Starting phenix.real_space_refine on Fri Jan 16 13:19:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tcc_25808/01_2026/7tcc_25808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tcc_25808/01_2026/7tcc_25808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tcc_25808/01_2026/7tcc_25808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tcc_25808/01_2026/7tcc_25808.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tcc_25808/01_2026/7tcc_25808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tcc_25808/01_2026/7tcc_25808.map" } resolution = 3.86 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= 0.023 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 174 5.16 5 C 23828 2.51 5 N 6234 2.21 5 O 7257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37493 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "B" Number of atoms: 8735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8735 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 57, 'TRANS': 1058} Chain breaks: 2 Chain: "C" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "D" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 932 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 830 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 990 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 806 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "O" Number of atoms: 932 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "P" Number of atoms: 830 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "F" Number of atoms: 932 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 830 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} 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: "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: "Y" 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: "Z" 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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.92, per 1000 atoms: 0.24 Number of scatterers: 37493 At special positions: 0 Unit cell: (168.435, 163.305, 237.69, 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 174 16.00 O 7257 8.00 N 6234 7.00 C 23828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=2.04 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 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 A 840 " - pdb=" SG CYS A 851 " distance=2.04 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=2.04 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 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 97 " - pdb=" SG CYS J 100B" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 97 " - pdb=" SG CYS O 100B" distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 100B" distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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 I 1 " - " NAG I 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 122 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 122 " " NAG I 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " " NAG S 1 " - " ASN A 801 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN C 331 " " NAG b 1 " - " ASN C 801 " Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8762 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 80 sheets defined 18.7% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 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 removed outlier: 3.677A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.063A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 628 Processing helix chain 'A' and resid 630 through 638 removed outlier: 4.564A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.729A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) 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: 3.589A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 849 through 855 removed outlier: 3.588A pdb=" N GLN A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 removed outlier: 4.253A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.640A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.816A pdb=" N VAL A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.187A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 Processing helix chain 'A' and resid 976 through 983 removed outlier: 4.062A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.593A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.567A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.692A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.948A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 626 Processing helix chain 'B' and resid 630 through 636 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.642A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) 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: 3.736A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.506A pdb=" N THR B 827 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.518A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.741A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 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 977 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.983A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.134A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.144A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.513A pdb=" N ASP C 571 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 568 through 572' Processing helix chain 'C' and resid 619 through 628 removed outlier: 3.509A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.849A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.767A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.922A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.924A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.645A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.094A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 916 removed outlier: 3.537A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.762A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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: 3.725A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.798A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.601A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.637A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.828A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.601A pdb=" N THR M 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 34 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.690A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.577A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.829A 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: 4.081A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 156 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.081A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.295A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.678A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.848A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.160A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 727 removed outlier: 7.006A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 727 removed outlier: 7.006A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.670A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.033A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.798A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 141 through 146 removed outlier: 6.982A pdb=" N ASP B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.819A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 7.572A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.928A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.928A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.335A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.384A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.683A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.677A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.916A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.554A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.229A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 126 through 129 Processing sheet with id=AD8, first strand: chain 'C' and resid 310 through 318 removed outlier: 5.607A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.822A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.924A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.106A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.841A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.668A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.866A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.232A pdb=" N GLY D 33 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.853A pdb=" N VAL D 115 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AF2, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.596A pdb=" N GLN E 39 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.751A pdb=" N LEU E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 100 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.884A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 33 through 38 removed outlier: 6.701A pdb=" N VAL J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TRP J 50 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE J 48 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN J 58 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP J 50 " --> pdb=" O ASN J 56 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN J 56 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL J 52 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 93 through 94 removed outlier: 3.677A pdb=" N ILE J 102 " --> pdb=" O ALA J 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'K' and resid 19 through 23 removed outlier: 3.964A pdb=" N ALA K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 53 through 54 removed outlier: 4.385A pdb=" N SER K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR K 49 " --> pdb=" O SER K 53 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG4, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.935A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.935A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.596A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AG8, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AG9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'M' and resid 58 through 60 removed outlier: 5.373A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AH3, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.077A pdb=" N PHE N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN N 39 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N THR N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.077A pdb=" N PHE N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AH6, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'O' and resid 34 through 38 removed outlier: 6.481A pdb=" N VAL O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TRP O 50 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.627A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'P' and resid 18 through 24 Processing sheet with id=AI1, first strand: chain 'P' and resid 53 through 54 removed outlier: 4.082A pdb=" N SER P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR P 49 " --> pdb=" O SER P 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU P 47 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AI3, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.497A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'F' and resid 33 through 39 removed outlier: 5.336A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP F 50 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN F 58 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 93 through 94 Processing sheet with id=AI6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.475A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'G' and resid 20 through 23 Processing sheet with id=AI8, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.972A pdb=" N SER G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL G 85 " --> pdb=" O GLN G 38 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3327 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: 9.65 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 2363 1.23 - 1.38: 12607 1.38 - 1.53: 21715 1.53 - 1.68: 1461 1.68 - 1.83: 228 Bond restraints: 38374 Sorted by residual: bond pdb=" CG PRO G 8 " pdb=" CD PRO G 8 " ideal model delta sigma weight residual 1.503 1.085 0.418 3.40e-02 8.65e+02 1.51e+02 bond pdb=" N PRO G 8 " pdb=" CD PRO G 8 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.54e+00 ... (remaining 38369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.62: 52102 4.62 - 9.24: 93 9.24 - 13.86: 4 13.86 - 18.48: 2 18.48 - 23.09: 1 Bond angle restraints: 52202 Sorted by residual: angle pdb=" N PRO G 8 " pdb=" CD PRO G 8 " pdb=" CG PRO G 8 " ideal model delta sigma weight residual 103.20 80.11 23.09 1.50e+00 4.44e-01 2.37e+02 angle pdb=" CA PRO G 8 " pdb=" CB PRO G 8 " pdb=" CG PRO G 8 " ideal model delta sigma weight residual 104.50 88.08 16.42 1.90e+00 2.77e-01 7.47e+01 angle pdb=" CA PRO G 8 " pdb=" N PRO G 8 " pdb=" CD PRO G 8 " ideal model delta sigma weight residual 112.00 101.55 10.45 1.40e+00 5.10e-01 5.58e+01 angle pdb=" C ILE A 95 " pdb=" N GLU A 96 " pdb=" CA GLU A 96 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 125.00 109.57 15.43 4.10e+00 5.95e-02 1.42e+01 ... (remaining 52197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 22687 33.33 - 66.65: 530 66.65 - 99.98: 50 99.98 - 133.31: 0 133.31 - 166.64: 1 Dihedral angle restraints: 23268 sinusoidal: 9544 harmonic: 13724 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -2.06 -83.94 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 29.21 63.79 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 31.64 61.36 1 1.00e+01 1.00e-02 5.00e+01 ... (remaining 23265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5013 0.064 - 0.128: 873 0.128 - 0.192: 54 0.192 - 0.256: 3 0.256 - 0.320: 5 Chirality restraints: 5948 Sorted by residual: chirality pdb=" CB ILE G 2 " pdb=" CA ILE G 2 " pdb=" CG1 ILE G 2 " pdb=" CG2 ILE G 2 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PRO C 527 " pdb=" N PRO C 527 " pdb=" C PRO C 527 " pdb=" CB PRO C 527 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE A 95 " pdb=" CA ILE A 95 " pdb=" CG1 ILE A 95 " pdb=" CG2 ILE A 95 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 5945 not shown) Planarity restraints: 6711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.094 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO C 527 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 7 " -0.062 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO G 8 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO G 8 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 8 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 37 " 0.023 2.00e-02 2.50e+03 1.84e-02 8.42e+00 pdb=" CG TRP E 37 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 37 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 37 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 37 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 37 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 37 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 37 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 37 " -0.003 2.00e-02 2.50e+03 ... (remaining 6708 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 578 2.61 - 3.18: 34095 3.18 - 3.75: 58088 3.75 - 4.33: 76658 4.33 - 4.90: 123511 Nonbonded interactions: 292930 Sorted by model distance: nonbonded pdb=" O LYS A 97 " pdb=" ND2 ASN A 188 " model vdw 2.032 3.120 nonbonded pdb=" O LEU A 293 " pdb=" OG1 THR A 632 " model vdw 2.122 3.040 nonbonded pdb=" OG SER C 605 " pdb=" OE1 GLN C 607 " model vdw 2.130 3.040 nonbonded pdb=" NZ LYS C 206 " pdb=" OG1 THR C 208 " model vdw 2.133 3.120 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.151 3.040 ... (remaining 292925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 213 or resid 214B through 1304)) selection = (chain 'B' and resid 14 through 1304) selection = (chain 'C' and (resid 14 through 213 or resid 214B through 1304)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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 group one per residue 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: 14.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.240 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.418 38469 Z= 0.171 Angle : 0.707 23.095 52433 Z= 0.366 Chirality : 0.047 0.320 5948 Planarity : 0.005 0.146 6683 Dihedral : 14.113 166.636 14344 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.64 % Favored : 91.02 % Rotamer: Outliers : 0.02 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4712 helix: 0.98 (0.21), residues: 705 sheet: -0.55 (0.15), residues: 1165 loop : -2.03 (0.11), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 466 TYR 0.022 0.001 TYR H 109 PHE 0.027 0.001 PHE C 400 TRP 0.050 0.002 TRP E 37 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00394 (38374) covalent geometry : angle 0.69277 (52202) SS BOND : bond 0.00370 ( 54) SS BOND : angle 1.47422 ( 108) hydrogen bonds : bond 0.17867 ( 1195) hydrogen bonds : angle 7.84927 ( 3327) link_BETA1-4 : bond 0.00365 ( 13) link_BETA1-4 : angle 1.31685 ( 39) link_NAG-ASN : bond 0.00376 ( 28) link_NAG-ASN : angle 3.16516 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.6803 (mpp) cc_final: 0.6425 (mpp) REVERT: C 177 MET cc_start: 0.7748 (tmm) cc_final: 0.7365 (mmm) REVERT: L 94 MET cc_start: 0.9154 (mmp) cc_final: 0.8799 (mmm) REVERT: M 113 MET cc_start: 0.8375 (pmm) cc_final: 0.8175 (pmm) REVERT: G 77 ARG cc_start: 0.6271 (mpp-170) cc_final: 0.5544 (tpt170) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.2345 time to fit residues: 53.8172 Evaluate side-chains 98 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.0050 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1011 GLN B 52 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN L 6 GLN M 3 GLN M 82 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN F 6 GLN F 56 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.073494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.046017 restraints weight = 348081.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.045177 restraints weight = 223914.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044918 restraints weight = 159655.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044918 restraints weight = 131118.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044918 restraints weight = 131118.496| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 38469 Z= 0.258 Angle : 0.737 12.466 52433 Z= 0.377 Chirality : 0.046 0.254 5948 Planarity : 0.005 0.118 6683 Dihedral : 6.536 57.200 6014 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.31 % Favored : 89.33 % Rotamer: Outliers : 0.39 % Allowed : 8.82 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.12), residues: 4712 helix: 0.73 (0.20), residues: 713 sheet: -0.69 (0.15), residues: 1124 loop : -1.99 (0.11), residues: 2875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.021 0.002 TYR A 421 PHE 0.028 0.002 PHE A 759 TRP 0.022 0.002 TRP A 258 HIS 0.010 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00546 (38374) covalent geometry : angle 0.72240 (52202) SS BOND : bond 0.00524 ( 54) SS BOND : angle 1.33417 ( 108) hydrogen bonds : bond 0.04969 ( 1195) hydrogen bonds : angle 6.57099 ( 3327) link_BETA1-4 : bond 0.00346 ( 13) link_BETA1-4 : angle 1.21496 ( 39) link_NAG-ASN : bond 0.00655 ( 28) link_NAG-ASN : angle 3.36685 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.9026 (tmm160) cc_final: 0.8781 (mmp-170) REVERT: B 1050 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7945 (mtm) REVERT: C 177 MET cc_start: 0.7860 (tmm) cc_final: 0.7646 (mmm) REVERT: E 37 TRP cc_start: 0.5870 (m100) cc_final: 0.5207 (m100) REVERT: L 94 MET cc_start: 0.9325 (mmp) cc_final: 0.8811 (mmp) REVERT: G 77 ARG cc_start: 0.6304 (mpp-170) cc_final: 0.5694 (tpt170) outliers start: 16 outliers final: 5 residues processed: 115 average time/residue: 0.2312 time to fit residues: 45.1065 Evaluate side-chains 100 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain O residue 101 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 352 optimal weight: 20.0000 chunk 358 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 450 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 349 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 314 GLN B 580 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 394 ASN ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.072407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045075 restraints weight = 353791.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.044569 restraints weight = 228690.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.044564 restraints weight = 177597.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.044439 restraints weight = 120636.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.044424 restraints weight = 115017.062| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 38469 Z= 0.285 Angle : 0.748 16.535 52433 Z= 0.381 Chirality : 0.046 0.234 5948 Planarity : 0.005 0.154 6683 Dihedral : 6.306 55.397 6014 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.76 % Favored : 89.88 % Rotamer: Outliers : 1.52 % Allowed : 13.78 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.12), residues: 4712 helix: 0.52 (0.19), residues: 715 sheet: -0.88 (0.15), residues: 1158 loop : -2.07 (0.11), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 246 TYR 0.021 0.002 TYR H 109 PHE 0.028 0.002 PHE A 759 TRP 0.023 0.002 TRP E 37 HIS 0.006 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00598 (38374) covalent geometry : angle 0.73340 (52202) SS BOND : bond 0.00566 ( 54) SS BOND : angle 1.28263 ( 108) hydrogen bonds : bond 0.04852 ( 1195) hydrogen bonds : angle 6.44656 ( 3327) link_BETA1-4 : bond 0.00411 ( 13) link_BETA1-4 : angle 1.40191 ( 39) link_NAG-ASN : bond 0.00694 ( 28) link_NAG-ASN : angle 3.43998 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 100 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 VAL cc_start: 0.5052 (OUTLIER) cc_final: 0.4716 (m) REVERT: A 1050 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8030 (mtm) REVERT: B 177 MET cc_start: 0.6391 (mpp) cc_final: 0.5814 (mpp) REVERT: B 827 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8491 (p) REVERT: C 177 MET cc_start: 0.8018 (tmm) cc_final: 0.7608 (mmm) REVERT: C 1050 MET cc_start: 0.8654 (ptp) cc_final: 0.7980 (mtm) REVERT: H 34 MET cc_start: 0.8440 (mmm) cc_final: 0.8158 (tmm) REVERT: H 83 MET cc_start: 0.4526 (mmm) cc_final: 0.4319 (mmt) REVERT: H 113 MET cc_start: 0.7351 (tpp) cc_final: 0.6708 (tpp) REVERT: L 94 MET cc_start: 0.9310 (mmp) cc_final: 0.8836 (mmp) REVERT: M 51 ILE cc_start: -0.0602 (OUTLIER) cc_final: -0.1110 (mp) REVERT: G 77 ARG cc_start: 0.6376 (mpp-170) cc_final: 0.5790 (tpt170) outliers start: 62 outliers final: 25 residues processed: 153 average time/residue: 0.2230 time to fit residues: 58.6000 Evaluate side-chains 121 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain F residue 108 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 293 optimal weight: 4.9990 chunk 416 optimal weight: 30.0000 chunk 216 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 345 optimal weight: 40.0000 chunk 394 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 432 optimal weight: 30.0000 chunk 433 optimal weight: 0.8980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.072514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.045717 restraints weight = 351678.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044833 restraints weight = 220371.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.045069 restraints weight = 152498.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045057 restraints weight = 109689.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.045047 restraints weight = 105539.763| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 38469 Z= 0.219 Angle : 0.684 11.977 52433 Z= 0.349 Chirality : 0.045 0.236 5948 Planarity : 0.005 0.136 6683 Dihedral : 5.991 54.418 6014 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.72 % Favored : 89.92 % Rotamer: Outliers : 1.62 % Allowed : 16.21 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4712 helix: 0.72 (0.20), residues: 721 sheet: -0.87 (0.15), residues: 1132 loop : -2.05 (0.11), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 466 TYR 0.021 0.001 TYR H 109 PHE 0.024 0.001 PHE A 759 TRP 0.020 0.002 TRP E 37 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00463 (38374) covalent geometry : angle 0.67067 (52202) SS BOND : bond 0.00490 ( 54) SS BOND : angle 1.12030 ( 108) hydrogen bonds : bond 0.04356 ( 1195) hydrogen bonds : angle 6.15387 ( 3327) link_BETA1-4 : bond 0.00247 ( 13) link_BETA1-4 : angle 1.23838 ( 39) link_NAG-ASN : bond 0.00484 ( 28) link_NAG-ASN : angle 3.19788 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 99 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 414 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.3395 (pm20) REVERT: C 177 MET cc_start: 0.7983 (tmm) cc_final: 0.7591 (mmm) REVERT: C 900 MET cc_start: 0.9047 (mmp) cc_final: 0.8727 (mmt) REVERT: C 1050 MET cc_start: 0.8243 (ptp) cc_final: 0.8006 (mtm) REVERT: H 34 MET cc_start: 0.8336 (mmm) cc_final: 0.8121 (tmm) REVERT: H 83 MET cc_start: 0.4485 (mmm) cc_final: 0.4172 (mmt) REVERT: L 94 MET cc_start: 0.9338 (mmp) cc_final: 0.8812 (mmp) REVERT: M 51 ILE cc_start: -0.0629 (OUTLIER) cc_final: -0.1185 (mp) REVERT: M 83 MET cc_start: 0.0531 (mmp) cc_final: 0.0292 (mmp) REVERT: G 77 ARG cc_start: 0.6428 (mpp-170) cc_final: 0.5806 (tpt170) outliers start: 66 outliers final: 33 residues processed: 155 average time/residue: 0.2194 time to fit residues: 58.5251 Evaluate side-chains 125 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 321 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 317 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 410 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.072806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046579 restraints weight = 350324.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.045388 restraints weight = 219786.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.045641 restraints weight = 144782.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.045733 restraints weight = 106154.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.046032 restraints weight = 98004.798| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 38469 Z= 0.168 Angle : 0.647 9.668 52433 Z= 0.329 Chirality : 0.044 0.232 5948 Planarity : 0.005 0.128 6683 Dihedral : 5.709 52.866 6014 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.00 % Favored : 90.66 % Rotamer: Outliers : 2.16 % Allowed : 16.53 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.12), residues: 4712 helix: 0.97 (0.20), residues: 720 sheet: -0.80 (0.15), residues: 1141 loop : -2.00 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 466 TYR 0.021 0.001 TYR H 109 PHE 0.021 0.001 PHE A 759 TRP 0.032 0.001 TRP E 37 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00361 (38374) covalent geometry : angle 0.63480 (52202) SS BOND : bond 0.00472 ( 54) SS BOND : angle 0.99171 ( 108) hydrogen bonds : bond 0.04129 ( 1195) hydrogen bonds : angle 5.90023 ( 3327) link_BETA1-4 : bond 0.00198 ( 13) link_BETA1-4 : angle 1.18691 ( 39) link_NAG-ASN : bond 0.00435 ( 28) link_NAG-ASN : angle 2.97012 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 96 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.8925 (tp) REVERT: B 414 GLN cc_start: 0.5654 (OUTLIER) cc_final: 0.4113 (pm20) REVERT: B 827 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8334 (p) REVERT: B 1050 MET cc_start: 0.8396 (ptp) cc_final: 0.7501 (mtm) REVERT: C 177 MET cc_start: 0.7979 (tmm) cc_final: 0.7500 (mmm) REVERT: C 1039 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8179 (mtm180) REVERT: C 1050 MET cc_start: 0.8410 (ptp) cc_final: 0.7979 (mtm) REVERT: D 106 LEU cc_start: 0.3431 (OUTLIER) cc_final: 0.3200 (pp) REVERT: H 113 MET cc_start: 0.6756 (tpp) cc_final: 0.5972 (tpp) REVERT: L 94 MET cc_start: 0.9276 (mmp) cc_final: 0.8805 (mmp) REVERT: M 51 ILE cc_start: -0.1041 (OUTLIER) cc_final: -0.1518 (mp) REVERT: G 77 ARG cc_start: 0.6529 (mpp-170) cc_final: 0.5794 (tpt170) outliers start: 88 outliers final: 47 residues processed: 177 average time/residue: 0.2156 time to fit residues: 65.4501 Evaluate side-chains 144 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 91 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain F residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 238 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 43 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 414 optimal weight: 30.0000 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.072444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045572 restraints weight = 351446.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.044892 restraints weight = 223709.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044750 restraints weight = 161577.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.044603 restraints weight = 121029.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.044603 restraints weight = 110751.585| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 38469 Z= 0.186 Angle : 0.660 10.956 52433 Z= 0.334 Chirality : 0.044 0.298 5948 Planarity : 0.005 0.122 6683 Dihedral : 5.620 49.580 6014 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.68 % Favored : 89.96 % Rotamer: Outliers : 2.58 % Allowed : 17.36 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.12), residues: 4712 helix: 0.97 (0.20), residues: 723 sheet: -0.82 (0.15), residues: 1173 loop : -2.01 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.022 0.001 TYR H 109 PHE 0.023 0.001 PHE A 759 TRP 0.018 0.001 TRP E 37 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00397 (38374) covalent geometry : angle 0.64845 (52202) SS BOND : bond 0.00628 ( 54) SS BOND : angle 1.15498 ( 108) hydrogen bonds : bond 0.04070 ( 1195) hydrogen bonds : angle 5.85186 ( 3327) link_BETA1-4 : bond 0.00204 ( 13) link_BETA1-4 : angle 1.24073 ( 39) link_NAG-ASN : bond 0.00402 ( 28) link_NAG-ASN : angle 2.89428 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 95 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8872 (tp) REVERT: A 177 MET cc_start: 0.5163 (mmt) cc_final: 0.4817 (mmp) REVERT: A 836 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7323 (tp-100) REVERT: B 414 GLN cc_start: 0.5059 (OUTLIER) cc_final: 0.3341 (pm20) REVERT: B 827 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8483 (p) REVERT: C 177 MET cc_start: 0.7949 (tmm) cc_final: 0.7538 (mmm) REVERT: C 270 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 900 MET cc_start: 0.9034 (mmp) cc_final: 0.8421 (mmt) REVERT: C 1034 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9468 (mm) REVERT: C 1039 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8186 (mtm180) REVERT: C 1050 MET cc_start: 0.8252 (ptp) cc_final: 0.7696 (mtm) REVERT: H 113 MET cc_start: 0.7042 (tpp) cc_final: 0.6277 (tpp) REVERT: L 94 MET cc_start: 0.9305 (mmp) cc_final: 0.8770 (mmp) REVERT: M 51 ILE cc_start: -0.0247 (OUTLIER) cc_final: -0.0744 (mp) REVERT: G 77 ARG cc_start: 0.6380 (mpp-170) cc_final: 0.5759 (tpt170) outliers start: 105 outliers final: 61 residues processed: 191 average time/residue: 0.2156 time to fit residues: 71.5517 Evaluate side-chains 160 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 91 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain O residue 101 ASP Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 306 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 301 optimal weight: 0.9980 chunk 325 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 322 optimal weight: 0.8980 chunk 347 optimal weight: 50.0000 chunk 424 optimal weight: 0.0040 chunk 238 optimal weight: 9.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.072926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046414 restraints weight = 348852.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.046755 restraints weight = 215560.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.045967 restraints weight = 162789.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.046008 restraints weight = 123788.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.046315 restraints weight = 99252.280| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 38469 Z= 0.135 Angle : 0.635 11.302 52433 Z= 0.321 Chirality : 0.044 0.263 5948 Planarity : 0.005 0.118 6683 Dihedral : 5.352 45.952 6014 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.45 % Favored : 91.17 % Rotamer: Outliers : 2.21 % Allowed : 18.05 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.12), residues: 4712 helix: 1.16 (0.20), residues: 724 sheet: -0.69 (0.15), residues: 1150 loop : -1.96 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.021 0.001 TYR H 109 PHE 0.015 0.001 PHE A 759 TRP 0.042 0.001 TRP E 37 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00295 (38374) covalent geometry : angle 0.62435 (52202) SS BOND : bond 0.00523 ( 54) SS BOND : angle 1.15443 ( 108) hydrogen bonds : bond 0.03839 ( 1195) hydrogen bonds : angle 5.63043 ( 3327) link_BETA1-4 : bond 0.00299 ( 13) link_BETA1-4 : angle 1.14130 ( 39) link_NAG-ASN : bond 0.00375 ( 28) link_NAG-ASN : angle 2.72404 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 94 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8907 (tp) REVERT: B 130 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8274 (t) REVERT: B 293 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 303 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9139 (tt) REVERT: B 414 GLN cc_start: 0.5087 (OUTLIER) cc_final: 0.3459 (pm20) REVERT: B 827 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8495 (p) REVERT: C 177 MET cc_start: 0.7920 (tmm) cc_final: 0.7473 (mmm) REVERT: C 270 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8899 (mp) REVERT: C 900 MET cc_start: 0.9064 (mmp) cc_final: 0.8720 (mmt) REVERT: C 1050 MET cc_start: 0.8327 (ptp) cc_final: 0.7811 (mtm) REVERT: H 113 MET cc_start: 0.6791 (tpp) cc_final: 0.5989 (tpp) REVERT: L 94 MET cc_start: 0.9265 (mmp) cc_final: 0.8774 (mmp) REVERT: M 51 ILE cc_start: -0.0476 (OUTLIER) cc_final: -0.1024 (mp) REVERT: G 77 ARG cc_start: 0.6417 (mpp-170) cc_final: 0.5730 (tpt170) outliers start: 90 outliers final: 53 residues processed: 175 average time/residue: 0.2141 time to fit residues: 64.4821 Evaluate side-chains 151 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 90 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 318 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 368 optimal weight: 8.9990 chunk 386 optimal weight: 8.9990 chunk 411 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 290 optimal weight: 0.8980 chunk 309 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 381 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 658 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 82 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.072822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.045946 restraints weight = 348497.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.044918 restraints weight = 221939.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.044469 restraints weight = 156780.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.044459 restraints weight = 116308.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.044488 restraints weight = 104390.493| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 38469 Z= 0.137 Angle : 0.632 11.547 52433 Z= 0.317 Chirality : 0.044 0.249 5948 Planarity : 0.004 0.118 6683 Dihedral : 5.216 39.588 6014 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.85 % Favored : 90.79 % Rotamer: Outliers : 2.28 % Allowed : 18.44 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.12), residues: 4712 helix: 1.20 (0.20), residues: 724 sheet: -0.66 (0.15), residues: 1150 loop : -1.93 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.021 0.001 TYR H 109 PHE 0.017 0.001 PHE A 759 TRP 0.017 0.001 TRP O 47 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00302 (38374) covalent geometry : angle 0.62176 (52202) SS BOND : bond 0.00489 ( 54) SS BOND : angle 1.23065 ( 108) hydrogen bonds : bond 0.03755 ( 1195) hydrogen bonds : angle 5.57143 ( 3327) link_BETA1-4 : bond 0.00282 ( 13) link_BETA1-4 : angle 1.16662 ( 39) link_NAG-ASN : bond 0.00268 ( 28) link_NAG-ASN : angle 2.60520 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 97 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8890 (tp) REVERT: A 177 MET cc_start: 0.5129 (mmt) cc_final: 0.4718 (mmp) REVERT: A 836 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7054 (tp-100) REVERT: B 207 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.8058 (t-170) REVERT: B 293 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8572 (tt) REVERT: B 303 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9133 (tt) REVERT: B 414 GLN cc_start: 0.5001 (OUTLIER) cc_final: 0.3329 (pm20) REVERT: B 827 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8541 (p) REVERT: C 177 MET cc_start: 0.7856 (tmm) cc_final: 0.7526 (mmm) REVERT: C 270 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8880 (mp) REVERT: C 900 MET cc_start: 0.9019 (mmp) cc_final: 0.8738 (mmt) REVERT: C 1034 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9480 (mm) REVERT: C 1039 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8182 (mtm180) REVERT: C 1050 MET cc_start: 0.8357 (ptp) cc_final: 0.7810 (mtm) REVERT: E 37 TRP cc_start: 0.5015 (m100) cc_final: 0.4750 (m100) REVERT: H 113 MET cc_start: 0.6823 (tpp) cc_final: 0.6030 (tpp) REVERT: L 94 MET cc_start: 0.9290 (mmp) cc_final: 0.8790 (mmp) REVERT: G 77 ARG cc_start: 0.6375 (mpp-170) cc_final: 0.5909 (tpp-160) outliers start: 93 outliers final: 64 residues processed: 182 average time/residue: 0.2151 time to fit residues: 67.1416 Evaluate side-chains 165 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 91 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain P residue 54 ARG Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 366 optimal weight: 0.7980 chunk 437 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 448 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 445 optimal weight: 5.9990 chunk 253 optimal weight: 30.0000 chunk 128 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.072116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.045575 restraints weight = 353595.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045722 restraints weight = 225989.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.045509 restraints weight = 158473.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.045565 restraints weight = 153543.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.045430 restraints weight = 153313.552| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 38469 Z= 0.210 Angle : 0.678 11.729 52433 Z= 0.342 Chirality : 0.044 0.298 5948 Planarity : 0.005 0.117 6683 Dihedral : 5.382 40.995 6014 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.72 % Favored : 89.94 % Rotamer: Outliers : 2.16 % Allowed : 18.69 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4712 helix: 1.14 (0.20), residues: 716 sheet: -0.77 (0.15), residues: 1156 loop : -1.97 (0.11), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 509 TYR 0.022 0.001 TYR H 109 PHE 0.024 0.001 PHE A 759 TRP 0.036 0.001 TRP E 37 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00449 (38374) covalent geometry : angle 0.66664 (52202) SS BOND : bond 0.00544 ( 54) SS BOND : angle 1.32541 ( 108) hydrogen bonds : bond 0.03980 ( 1195) hydrogen bonds : angle 5.72832 ( 3327) link_BETA1-4 : bond 0.00242 ( 13) link_BETA1-4 : angle 1.31754 ( 39) link_NAG-ASN : bond 0.00475 ( 28) link_NAG-ASN : angle 2.77214 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 91 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5740 (mmt) cc_final: 0.5408 (mmp) REVERT: B 207 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7568 (t-170) REVERT: B 293 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8673 (tt) REVERT: B 303 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9126 (tt) REVERT: B 414 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.5481 (pm20) REVERT: B 827 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8693 (p) REVERT: C 270 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9103 (mp) REVERT: C 900 MET cc_start: 0.9111 (mmp) cc_final: 0.8829 (mmt) REVERT: C 1039 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8270 (mtm180) REVERT: C 1050 MET cc_start: 0.8418 (ptp) cc_final: 0.7666 (mtm) REVERT: H 113 MET cc_start: 0.7148 (tpp) cc_final: 0.6400 (tpp) REVERT: L 94 MET cc_start: 0.9198 (mmp) cc_final: 0.8789 (mmm) REVERT: O 2 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6706 (mmt) REVERT: G 77 ARG cc_start: 0.6377 (mpp-170) cc_final: 0.5933 (tpp-160) outliers start: 88 outliers final: 65 residues processed: 174 average time/residue: 0.2075 time to fit residues: 62.9631 Evaluate side-chains 163 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 90 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 271 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 348 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 339 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.072541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.046367 restraints weight = 349585.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046200 restraints weight = 227779.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.046383 restraints weight = 166406.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.045709 restraints weight = 123291.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.045582 restraints weight = 101552.471| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 38469 Z= 0.147 Angle : 0.647 12.448 52433 Z= 0.324 Chirality : 0.044 0.243 5948 Planarity : 0.005 0.117 6683 Dihedral : 5.220 39.696 6014 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.68 % Favored : 90.98 % Rotamer: Outliers : 2.06 % Allowed : 18.86 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4712 helix: 1.17 (0.20), residues: 728 sheet: -0.68 (0.15), residues: 1162 loop : -1.91 (0.11), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 905 TYR 0.021 0.001 TYR H 109 PHE 0.016 0.001 PHE A 759 TRP 0.025 0.001 TRP E 37 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00322 (38374) covalent geometry : angle 0.63690 (52202) SS BOND : bond 0.00475 ( 54) SS BOND : angle 1.19261 ( 108) hydrogen bonds : bond 0.03799 ( 1195) hydrogen bonds : angle 5.58850 ( 3327) link_BETA1-4 : bond 0.00281 ( 13) link_BETA1-4 : angle 1.14470 ( 39) link_NAG-ASN : bond 0.00284 ( 28) link_NAG-ASN : angle 2.61156 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9424 Ramachandran restraints generated. 4712 Oldfield, 0 Emsley, 4712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 91 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8885 (tp) REVERT: B 207 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.8022 (t-170) REVERT: B 293 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8569 (tt) REVERT: B 303 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9106 (tt) REVERT: B 414 GLN cc_start: 0.4957 (OUTLIER) cc_final: 0.3395 (pm20) REVERT: B 827 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 270 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8890 (mp) REVERT: C 900 MET cc_start: 0.9086 (mmp) cc_final: 0.8807 (mmt) REVERT: C 1039 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8212 (mtm180) REVERT: C 1050 MET cc_start: 0.8347 (ptp) cc_final: 0.7944 (mtm) REVERT: H 113 MET cc_start: 0.6748 (tpp) cc_final: 0.5956 (tpp) REVERT: L 94 MET cc_start: 0.9240 (mmp) cc_final: 0.8704 (mmp) REVERT: O 2 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6543 (mmt) REVERT: G 77 ARG cc_start: 0.6414 (mpp-170) cc_final: 0.5917 (tpp-160) outliers start: 84 outliers final: 66 residues processed: 169 average time/residue: 0.2220 time to fit residues: 64.7531 Evaluate side-chains 165 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 90 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain O residue 2 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 230 optimal weight: 1.9990 chunk 435 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 323 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 218 optimal weight: 0.1980 chunk 356 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 462 optimal weight: 2.9990 chunk 299 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 836 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.073133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.046138 restraints weight = 350281.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.045219 restraints weight = 211788.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.045304 restraints weight = 141117.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.045327 restraints weight = 112218.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.045308 restraints weight = 108429.474| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 38469 Z= 0.113 Angle : 0.643 12.279 52433 Z= 0.319 Chirality : 0.044 0.245 5948 Planarity : 0.005 0.118 6683 Dihedral : 4.959 36.819 6014 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.21 % Favored : 91.45 % Rotamer: Outliers : 1.72 % Allowed : 19.38 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4712 helix: 1.29 (0.20), residues: 721 sheet: -0.57 (0.15), residues: 1170 loop : -1.86 (0.11), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.052 0.001 TYR A 837 PHE 0.014 0.001 PHE G 62 TRP 0.079 0.001 TRP E 37 HIS 0.004 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00252 (38374) covalent geometry : angle 0.63312 (52202) SS BOND : bond 0.00460 ( 54) SS BOND : angle 1.28796 ( 108) hydrogen bonds : bond 0.03602 ( 1195) hydrogen bonds : angle 5.39560 ( 3327) link_BETA1-4 : bond 0.00432 ( 13) link_BETA1-4 : angle 1.14066 ( 39) link_NAG-ASN : bond 0.00257 ( 28) link_NAG-ASN : angle 2.42118 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11292.34 seconds wall clock time: 193 minutes 54.86 seconds (11634.86 seconds total)