Starting phenix.real_space_refine on Fri Mar 6 15:29:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mxp_24075/03_2026/7mxp_24075.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mxp_24075/03_2026/7mxp_24075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mxp_24075/03_2026/7mxp_24075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mxp_24075/03_2026/7mxp_24075.map" model { file = "/net/cci-nas-00/data/ceres_data/7mxp_24075/03_2026/7mxp_24075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mxp_24075/03_2026/7mxp_24075.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.028 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 135 5.16 5 C 20115 2.51 5 N 5207 2.21 5 O 6207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31664 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8555 Classifications: {'peptide': 1098} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1044} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8577 Classifications: {'peptide': 1101} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1047} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8494 Classifications: {'peptide': 1090} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 53, 'TRANS': 1036} Chain breaks: 5 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {'BMA': 2, 'FUC': 1, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {'BMA': 2, 'FUC': 1, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 99 Unusual residues: {'BMA': 2, 'FUC': 1, 'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.29, per 1000 atoms: 0.23 Number of scatterers: 31664 At special positions: 0 Unit cell: (193.67, 200.09, 187.25, 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 135 16.00 O 6207 8.00 N 5207 7.00 C 20115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 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=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA N 3 " - " MAN N 4 " BETA1-2 " BMA E 3 " - " NAG E 6 " " MAN E 4 " - " NAG E 5 " " BMA F 3 " - " NAG F 6 " " MAN F 4 " - " NAG F 5 " " BMA N 3 " - " NAG N 6 " " MAN N 4 " - " NAG N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA1-6 " NAG E 1 " - " FUC E 8 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " BMA E 3 " - " BMA E 7 " " NAG F 1 " - " FUC F 8 " " BMA F 3 " - " BMA F 7 " " NAG N 1 " - " FUC N 8 " " BMA N 3 " - " BMA N 7 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 165 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 165 " " NAG D 1 " - " ASN B 149 " " NAG E 1 " - " ASN B 17 " " NAG F 1 " - " ASN A 17 " " NAG M 1 " - " ASN A 149 " " NAG N 1 " - " ASN C 17 " " NAG O 1 " - " ASN C 149 " " NAG Y 1 " - " ASN C 122 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7356 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 56 sheets defined 18.3% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.632A pdb=" N LEU A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.668A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.508A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 387' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 751 through 757 removed outlier: 3.961A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.953A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.536A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.534A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.612A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 963 removed outlier: 3.532A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.521A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.951A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A1011 " --> pdb=" O TYR A1007 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.663A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.132A 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 416 through 422 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.830A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.675A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.910A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.703A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.806A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.845A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 4.086A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.777A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.928A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 removed outlier: 3.533A pdb=" N GLU B 988 " --> pdb=" O ASP B 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 989 through 1033 removed outlier: 4.696A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.298A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.533A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 4.035A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.573A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.527A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.140A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 946 through 968 removed outlier: 3.828A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.435A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 28 removed outlier: 4.093A pdb=" N LEU J 27 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER J 28 " --> pdb=" O ASP J 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 24 through 28' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.525A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 removed outlier: 4.046A pdb=" N LYS I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'K' and resid 24 through 28 removed outlier: 4.104A pdb=" N SER K 28 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.153A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 8.785A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.553A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.121A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.938A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.992A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.486A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.486A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.045A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.526A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.549A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.096A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 356 through 358 removed outlier: 5.136A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.589A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.782A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 removed outlier: 5.922A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.663A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.663A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.187A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.620A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.802A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 50 through 55 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 84 through 85 removed outlier: 7.140A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 318 removed outlier: 3.511A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.675A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.623A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.823A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.556A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.743A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1047 through 1048 removed outlier: 4.022A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.986A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL G 109 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA G 88 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 32 through 35 Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.969A pdb=" N SER I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.643A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 43 through 47 removed outlier: 7.109A pdb=" N TRP K 34 " --> pdb=" O VAL K 46 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.071A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.699A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY H 33 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 11 removed outlier: 7.122A pdb=" N VAL L 10 " --> pdb=" O THR L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.873A pdb=" N CYS L 22 " --> pdb=" O ILE L 70 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 45 through 47 removed outlier: 7.123A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 983 hydrogen bonds defined for protein. 2682 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: 10.10 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7384 1.33 - 1.46: 9748 1.46 - 1.59: 15088 1.59 - 1.72: 5 1.72 - 1.84: 171 Bond restraints: 32396 Sorted by residual: bond pdb=" C LYS B 986 " pdb=" N VAL B 987 " ideal model delta sigma weight residual 1.335 1.454 -0.119 1.09e-02 8.42e+03 1.19e+02 bond pdb=" C LYS C 986 " pdb=" N VAL C 987 " ideal model delta sigma weight residual 1.335 1.446 -0.111 1.21e-02 6.83e+03 8.38e+01 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.519 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" N VAL B 289 " pdb=" CA VAL B 289 " ideal model delta sigma weight residual 1.459 1.522 -0.063 1.22e-02 6.72e+03 2.70e+01 ... (remaining 32391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 43069 4.22 - 8.44: 905 8.44 - 12.66: 93 12.66 - 16.88: 13 16.88 - 21.10: 2 Bond angle restraints: 44082 Sorted by residual: angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 121.14 -7.34 1.00e+00 1.00e+00 5.38e+01 angle pdb=" CA VAL B 42 " pdb=" CB VAL B 42 " pdb=" CG1 VAL B 42 " ideal model delta sigma weight residual 110.40 122.57 -12.17 1.70e+00 3.46e-01 5.12e+01 angle pdb=" CG1 ILE A 624 " pdb=" CB ILE A 624 " pdb=" CG2 ILE A 624 " ideal model delta sigma weight residual 110.70 89.60 21.10 3.00e+00 1.11e-01 4.95e+01 angle pdb=" N LYS C 986 " pdb=" CA LYS C 986 " pdb=" C LYS C 986 " ideal model delta sigma weight residual 111.71 119.41 -7.70 1.15e+00 7.56e-01 4.49e+01 angle pdb=" C GLY B 744 " pdb=" N ASP B 745 " pdb=" CA ASP B 745 " ideal model delta sigma weight residual 122.08 131.59 -9.51 1.47e+00 4.63e-01 4.18e+01 ... (remaining 44077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 18178 21.14 - 42.29: 1415 42.29 - 63.43: 199 63.43 - 84.57: 89 84.57 - 105.72: 60 Dihedral angle restraints: 19941 sinusoidal: 8455 harmonic: 11486 Sorted by residual: dihedral pdb=" CA ASP C 294 " pdb=" C ASP C 294 " pdb=" N PRO C 295 " pdb=" CA PRO C 295 " ideal model delta harmonic sigma weight residual -180.00 -120.07 -59.93 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA LEU C 293 " pdb=" C LEU C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 123.97 56.03 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA ASP A 290 " pdb=" C ASP A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta harmonic sigma weight residual -180.00 -124.36 -55.64 0 5.00e+00 4.00e-02 1.24e+02 ... (remaining 19938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4813 0.149 - 0.299: 261 0.299 - 0.448: 34 0.448 - 0.598: 12 0.598 - 0.747: 2 Chirality restraints: 5122 Sorted by residual: chirality pdb=" CB ILE B 119 " pdb=" CA ILE B 119 " pdb=" CG1 ILE B 119 " pdb=" CG2 ILE B 119 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CB VAL K 74 " pdb=" CA VAL K 74 " pdb=" CG1 VAL K 74 " pdb=" CG2 VAL K 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" CB ILE C 794 " pdb=" CA ILE C 794 " pdb=" CG1 ILE C 794 " pdb=" CG2 ILE C 794 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.19e+00 ... (remaining 5119 not shown) Planarity restraints: 5643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 285 " 0.034 2.00e-02 2.50e+03 7.10e-02 5.04e+01 pdb=" C ILE B 285 " -0.123 2.00e-02 2.50e+03 pdb=" O ILE B 285 " 0.049 2.00e-02 2.50e+03 pdb=" N THR B 286 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 855 " -0.021 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C PHE B 855 " 0.076 2.00e-02 2.50e+03 pdb=" O PHE B 855 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN B 856 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 42 " -0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C VAL B 42 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL B 42 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 43 " -0.024 2.00e-02 2.50e+03 ... (remaining 5640 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8818 2.80 - 3.33: 26603 3.33 - 3.85: 59817 3.85 - 4.38: 62986 4.38 - 4.90: 105580 Nonbonded interactions: 263804 Sorted by model distance: nonbonded pdb=" O LEU B 276 " pdb=" N ALA B 288 " model vdw 2.280 3.120 nonbonded pdb=" O PHE L 61 " pdb=" OG1 THR L 73 " model vdw 2.294 3.040 nonbonded pdb=" NE2 GLN H 81 " pdb=" OG1 THR H 82A" model vdw 2.315 3.120 nonbonded pdb=" O LEU C 877 " pdb=" OG1 THR C 881 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR A 396 " pdb=" O ILE B 231 " model vdw 2.334 3.040 ... (remaining 263799 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 828 or resid 851 or resid 855 through 1309)) selection = (chain 'B' and (resid 14 through 828 or resid 840 or resid 855 through 1309)) selection = (chain 'C' and (resid 14 through 828 or resid 851 or resid 855 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 9.010 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.010 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.010 0.119 32499 Z= 0.472 Angle : 1.502 21.103 44345 Z= 0.816 Chirality : 0.084 0.747 5122 Planarity : 0.010 0.100 5612 Dihedral : 16.723 105.716 12447 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.50 % Favored : 91.35 % Rotamer: Outliers : 0.23 % Allowed : 1.09 % Favored : 98.68 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.69 % Twisted General : 0.67 % 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: -3.74 (0.11), residues: 3919 helix: -3.23 (0.14), residues: 632 sheet: -1.64 (0.17), residues: 826 loop : -2.71 (0.10), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG C 634 TYR 0.044 0.004 TYR B 204 PHE 0.055 0.004 PHE J 48 TRP 0.046 0.005 TRP K 34 HIS 0.015 0.003 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00959 (32396) covalent geometry : angle 1.46956 (44082) SS BOND : bond 0.00707 ( 46) SS BOND : angle 2.87248 ( 92) hydrogen bonds : bond 0.24563 ( 940) hydrogen bonds : angle 10.57133 ( 2682) link_ALPHA1-3 : bond 0.00384 ( 3) link_ALPHA1-3 : angle 2.53132 ( 9) link_BETA1-2 : bond 0.00786 ( 6) link_BETA1-2 : angle 3.07332 ( 18) link_BETA1-4 : bond 0.01305 ( 11) link_BETA1-4 : angle 4.32555 ( 33) link_BETA1-6 : bond 0.00908 ( 6) link_BETA1-6 : angle 2.81139 ( 18) link_NAG-ASN : bond 0.01417 ( 31) link_NAG-ASN : angle 5.72713 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 650 LEU cc_start: 0.9650 (pt) cc_final: 0.9248 (tp) REVERT: A 740 MET cc_start: 0.9681 (tpt) cc_final: 0.9453 (tpp) REVERT: A 902 MET cc_start: 0.9649 (mmp) cc_final: 0.9430 (mmm) REVERT: A 1029 MET cc_start: 0.9528 (mtm) cc_final: 0.9115 (mtm) REVERT: B 106 PHE cc_start: 0.9358 (m-80) cc_final: 0.9143 (m-80) REVERT: B 117 LEU cc_start: 0.9686 (tp) cc_final: 0.9294 (tp) REVERT: B 740 MET cc_start: 0.9338 (tpt) cc_final: 0.8716 (tpp) REVERT: C 177 MET cc_start: 0.9030 (pmm) cc_final: 0.8822 (pmm) REVERT: C 900 MET cc_start: 0.9681 (mpp) cc_final: 0.9460 (ptp) REVERT: C 1010 GLN cc_start: 0.9664 (tp-100) cc_final: 0.9353 (tp-100) REVERT: G 82 MET cc_start: 0.2979 (ptt) cc_final: 0.2516 (ptt) REVERT: I 18 LEU cc_start: 0.8270 (tp) cc_final: 0.7773 (tt) REVERT: I 100 PHE cc_start: 0.7640 (m-80) cc_final: 0.7168 (m-10) REVERT: H 105 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9138 (pm20) outliers start: 8 outliers final: 2 residues processed: 106 average time/residue: 0.2197 time to fit residues: 38.0050 Evaluate side-chains 68 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 66 HIS A 173 GLN A 824 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN B 146 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1010 GLN B1058 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN I 13 GLN I 73 ASN L 41 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.039219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.028789 restraints weight = 526679.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.029925 restraints weight = 322322.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.030715 restraints weight = 229205.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031265 restraints weight = 177676.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.031645 restraints weight = 147084.684| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32499 Z= 0.153 Angle : 0.741 11.764 44345 Z= 0.379 Chirality : 0.047 0.333 5122 Planarity : 0.006 0.084 5612 Dihedral : 11.841 90.386 5520 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -2.96 (0.12), residues: 3919 helix: -1.39 (0.17), residues: 655 sheet: -1.60 (0.17), residues: 844 loop : -2.36 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 53 TYR 0.019 0.002 TYR A 917 PHE 0.020 0.001 PHE B 833 TRP 0.019 0.002 TRP K 34 HIS 0.005 0.001 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00315 (32396) covalent geometry : angle 0.71195 (44082) SS BOND : bond 0.00323 ( 46) SS BOND : angle 1.47589 ( 92) hydrogen bonds : bond 0.04778 ( 940) hydrogen bonds : angle 7.31426 ( 2682) link_ALPHA1-3 : bond 0.02034 ( 3) link_ALPHA1-3 : angle 2.57956 ( 9) link_BETA1-2 : bond 0.00456 ( 6) link_BETA1-2 : angle 1.17705 ( 18) link_BETA1-4 : bond 0.00901 ( 11) link_BETA1-4 : angle 2.14510 ( 33) link_BETA1-6 : bond 0.00441 ( 6) link_BETA1-6 : angle 3.21618 ( 18) link_NAG-ASN : bond 0.00573 ( 31) link_NAG-ASN : angle 3.83396 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9343 (tpp) cc_final: 0.9137 (tpt) REVERT: A 1019 ARG cc_start: 0.9720 (ppt170) cc_final: 0.9427 (ttp80) REVERT: A 1029 MET cc_start: 0.9285 (mtm) cc_final: 0.8985 (mtm) REVERT: B 117 LEU cc_start: 0.9627 (tp) cc_final: 0.9392 (mm) REVERT: B 194 PHE cc_start: 0.8115 (m-10) cc_final: 0.7910 (m-80) REVERT: B 740 MET cc_start: 0.9173 (tpt) cc_final: 0.8262 (tpp) REVERT: C 118 LEU cc_start: 0.9817 (tt) cc_final: 0.9532 (mp) REVERT: C 1010 GLN cc_start: 0.9498 (tp-100) cc_final: 0.9199 (tp-100) REVERT: C 1050 MET cc_start: 0.9788 (pmm) cc_final: 0.9559 (pmm) REVERT: G 82 MET cc_start: 0.2133 (ptt) cc_final: 0.1749 (ptt) REVERT: I 100 PHE cc_start: 0.7681 (m-80) cc_final: 0.7329 (m-10) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 0.2199 time to fit residues: 33.3727 Evaluate side-chains 62 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 255 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 0.0170 chunk 261 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 361 optimal weight: 50.0000 chunk 257 optimal weight: 0.0060 chunk 49 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 371 optimal weight: 10.0000 overall best weight: 3.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS A1106 GLN B 66 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 935 GLN B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 540 ASN ** C 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 853 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 GLN I 73 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.037146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.027090 restraints weight = 542794.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.028075 restraints weight = 338891.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.028744 restraints weight = 244850.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.029244 restraints weight = 193719.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.029593 restraints weight = 163054.493| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 32499 Z= 0.219 Angle : 0.762 13.447 44345 Z= 0.390 Chirality : 0.046 0.271 5122 Planarity : 0.005 0.079 5612 Dihedral : 10.213 80.195 5520 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.94 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.13 % 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: -2.62 (0.12), residues: 3919 helix: -0.48 (0.19), residues: 657 sheet: -1.80 (0.17), residues: 871 loop : -2.16 (0.11), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 765 TYR 0.023 0.002 TYR C 369 PHE 0.028 0.002 PHE C 238 TRP 0.014 0.002 TRP K 34 HIS 0.007 0.002 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00442 (32396) covalent geometry : angle 0.73506 (44082) SS BOND : bond 0.00448 ( 46) SS BOND : angle 1.53084 ( 92) hydrogen bonds : bond 0.04853 ( 940) hydrogen bonds : angle 6.98985 ( 2682) link_ALPHA1-3 : bond 0.01492 ( 3) link_ALPHA1-3 : angle 1.58126 ( 9) link_BETA1-2 : bond 0.00843 ( 6) link_BETA1-2 : angle 1.39252 ( 18) link_BETA1-4 : bond 0.00613 ( 11) link_BETA1-4 : angle 2.20843 ( 33) link_BETA1-6 : bond 0.00696 ( 6) link_BETA1-6 : angle 2.57457 ( 18) link_NAG-ASN : bond 0.00772 ( 31) link_NAG-ASN : angle 3.85898 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9405 (tpp) cc_final: 0.9193 (tpp) REVERT: A 1019 ARG cc_start: 0.9765 (ppt170) cc_final: 0.9461 (ttp80) REVERT: A 1029 MET cc_start: 0.9375 (mtm) cc_final: 0.9016 (mtm) REVERT: B 117 LEU cc_start: 0.9512 (tp) cc_final: 0.9284 (mm) REVERT: B 194 PHE cc_start: 0.8340 (m-10) cc_final: 0.8123 (m-80) REVERT: B 740 MET cc_start: 0.9287 (tpt) cc_final: 0.8489 (tpp) REVERT: C 118 LEU cc_start: 0.9824 (tt) cc_final: 0.9536 (mp) REVERT: C 177 MET cc_start: 0.8690 (pmm) cc_final: 0.8485 (pmm) REVERT: C 1050 MET cc_start: 0.9782 (pmm) cc_final: 0.9526 (pmm) REVERT: G 82 MET cc_start: 0.2682 (ptt) cc_final: 0.2318 (ptt) REVERT: I 34 MET cc_start: 0.9094 (mpp) cc_final: 0.8567 (mpp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2199 time to fit residues: 30.3958 Evaluate side-chains 59 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 15 optimal weight: 6.9990 chunk 299 optimal weight: 0.4980 chunk 373 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 370 optimal weight: 6.9990 chunk 342 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 355 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A1011 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 448 ASN C 784 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 30 HIS ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.036915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.026989 restraints weight = 538877.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.027972 restraints weight = 334588.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.028594 restraints weight = 240697.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.029116 restraints weight = 190659.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.029465 restraints weight = 160725.237| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 32499 Z= 0.181 Angle : 0.713 12.781 44345 Z= 0.361 Chirality : 0.047 0.418 5122 Planarity : 0.005 0.074 5612 Dihedral : 9.044 67.499 5520 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.37 % Favored : 92.60 % Rotamer: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.05 % 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: -2.41 (0.12), residues: 3919 helix: -0.09 (0.19), residues: 669 sheet: -1.66 (0.17), residues: 836 loop : -2.10 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 53 TYR 0.027 0.002 TYR C 369 PHE 0.027 0.002 PHE A 559 TRP 0.013 0.002 TRP C 436 HIS 0.009 0.001 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.00370 (32396) covalent geometry : angle 0.68454 (44082) SS BOND : bond 0.00275 ( 46) SS BOND : angle 1.46621 ( 92) hydrogen bonds : bond 0.04274 ( 940) hydrogen bonds : angle 6.70206 ( 2682) link_ALPHA1-3 : bond 0.01407 ( 3) link_ALPHA1-3 : angle 1.86683 ( 9) link_BETA1-2 : bond 0.00542 ( 6) link_BETA1-2 : angle 1.20302 ( 18) link_BETA1-4 : bond 0.00544 ( 11) link_BETA1-4 : angle 2.28632 ( 33) link_BETA1-6 : bond 0.00546 ( 6) link_BETA1-6 : angle 2.35979 ( 18) link_NAG-ASN : bond 0.00656 ( 31) link_NAG-ASN : angle 3.82170 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9740 (ppt170) cc_final: 0.9431 (ttp80) REVERT: A 1029 MET cc_start: 0.9274 (mtm) cc_final: 0.8890 (mtm) REVERT: B 117 LEU cc_start: 0.9511 (tp) cc_final: 0.9219 (mm) REVERT: B 740 MET cc_start: 0.9292 (tpt) cc_final: 0.8468 (tpp) REVERT: C 118 LEU cc_start: 0.9816 (tt) cc_final: 0.9464 (mp) REVERT: C 1050 MET cc_start: 0.9777 (pmm) cc_final: 0.9501 (pmm) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.2219 time to fit residues: 31.1428 Evaluate side-chains 57 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 341 optimal weight: 30.0000 chunk 38 optimal weight: 0.6980 chunk 388 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 580 GLN B 703 ASN B 955 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 784 GLN C 787 GLN C 907 ASN C 955 ASN C 992 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.034370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.024829 restraints weight = 565756.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.025750 restraints weight = 363402.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.026372 restraints weight = 267533.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.026808 restraints weight = 214165.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.027064 restraints weight = 182664.350| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 32499 Z= 0.310 Angle : 0.851 14.230 44345 Z= 0.438 Chirality : 0.048 0.334 5122 Planarity : 0.006 0.071 5612 Dihedral : 8.921 59.323 5520 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.54 % Favored : 90.43 % Rotamer: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.11 % 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: -2.64 (0.12), residues: 3919 helix: -0.43 (0.19), residues: 658 sheet: -1.92 (0.17), residues: 801 loop : -2.16 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 53 TYR 0.038 0.003 TYR C 917 PHE 0.027 0.003 PHE A 59 TRP 0.020 0.003 TRP C 104 HIS 0.014 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00625 (32396) covalent geometry : angle 0.82442 (44082) SS BOND : bond 0.00764 ( 46) SS BOND : angle 2.13094 ( 92) hydrogen bonds : bond 0.05043 ( 940) hydrogen bonds : angle 7.21581 ( 2682) link_ALPHA1-3 : bond 0.01594 ( 3) link_ALPHA1-3 : angle 1.51361 ( 9) link_BETA1-2 : bond 0.00843 ( 6) link_BETA1-2 : angle 1.63191 ( 18) link_BETA1-4 : bond 0.00715 ( 11) link_BETA1-4 : angle 2.26177 ( 33) link_BETA1-6 : bond 0.00608 ( 6) link_BETA1-6 : angle 2.35281 ( 18) link_NAG-ASN : bond 0.00918 ( 31) link_NAG-ASN : angle 3.91289 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9734 (ppt170) cc_final: 0.9450 (ttp80) REVERT: A 1029 MET cc_start: 0.9310 (mtm) cc_final: 0.9105 (mtp) REVERT: B 117 LEU cc_start: 0.9570 (tp) cc_final: 0.9296 (mm) REVERT: B 177 MET cc_start: 0.8160 (pmm) cc_final: 0.7952 (pmm) REVERT: B 740 MET cc_start: 0.9408 (tpt) cc_final: 0.8581 (tpp) REVERT: C 118 LEU cc_start: 0.9805 (tt) cc_final: 0.9435 (mp) REVERT: C 177 MET cc_start: 0.8664 (pmm) cc_final: 0.8406 (pmm) REVERT: C 1050 MET cc_start: 0.9762 (pmm) cc_final: 0.9454 (pmm) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1994 time to fit residues: 25.5270 Evaluate side-chains 58 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 356 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 353 optimal weight: 0.2980 chunk 69 optimal weight: 8.9990 chunk 384 optimal weight: 6.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1106 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 992 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.035434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.025880 restraints weight = 548411.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.026829 restraints weight = 343358.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.027468 restraints weight = 248377.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.027913 restraints weight = 196426.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.028242 restraints weight = 165250.439| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 32499 Z= 0.185 Angle : 0.723 12.878 44345 Z= 0.367 Chirality : 0.048 0.471 5122 Planarity : 0.005 0.059 5612 Dihedral : 8.510 59.287 5520 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.09 % Favored : 91.89 % Rotamer: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.46 (0.13), residues: 3919 helix: 0.06 (0.20), residues: 668 sheet: -1.89 (0.17), residues: 787 loop : -2.12 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 71 TYR 0.026 0.002 TYR B 38 PHE 0.030 0.002 PHE A 559 TRP 0.037 0.002 TRP G 52 HIS 0.007 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00381 (32396) covalent geometry : angle 0.69593 (44082) SS BOND : bond 0.00348 ( 46) SS BOND : angle 1.71206 ( 92) hydrogen bonds : bond 0.04229 ( 940) hydrogen bonds : angle 6.83501 ( 2682) link_ALPHA1-3 : bond 0.01337 ( 3) link_ALPHA1-3 : angle 1.68682 ( 9) link_BETA1-2 : bond 0.00561 ( 6) link_BETA1-2 : angle 1.28980 ( 18) link_BETA1-4 : bond 0.00602 ( 11) link_BETA1-4 : angle 2.14930 ( 33) link_BETA1-6 : bond 0.00530 ( 6) link_BETA1-6 : angle 2.14665 ( 18) link_NAG-ASN : bond 0.00599 ( 31) link_NAG-ASN : angle 3.72841 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9713 (ppt170) cc_final: 0.9445 (ttp80) REVERT: A 1029 MET cc_start: 0.9256 (mtm) cc_final: 0.8868 (mtm) REVERT: B 106 PHE cc_start: 0.9100 (m-80) cc_final: 0.8824 (m-80) REVERT: B 117 LEU cc_start: 0.9482 (tp) cc_final: 0.9020 (tp) REVERT: B 697 MET cc_start: 0.9193 (tpt) cc_final: 0.8855 (tpp) REVERT: B 740 MET cc_start: 0.9376 (tpt) cc_final: 0.8508 (tpp) REVERT: B 869 MET cc_start: 0.9528 (mtp) cc_final: 0.9326 (mtp) REVERT: C 118 LEU cc_start: 0.9810 (tt) cc_final: 0.9411 (mp) REVERT: C 177 MET cc_start: 0.8634 (pmm) cc_final: 0.8407 (pmm) REVERT: C 1050 MET cc_start: 0.9758 (pmm) cc_final: 0.9410 (pmm) outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.2114 time to fit residues: 28.2629 Evaluate side-chains 58 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 231 optimal weight: 7.9990 chunk 337 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 287 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.034400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.025065 restraints weight = 561537.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.025963 restraints weight = 352758.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.026589 restraints weight = 256090.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.027031 restraints weight = 202983.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.027306 restraints weight = 171557.936| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 32499 Z= 0.233 Angle : 0.758 11.947 44345 Z= 0.388 Chirality : 0.047 0.382 5122 Planarity : 0.005 0.065 5612 Dihedral : 8.291 59.645 5520 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.00 % Favored : 89.97 % Rotamer: Outliers : 0.03 % Allowed : 2.08 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.53 (0.13), residues: 3919 helix: -0.13 (0.20), residues: 677 sheet: -1.89 (0.18), residues: 776 loop : -2.15 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 454 TYR 0.022 0.002 TYR B 38 PHE 0.020 0.002 PHE C 55 TRP 0.025 0.002 TRP G 52 HIS 0.015 0.002 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00482 (32396) covalent geometry : angle 0.73245 (44082) SS BOND : bond 0.00397 ( 46) SS BOND : angle 1.79801 ( 92) hydrogen bonds : bond 0.04413 ( 940) hydrogen bonds : angle 6.96437 ( 2682) link_ALPHA1-3 : bond 0.01498 ( 3) link_ALPHA1-3 : angle 1.51080 ( 9) link_BETA1-2 : bond 0.00723 ( 6) link_BETA1-2 : angle 1.44759 ( 18) link_BETA1-4 : bond 0.00662 ( 11) link_BETA1-4 : angle 2.03972 ( 33) link_BETA1-6 : bond 0.00536 ( 6) link_BETA1-6 : angle 2.13581 ( 18) link_NAG-ASN : bond 0.00695 ( 31) link_NAG-ASN : angle 3.67183 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9724 (ppt170) cc_final: 0.9428 (ttp80) REVERT: A 1029 MET cc_start: 0.9293 (mtm) cc_final: 0.9052 (mtp) REVERT: B 117 LEU cc_start: 0.9574 (tp) cc_final: 0.9342 (mm) REVERT: B 177 MET cc_start: 0.8152 (pmm) cc_final: 0.7900 (pmm) REVERT: B 740 MET cc_start: 0.9418 (tpt) cc_final: 0.8569 (tpp) REVERT: C 118 LEU cc_start: 0.9803 (tt) cc_final: 0.9457 (mp) REVERT: C 177 MET cc_start: 0.8603 (pmm) cc_final: 0.8388 (pmm) REVERT: C 1050 MET cc_start: 0.9753 (pmm) cc_final: 0.9413 (pmm) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.1938 time to fit residues: 23.7755 Evaluate side-chains 56 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 42 optimal weight: 7.9990 chunk 361 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 297 optimal weight: 0.9990 chunk 324 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 613 GLN C1023 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1119 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.033366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.024388 restraints weight = 572591.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.025167 restraints weight = 360984.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.025730 restraints weight = 262350.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.026133 restraints weight = 209268.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.026435 restraints weight = 177415.782| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 32499 Z= 0.266 Angle : 0.810 13.008 44345 Z= 0.414 Chirality : 0.048 0.367 5122 Planarity : 0.005 0.060 5612 Dihedral : 8.310 59.981 5520 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.74 % Favored : 89.23 % Rotamer: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.74 (0.13), residues: 3919 helix: -0.39 (0.19), residues: 670 sheet: -1.99 (0.17), residues: 784 loop : -2.27 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 71 TYR 0.034 0.003 TYR B 38 PHE 0.026 0.002 PHE B 106 TRP 0.043 0.003 TRP K 34 HIS 0.013 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00543 (32396) covalent geometry : angle 0.78295 (44082) SS BOND : bond 0.00430 ( 46) SS BOND : angle 1.88240 ( 92) hydrogen bonds : bond 0.04693 ( 940) hydrogen bonds : angle 7.22620 ( 2682) link_ALPHA1-3 : bond 0.01833 ( 3) link_ALPHA1-3 : angle 1.54813 ( 9) link_BETA1-2 : bond 0.00571 ( 6) link_BETA1-2 : angle 1.58942 ( 18) link_BETA1-4 : bond 0.00749 ( 11) link_BETA1-4 : angle 2.02736 ( 33) link_BETA1-6 : bond 0.00504 ( 6) link_BETA1-6 : angle 2.16764 ( 18) link_NAG-ASN : bond 0.00878 ( 31) link_NAG-ASN : angle 3.95316 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9735 (ppt170) cc_final: 0.9439 (ttp80) REVERT: A 1029 MET cc_start: 0.9255 (mtm) cc_final: 0.9019 (mtp) REVERT: B 106 PHE cc_start: 0.8942 (m-80) cc_final: 0.8675 (m-80) REVERT: B 117 LEU cc_start: 0.9619 (tp) cc_final: 0.9202 (tp) REVERT: B 177 MET cc_start: 0.8046 (pmm) cc_final: 0.7761 (pmm) REVERT: B 697 MET cc_start: 0.9278 (tpt) cc_final: 0.8994 (tpp) REVERT: B 740 MET cc_start: 0.9447 (tpt) cc_final: 0.8591 (tpp) REVERT: B 869 MET cc_start: 0.9470 (mtp) cc_final: 0.9267 (mtp) REVERT: C 118 LEU cc_start: 0.9825 (tt) cc_final: 0.9470 (mp) REVERT: C 177 MET cc_start: 0.8513 (pmm) cc_final: 0.8282 (pmm) REVERT: C 1050 MET cc_start: 0.9751 (pmm) cc_final: 0.9444 (pmm) REVERT: I 34 MET cc_start: 0.9458 (mmp) cc_final: 0.9196 (mmm) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.2166 time to fit residues: 26.6424 Evaluate side-chains 57 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 191 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 254 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 350 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B1010 GLN B1036 GLN C 164 ASN C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.035317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.025994 restraints weight = 550059.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.026984 restraints weight = 334469.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.027657 restraints weight = 235429.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.028118 restraints weight = 182133.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.028460 restraints weight = 151674.267| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32499 Z= 0.137 Angle : 0.707 14.697 44345 Z= 0.355 Chirality : 0.048 0.476 5122 Planarity : 0.005 0.062 5612 Dihedral : 7.846 59.618 5520 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.41 (0.13), residues: 3919 helix: 0.22 (0.20), residues: 678 sheet: -1.86 (0.17), residues: 810 loop : -2.14 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 78 TYR 0.035 0.002 TYR L 31 PHE 0.028 0.002 PHE L 61 TRP 0.032 0.002 TRP K 34 HIS 0.008 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00298 (32396) covalent geometry : angle 0.67847 (44082) SS BOND : bond 0.00336 ( 46) SS BOND : angle 1.76651 ( 92) hydrogen bonds : bond 0.03838 ( 940) hydrogen bonds : angle 6.59689 ( 2682) link_ALPHA1-3 : bond 0.01359 ( 3) link_ALPHA1-3 : angle 1.60989 ( 9) link_BETA1-2 : bond 0.00554 ( 6) link_BETA1-2 : angle 1.34929 ( 18) link_BETA1-4 : bond 0.00624 ( 11) link_BETA1-4 : angle 1.90877 ( 33) link_BETA1-6 : bond 0.00553 ( 6) link_BETA1-6 : angle 1.87333 ( 18) link_NAG-ASN : bond 0.00647 ( 31) link_NAG-ASN : angle 3.76542 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9706 (ppt170) cc_final: 0.9409 (ttp80) REVERT: A 1029 MET cc_start: 0.9251 (mtm) cc_final: 0.8883 (mtm) REVERT: B 117 LEU cc_start: 0.9519 (tp) cc_final: 0.9281 (mm) REVERT: B 177 MET cc_start: 0.7872 (pmm) cc_final: 0.7556 (pmm) REVERT: B 194 PHE cc_start: 0.8732 (m-80) cc_final: 0.8312 (m-80) REVERT: B 697 MET cc_start: 0.9252 (tpt) cc_final: 0.8951 (tpp) REVERT: C 177 MET cc_start: 0.8524 (pmm) cc_final: 0.8322 (pmm) REVERT: C 1050 MET cc_start: 0.9707 (pmm) cc_final: 0.9325 (pmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2096 time to fit residues: 27.7796 Evaluate side-chains 60 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 168 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 384 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 369 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 387 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 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 = 0.3194 r_free = 0.3194 target = 0.034260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.025190 restraints weight = 562679.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.026046 restraints weight = 348102.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.026607 restraints weight = 247298.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.027060 restraints weight = 193508.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.027366 restraints weight = 162303.355| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 32499 Z= 0.182 Angle : 0.716 11.903 44345 Z= 0.364 Chirality : 0.047 0.510 5122 Planarity : 0.005 0.065 5612 Dihedral : 7.848 58.937 5520 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.24 % Favored : 90.74 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.42 (0.13), residues: 3919 helix: 0.13 (0.20), residues: 680 sheet: -1.85 (0.17), residues: 816 loop : -2.13 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 319 TYR 0.028 0.002 TYR B 38 PHE 0.025 0.002 PHE C 275 TRP 0.029 0.002 TRP K 34 HIS 0.009 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00385 (32396) covalent geometry : angle 0.69001 (44082) SS BOND : bond 0.00341 ( 46) SS BOND : angle 1.66742 ( 92) hydrogen bonds : bond 0.03992 ( 940) hydrogen bonds : angle 6.66075 ( 2682) link_ALPHA1-3 : bond 0.01315 ( 3) link_ALPHA1-3 : angle 1.30748 ( 9) link_BETA1-2 : bond 0.00574 ( 6) link_BETA1-2 : angle 1.54405 ( 18) link_BETA1-4 : bond 0.00650 ( 11) link_BETA1-4 : angle 1.83775 ( 33) link_BETA1-6 : bond 0.00494 ( 6) link_BETA1-6 : angle 1.95075 ( 18) link_NAG-ASN : bond 0.00605 ( 31) link_NAG-ASN : angle 3.69650 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7838 Ramachandran restraints generated. 3919 Oldfield, 0 Emsley, 3919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.9729 (ppt170) cc_final: 0.9426 (ttp80) REVERT: A 1029 MET cc_start: 0.9218 (mtm) cc_final: 0.8787 (mtm) REVERT: B 106 PHE cc_start: 0.8959 (m-80) cc_final: 0.8660 (m-80) REVERT: B 117 LEU cc_start: 0.9551 (tp) cc_final: 0.9010 (tp) REVERT: B 177 MET cc_start: 0.8028 (pmm) cc_final: 0.7730 (pmm) REVERT: B 194 PHE cc_start: 0.8655 (m-80) cc_final: 0.8279 (m-80) REVERT: B 697 MET cc_start: 0.9225 (tpt) cc_final: 0.8924 (tpp) REVERT: C 177 MET cc_start: 0.8463 (pmm) cc_final: 0.8221 (pmm) REVERT: C 1050 MET cc_start: 0.9715 (pmm) cc_final: 0.9332 (pmm) REVERT: G 34 MET cc_start: -0.3691 (pmm) cc_final: -0.3913 (pmm) REVERT: I 34 MET cc_start: 0.9377 (mmp) cc_final: 0.9154 (mmm) outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.2095 time to fit residues: 26.4437 Evaluate side-chains 57 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 348 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 171 optimal weight: 0.0060 chunk 92 optimal weight: 3.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 824 ASN A1005 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 613 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.034799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.025703 restraints weight = 545498.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.026555 restraints weight = 337027.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.027167 restraints weight = 238332.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.027601 restraints weight = 185979.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.027836 restraints weight = 155068.352| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32499 Z= 0.147 Angle : 0.678 11.154 44345 Z= 0.343 Chirality : 0.046 0.435 5122 Planarity : 0.004 0.061 5612 Dihedral : 7.707 59.052 5520 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.96 % Favored : 91.02 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.33 (0.13), residues: 3919 helix: 0.33 (0.20), residues: 680 sheet: -1.77 (0.17), residues: 835 loop : -2.12 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 319 TYR 0.026 0.002 TYR B 38 PHE 0.034 0.002 PHE J 61 TRP 0.028 0.002 TRP K 34 HIS 0.009 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00314 (32396) covalent geometry : angle 0.65300 (44082) SS BOND : bond 0.00334 ( 46) SS BOND : angle 1.53915 ( 92) hydrogen bonds : bond 0.03757 ( 940) hydrogen bonds : angle 6.45809 ( 2682) link_ALPHA1-3 : bond 0.01301 ( 3) link_ALPHA1-3 : angle 1.37024 ( 9) link_BETA1-2 : bond 0.00516 ( 6) link_BETA1-2 : angle 1.49134 ( 18) link_BETA1-4 : bond 0.00636 ( 11) link_BETA1-4 : angle 1.79395 ( 33) link_BETA1-6 : bond 0.00477 ( 6) link_BETA1-6 : angle 1.82479 ( 18) link_NAG-ASN : bond 0.00517 ( 31) link_NAG-ASN : angle 3.47411 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.24 seconds wall clock time: 102 minutes 32.07 seconds (6152.07 seconds total)