Planarity : 0.004 0.053 4998 Dihedral : 5.266 52.990 5025 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.92 % Allowed : 14.27 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3441 helix: 2.22 (0.20), residues: 676 sheet: -0.01 (0.17), residues: 897 loop : -0.35 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 118 TYR 0.025 0.001 TYR A 904 PHE 0.026 0.001 PHE A 65 TRP 0.043 0.002 TRP B 104 HIS 0.002 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00396 (28770) covalent geometry : angle 0.59826 (39147) SS BOND : bond 0.00137 ( 45) SS BOND : angle 0.78115 ( 90) hydrogen bonds : bond 0.04028 ( 1155) hydrogen bonds : angle 5.58404 ( 3321) link_BETA1-4 : bond 0.00256 ( 18) link_BETA1-4 : angle 1.09404 ( 54) link_NAG-ASN : bond 0.00540 ( 42) link_NAG-ASN : angle 2.64814 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13623.37 seconds wall clock time: 231 minutes 55.89 seconds (13915.89 seconds total)