Starting phenix.real_space_refine on Fri Mar 6 09:31:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6e_23693/03_2026/7m6e_23693_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6e_23693/03_2026/7m6e_23693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m6e_23693/03_2026/7m6e_23693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6e_23693/03_2026/7m6e_23693.map" model { file = "/net/cci-nas-00/data/ceres_data/7m6e_23693/03_2026/7m6e_23693_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6e_23693/03_2026/7m6e_23693_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 138 5.16 5 C 18992 2.51 5 N 4915 2.21 5 O 5751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s 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: 29796 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "E" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 802 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 802 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 802 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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 Time building chain proxies: 6.48, per 1000 atoms: 0.22 Number of scatterers: 29796 At special positions: 0 Unit cell: (145.123, 139.909, 184.228, 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 138 16.00 O 5751 8.00 N 4915 7.00 C 18992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.07 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=2.02 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.07 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=2.02 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.07 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.05 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.02 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=1, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 343 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG D 301 " - " ASN E 343 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 61 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG I 1 " - " ASN B 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 65 sheets defined 21.3% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.753A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.105A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.019A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.544A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.941A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.137A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.753A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.105A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.018A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.544A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.326A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.942A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.137A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.870A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 344 removed outlier: 3.723A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 383 through 390 removed outlier: 4.105A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 409 removed outlier: 4.019A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.544A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.326A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 919 " --> pdb=" O VAL E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 966 removed outlier: 3.942A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 966 " --> pdb=" O LEU E 962 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.137A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.871A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.871A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.527A pdb=" N ASP C 81 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 82 " --> pdb=" O SER C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.527A pdb=" N ASP G 81 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU G 82 " --> pdb=" O SER G 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 78 through 82' Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.527A pdb=" N ASP L 81 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU L 82 " --> pdb=" O SER L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.883A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.457A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.560A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 141 removed outlier: 3.520A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.901A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.344A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.501A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.501A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.816A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.704A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.801A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (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 788 through 790 removed outlier: 6.027A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.883A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.458A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.560A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 141 removed outlier: 3.518A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.901A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.343A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.500A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.500A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.815A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.704A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.771A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.496A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AD7, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.682A pdb=" N ASP D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 51 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.883A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 90 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 96 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 189 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR E 208 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 191 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 206 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.458A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.559A pdb=" N ILE E 105 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 132 through 141 removed outlier: 3.519A pdb=" N GLU E 132 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.900A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 325 through 328 removed outlier: 5.344A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.763A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.763A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.815A pdb=" N TYR E 453 " --> pdb=" O GLN E 493 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.704A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 711 through 713 Processing sheet with id=AF1, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.715A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.495A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.682A pdb=" N ASP F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE F 51 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN F 96 " --> pdb=" O MET F 100H" (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET F 100H" --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 99 through 100 removed outlier: 3.538A pdb=" N SER F 100C" --> pdb=" O ASN F 100 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.494A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AG1, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.682A pdb=" N ASP H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE H 51 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLN H 96 " --> pdb=" O MET H 100H" (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET H 100H" --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AG3, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.514A pdb=" N ALA C 10 " --> pdb=" O THR C 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AG5, first strand: chain 'C' and resid 33 through 37 Processing sheet with id=AG6, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.515A pdb=" N ALA G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'G' and resid 17 through 23 Processing sheet with id=AG8, first strand: chain 'G' and resid 33 through 37 Processing sheet with id=AG9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.515A pdb=" N ALA L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AH2, first strand: chain 'L' and resid 33 through 37 1129 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.46 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 4834 1.30 - 1.45: 9326 1.45 - 1.60: 16170 1.60 - 1.75: 6 1.75 - 1.90: 171 Bond restraints: 30507 Sorted by residual: bond pdb=" C PRO A 295 " pdb=" O PRO A 295 " ideal model delta sigma weight residual 1.238 1.154 0.083 1.24e-02 6.50e+03 4.49e+01 bond pdb=" C PRO E 295 " pdb=" O PRO E 295 " ideal model delta sigma weight residual 1.238 1.156 0.081 1.24e-02 6.50e+03 4.28e+01 bond pdb=" C PRO B 295 " pdb=" O PRO B 295 " ideal model delta sigma weight residual 1.237 1.157 0.080 1.32e-02 5.74e+03 3.66e+01 bond pdb=" C GLN A 935 " pdb=" O GLN A 935 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.15e-02 7.56e+03 1.56e+01 bond pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " ideal model delta sigma weight residual 1.808 1.679 0.129 3.30e-02 9.18e+02 1.54e+01 ... (remaining 30502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.32: 41198 5.32 - 10.64: 345 10.64 - 15.96: 12 15.96 - 21.29: 0 21.29 - 26.61: 1 Bond angle restraints: 41556 Sorted by residual: angle pdb=" C ASN E 343 " pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta sigma weight residual 110.17 83.56 26.61 2.04e+00 2.40e-01 1.70e+02 angle pdb=" C ASN A 343 " pdb=" CA ASN A 343 " pdb=" CB ASN A 343 " ideal model delta sigma weight residual 110.88 98.42 12.46 1.57e+00 4.06e-01 6.30e+01 angle pdb=" CA CYS A 488 " pdb=" CB CYS A 488 " pdb=" SG CYS A 488 " ideal model delta sigma weight residual 114.40 129.42 -15.02 2.30e+00 1.89e-01 4.26e+01 angle pdb=" CA CYS E 488 " pdb=" CB CYS E 488 " pdb=" SG CYS E 488 " ideal model delta sigma weight residual 114.40 129.41 -15.01 2.30e+00 1.89e-01 4.26e+01 angle pdb=" CA TRP D 97 " pdb=" CB TRP D 97 " pdb=" CG TRP D 97 " ideal model delta sigma weight residual 113.60 125.99 -12.39 1.90e+00 2.77e-01 4.25e+01 ... (remaining 41551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17246 17.95 - 35.90: 889 35.90 - 53.84: 256 53.84 - 71.79: 91 71.79 - 89.74: 33 Dihedral angle restraints: 18515 sinusoidal: 7520 harmonic: 10995 Sorted by residual: dihedral pdb=" C ASN E 343 " pdb=" N ASN E 343 " pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta harmonic sigma weight residual -122.60 -90.59 -32.01 0 2.50e+00 1.60e-01 1.64e+02 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -13.46 -72.54 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -13.49 -72.51 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 18512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 4700 0.235 - 0.469: 61 0.469 - 0.704: 1 0.704 - 0.939: 0 0.939 - 1.173: 6 Chirality restraints: 4768 Sorted by residual: chirality pdb=" C1 FUC I 3 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 3 " pdb=" O5 FUC I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.18e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.54e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.44e+01 ... (remaining 4765 not shown) Planarity restraints: 5362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " -0.182 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C7 NAG A1311 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " -0.132 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " 0.252 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.009 2.00e-02 2.50e+03 6.31e-02 4.98e+01 pdb=" CG ASN B 61 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.084 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.009 2.00e-02 2.50e+03 6.28e-02 4.93e+01 pdb=" CG ASN A 61 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.083 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.065 2.00e-02 2.50e+03 ... (remaining 5359 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 288 2.60 - 3.17: 25300 3.17 - 3.75: 45372 3.75 - 4.32: 64312 4.32 - 4.90: 107345 Nonbonded interactions: 242617 Sorted by model distance: nonbonded pdb=" OD2 ASP B 420 " pdb=" OH TYR E 369 " model vdw 2.022 3.040 nonbonded pdb=" OD2 ASP A 420 " pdb=" OH TYR B 369 " model vdw 2.026 3.040 nonbonded pdb=" OD1 ASP D 86 " pdb=" OH TYR D 90 " model vdw 2.034 3.040 nonbonded pdb=" OD1 ASP H 86 " pdb=" OH TYR H 90 " model vdw 2.034 3.040 nonbonded pdb=" OD1 ASP F 86 " pdb=" OH TYR F 90 " model vdw 2.034 3.040 ... (remaining 242612 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 15 through 1310) selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } ncs_group { reference = (chain 'D' and resid 2 through 112) selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.960 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 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 0.158 30591 Z= 0.448 Angle : 1.479 26.915 41757 Z= 0.828 Chirality : 0.087 1.173 4768 Planarity : 0.010 0.153 5329 Dihedral : 13.076 89.741 11321 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 1.03 % Allowed : 1.21 % Favored : 97.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 3735 helix: 0.43 (0.18), residues: 618 sheet: -0.17 (0.16), residues: 900 loop : -0.55 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.003 ARG L 78 TYR 0.084 0.005 TYR H 52 PHE 0.079 0.006 PHE B 497 TRP 0.077 0.006 TRP F 97 HIS 0.017 0.003 HIS D 100D Details of bonding type rmsd covalent geometry : bond 0.00960 (30507) covalent geometry : angle 1.36747 (41556) SS BOND : bond 0.01196 ( 48) SS BOND : angle 5.12953 ( 96) hydrogen bonds : bond 0.17545 ( 1098) hydrogen bonds : angle 8.91987 ( 3060) Misc. bond : bond 0.08628 ( 1) link_BETA1-4 : bond 0.00455 ( 1) link_BETA1-4 : angle 3.44235 ( 3) link_BETA1-6 : bond 0.00020 ( 1) link_BETA1-6 : angle 1.98128 ( 3) link_NAG-ASN : bond 0.02911 ( 33) link_NAG-ASN : angle 10.54937 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 582 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7494 (t60) cc_final: 0.6792 (t60) REVERT: A 187 LYS cc_start: 0.6448 (mmtt) cc_final: 0.6231 (tppt) REVERT: A 274 THR cc_start: 0.7463 (p) cc_final: 0.6401 (p) REVERT: A 360 ASN cc_start: 0.7481 (t0) cc_final: 0.7209 (t0) REVERT: A 373 SER cc_start: 0.8279 (p) cc_final: 0.8072 (p) REVERT: A 396 TYR cc_start: 0.7940 (m-80) cc_final: 0.7519 (m-80) REVERT: A 449 TYR cc_start: 0.6375 (m-10) cc_final: 0.6068 (m-10) REVERT: B 64 TRP cc_start: 0.7371 (t60) cc_final: 0.6932 (t60) REVERT: B 274 THR cc_start: 0.7574 (p) cc_final: 0.6618 (p) REVERT: B 437 ASN cc_start: 0.8586 (t0) cc_final: 0.8370 (t0) REVERT: B 858 LEU cc_start: 0.8821 (mp) cc_final: 0.8608 (mp) REVERT: B 900 MET cc_start: 0.5846 (mtp) cc_final: 0.5428 (mtp) REVERT: B 933 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7766 (mtpt) REVERT: B 994 ASP cc_start: 0.7878 (t0) cc_final: 0.7670 (t0) REVERT: B 1108 ASN cc_start: 0.7647 (m-40) cc_final: 0.7348 (m-40) REVERT: D 100 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6709 (t-90) REVERT: E 105 ILE cc_start: 0.6185 (mp) cc_final: 0.5977 (pt) REVERT: E 177 MET cc_start: 0.0802 (mpp) cc_final: 0.0591 (mpp) REVERT: E 274 THR cc_start: 0.7532 (p) cc_final: 0.6521 (p) REVERT: E 347 PHE cc_start: 0.6936 (m-10) cc_final: 0.6237 (m-80) REVERT: E 923 ILE cc_start: 0.6895 (tt) cc_final: 0.6659 (tt) REVERT: E 933 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7629 (mtpt) REVERT: E 960 ASN cc_start: 0.8488 (t0) cc_final: 0.8211 (t0) REVERT: F 94 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7841 (ptt-90) REVERT: F 101 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7259 (p0) REVERT: H 46 GLU cc_start: 0.6329 (mp0) cc_final: 0.5683 (mp0) REVERT: C 29 SER cc_start: 0.5469 (p) cc_final: 0.4858 (t) REVERT: G 82 GLU cc_start: 0.4153 (OUTLIER) cc_final: 0.3163 (pp20) REVERT: L 29 SER cc_start: 0.4845 (p) cc_final: 0.4303 (t) outliers start: 33 outliers final: 9 residues processed: 604 average time/residue: 0.1653 time to fit residues: 165.5970 Evaluate side-chains 425 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 411 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain E residue 933 LYS Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 196 ASN A 394 ASN A 498 GLN A 606 ASN A 777 ASN A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 52 GLN B 196 ASN B 370 ASN B 394 ASN B 498 GLN B 606 ASN B 777 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1011 GLN E 52 GLN E 196 ASN E 394 ASN E 498 GLN E 777 ASN E 901 GLN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1011 GLN C 36 GLN G 36 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.188325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.151437 restraints weight = 46869.907| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.96 r_work: 0.3752 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30591 Z= 0.173 Angle : 0.774 18.076 41757 Z= 0.389 Chirality : 0.054 0.807 4768 Planarity : 0.005 0.058 5329 Dihedral : 7.626 78.268 4838 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.37 % Allowed : 7.79 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3735 helix: 1.04 (0.19), residues: 627 sheet: 0.10 (0.15), residues: 954 loop : -0.56 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 509 TYR 0.018 0.002 TYR B1067 PHE 0.027 0.002 PHE B 168 TRP 0.050 0.003 TRP D 97 HIS 0.010 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00385 (30507) covalent geometry : angle 0.71960 (41556) SS BOND : bond 0.00403 ( 48) SS BOND : angle 2.06261 ( 96) hydrogen bonds : bond 0.05199 ( 1098) hydrogen bonds : angle 7.02854 ( 3060) Misc. bond : bond 0.00525 ( 1) link_BETA1-4 : bond 0.00113 ( 1) link_BETA1-4 : angle 1.18267 ( 3) link_BETA1-6 : bond 0.00824 ( 1) link_BETA1-6 : angle 1.98109 ( 3) link_NAG-ASN : bond 0.00735 ( 33) link_NAG-ASN : angle 5.57649 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 507 time to evaluate : 0.734 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 32 PHE cc_start: 0.7446 (m-10) cc_final: 0.7198 (m-10) REVERT: A 44 ARG cc_start: 0.8156 (ptp90) cc_final: 0.7865 (mtt180) REVERT: A 202 LYS cc_start: 0.6642 (tttm) cc_final: 0.6395 (tptm) REVERT: A 326 ILE cc_start: 0.8166 (mm) cc_final: 0.7731 (pt) REVERT: A 329 PHE cc_start: 0.7493 (m-10) cc_final: 0.7286 (m-10) REVERT: A 347 PHE cc_start: 0.7600 (m-10) cc_final: 0.7293 (m-80) REVERT: A 353 TRP cc_start: 0.8427 (p-90) cc_final: 0.7852 (p-90) REVERT: A 373 SER cc_start: 0.8590 (p) cc_final: 0.8366 (p) REVERT: A 396 TYR cc_start: 0.8435 (m-80) cc_final: 0.7675 (m-80) REVERT: A 794 ILE cc_start: 0.8687 (mm) cc_final: 0.8366 (tt) REVERT: B 32 PHE cc_start: 0.7355 (m-10) cc_final: 0.7065 (m-10) REVERT: B 64 TRP cc_start: 0.7370 (t60) cc_final: 0.6398 (t60) REVERT: B 437 ASN cc_start: 0.8968 (t0) cc_final: 0.8764 (t0) REVERT: B 472 ILE cc_start: 0.7245 (mm) cc_final: 0.6998 (mm) REVERT: B 777 ASN cc_start: 0.6928 (m-40) cc_final: 0.6661 (m110) REVERT: B 900 MET cc_start: 0.5791 (mtp) cc_final: 0.5094 (mtp) REVERT: B 902 MET cc_start: 0.8177 (tpt) cc_final: 0.7562 (tpt) REVERT: B 933 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7533 (mmtm) REVERT: B 994 ASP cc_start: 0.8201 (t0) cc_final: 0.7806 (t0) REVERT: B 1108 ASN cc_start: 0.7990 (m-40) cc_final: 0.7564 (t0) REVERT: E 32 PHE cc_start: 0.7530 (m-10) cc_final: 0.7260 (m-10) REVERT: E 44 ARG cc_start: 0.8232 (ptp90) cc_final: 0.7684 (mtt180) REVERT: E 177 MET cc_start: 0.2055 (mpp) cc_final: 0.1789 (mpp) REVERT: E 332 ILE cc_start: 0.7988 (mt) cc_final: 0.7649 (mm) REVERT: E 353 TRP cc_start: 0.8472 (p-90) cc_final: 0.7844 (p-90) REVERT: H 86 ASP cc_start: 0.6240 (OUTLIER) cc_final: 0.5728 (t0) REVERT: H 107 THR cc_start: 0.6482 (m) cc_final: 0.6126 (m) REVERT: L 6 GLN cc_start: 0.6888 (mt0) cc_final: 0.6685 (mt0) REVERT: L 29 SER cc_start: 0.5086 (p) cc_final: 0.4865 (p) REVERT: L 82 GLU cc_start: 0.3163 (mm-30) cc_final: 0.2781 (pp20) outliers start: 76 outliers final: 46 residues processed: 547 average time/residue: 0.1680 time to fit residues: 152.2437 Evaluate side-chains 458 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 410 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 737 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 96 optimal weight: 0.0670 chunk 205 optimal weight: 4.9990 chunk 212 optimal weight: 0.0970 chunk 316 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 0.0000 chunk 369 optimal weight: 7.9990 chunk 362 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 394 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 498 GLN B 901 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 394 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN C 36 GLN L 36 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.191619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.159915 restraints weight = 45551.436| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.44 r_work: 0.3830 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30591 Z= 0.132 Angle : 0.674 15.528 41757 Z= 0.336 Chirality : 0.049 0.630 4768 Planarity : 0.004 0.045 5329 Dihedral : 6.822 54.431 4811 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.34 % Allowed : 10.93 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 3735 helix: 1.52 (0.20), residues: 606 sheet: 0.05 (0.15), residues: 996 loop : -0.49 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 94 TYR 0.018 0.002 TYR C 33 PHE 0.024 0.002 PHE E 168 TRP 0.035 0.002 TRP H 97 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00284 (30507) covalent geometry : angle 0.63174 (41556) SS BOND : bond 0.00523 ( 48) SS BOND : angle 1.35159 ( 96) hydrogen bonds : bond 0.04716 ( 1098) hydrogen bonds : angle 6.44646 ( 3060) Misc. bond : bond 0.00896 ( 1) link_BETA1-4 : bond 0.00900 ( 1) link_BETA1-4 : angle 1.11182 ( 3) link_BETA1-6 : bond 0.00475 ( 1) link_BETA1-6 : angle 1.16704 ( 3) link_NAG-ASN : bond 0.00732 ( 33) link_NAG-ASN : angle 4.73845 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 474 time to evaluate : 1.045 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 44 ARG cc_start: 0.8316 (ptp90) cc_final: 0.7882 (mtt90) REVERT: A 160 TYR cc_start: 0.6135 (p90) cc_final: 0.5912 (p90) REVERT: A 187 LYS cc_start: 0.6634 (mmtt) cc_final: 0.6386 (mmtp) REVERT: A 326 ILE cc_start: 0.8475 (mm) cc_final: 0.8139 (pt) REVERT: A 347 PHE cc_start: 0.7619 (m-10) cc_final: 0.7245 (m-80) REVERT: A 357 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7729 (ptm-80) REVERT: A 373 SER cc_start: 0.8500 (p) cc_final: 0.8288 (p) REVERT: A 396 TYR cc_start: 0.8613 (m-80) cc_final: 0.8115 (m-80) REVERT: B 32 PHE cc_start: 0.7530 (m-80) cc_final: 0.7295 (m-10) REVERT: B 44 ARG cc_start: 0.8537 (ptp90) cc_final: 0.8134 (mtt180) REVERT: B 360 ASN cc_start: 0.7493 (t0) cc_final: 0.7106 (t0) REVERT: B 902 MET cc_start: 0.8283 (tpt) cc_final: 0.7773 (tpt) REVERT: B 994 ASP cc_start: 0.8386 (t0) cc_final: 0.8021 (t0) REVERT: B 1108 ASN cc_start: 0.7696 (m-40) cc_final: 0.7450 (t0) REVERT: D 94 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8506 (ptt-90) REVERT: E 32 PHE cc_start: 0.7596 (m-80) cc_final: 0.7393 (m-10) REVERT: E 44 ARG cc_start: 0.8363 (ptp90) cc_final: 0.8006 (mtt90) REVERT: E 321 GLN cc_start: 0.8256 (mm-40) cc_final: 0.8026 (mm-40) REVERT: E 332 ILE cc_start: 0.7993 (mt) cc_final: 0.7681 (mm) REVERT: E 497 PHE cc_start: 0.6982 (m-80) cc_final: 0.6775 (m-10) REVERT: H 46 GLU cc_start: 0.6490 (mp0) cc_final: 0.6047 (mp0) REVERT: H 100 MET cc_start: 0.8469 (mtt) cc_final: 0.8247 (mtt) REVERT: C 16 GLN cc_start: 0.7560 (tp40) cc_final: 0.7324 (tp40) REVERT: C 86 TYR cc_start: 0.7525 (m-80) cc_final: 0.7259 (m-80) REVERT: G 6 GLN cc_start: 0.7008 (mt0) cc_final: 0.6650 (mt0) REVERT: G 68 THR cc_start: 0.7818 (p) cc_final: 0.7451 (t) REVERT: L 55 SER cc_start: 0.6137 (m) cc_final: 0.5772 (p) REVERT: L 82 GLU cc_start: 0.3428 (mm-30) cc_final: 0.2811 (pp20) outliers start: 75 outliers final: 49 residues processed: 517 average time/residue: 0.1668 time to fit residues: 142.5858 Evaluate side-chains 467 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 417 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 439 ASN Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain L residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 19 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 196 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 907 ASN B 913 GLN D 6 GLN E 52 GLN E 115 GLN E 196 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN E 913 GLN ** E1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN C 36 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.184310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148908 restraints weight = 45016.342| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.44 r_work: 0.3692 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30591 Z= 0.229 Angle : 0.726 12.688 41757 Z= 0.367 Chirality : 0.051 0.568 4768 Planarity : 0.005 0.052 5329 Dihedral : 6.709 54.172 4807 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.74 % Allowed : 11.43 % Favored : 84.83 % 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: -0.46 (0.13), residues: 3735 helix: 1.03 (0.20), residues: 618 sheet: -0.15 (0.15), residues: 996 loop : -0.75 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 509 TYR 0.024 0.002 TYR D 91 PHE 0.022 0.002 PHE H 100F TRP 0.036 0.002 TRP H 97 HIS 0.009 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00527 (30507) covalent geometry : angle 0.69037 (41556) SS BOND : bond 0.00627 ( 48) SS BOND : angle 1.75534 ( 96) hydrogen bonds : bond 0.04837 ( 1098) hydrogen bonds : angle 6.36764 ( 3060) Misc. bond : bond 0.00703 ( 1) link_BETA1-4 : bond 0.00177 ( 1) link_BETA1-4 : angle 1.39239 ( 3) link_BETA1-6 : bond 0.00655 ( 1) link_BETA1-6 : angle 1.53904 ( 3) link_NAG-ASN : bond 0.00683 ( 33) link_NAG-ASN : angle 4.38951 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 399 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0619 (mmt) cc_final: -0.1331 (tmm) REVERT: A 160 TYR cc_start: 0.5967 (p90) cc_final: 0.5758 (p90) REVERT: A 326 ILE cc_start: 0.8528 (mm) cc_final: 0.8249 (pt) REVERT: A 347 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: A 357 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7820 (ptm-80) REVERT: A 396 TYR cc_start: 0.8727 (m-80) cc_final: 0.8106 (m-80) REVERT: A 529 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7830 (tptt) REVERT: A 796 ASP cc_start: 0.6661 (t0) cc_final: 0.6168 (p0) REVERT: B 32 PHE cc_start: 0.7599 (m-80) cc_final: 0.7353 (m-10) REVERT: B 238 PHE cc_start: 0.3575 (OUTLIER) cc_final: 0.2884 (p90) REVERT: B 326 ILE cc_start: 0.8513 (mm) cc_final: 0.8276 (pt) REVERT: B 529 LYS cc_start: 0.8214 (ptmt) cc_final: 0.7907 (tptt) REVERT: B 574 ASP cc_start: 0.7414 (p0) cc_final: 0.6409 (t70) REVERT: B 796 ASP cc_start: 0.6342 (t0) cc_final: 0.5743 (p0) REVERT: B 900 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5660 (mtp) REVERT: B 902 MET cc_start: 0.8369 (tpt) cc_final: 0.7888 (tpt) REVERT: B 994 ASP cc_start: 0.8595 (t0) cc_final: 0.8193 (t0) REVERT: D 59 TYR cc_start: 0.8113 (m-80) cc_final: 0.7764 (m-80) REVERT: D 94 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8505 (ptt-90) REVERT: E 32 PHE cc_start: 0.7689 (m-80) cc_final: 0.7465 (m-10) REVERT: E 332 ILE cc_start: 0.8174 (mt) cc_final: 0.7825 (mm) REVERT: E 345 THR cc_start: 0.7932 (t) cc_final: 0.7705 (t) REVERT: E 529 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7799 (tttp) REVERT: E 796 ASP cc_start: 0.6424 (t0) cc_final: 0.5816 (p0) REVERT: E 994 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8322 (m-30) REVERT: F 46 GLU cc_start: 0.6384 (mp0) cc_final: 0.6145 (mp0) REVERT: H 46 GLU cc_start: 0.6773 (mp0) cc_final: 0.6556 (mp0) REVERT: H 86 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.6251 (t0) REVERT: H 89 MET cc_start: 0.7160 (tpt) cc_final: 0.6951 (tpt) REVERT: H 100 MET cc_start: 0.8485 (mtt) cc_final: 0.8278 (mtt) REVERT: C 82 GLU cc_start: 0.3458 (mm-30) cc_final: 0.2841 (pp20) REVERT: C 86 TYR cc_start: 0.7838 (m-80) cc_final: 0.7638 (m-80) REVERT: G 68 THR cc_start: 0.8017 (p) cc_final: 0.7605 (t) REVERT: L 46 PHE cc_start: 0.8294 (t80) cc_final: 0.7936 (t80) REVERT: L 55 SER cc_start: 0.6239 (m) cc_final: 0.5822 (p) REVERT: L 82 GLU cc_start: 0.3628 (mm-30) cc_final: 0.3121 (pp20) outliers start: 120 outliers final: 84 residues processed: 473 average time/residue: 0.1656 time to fit residues: 130.7053 Evaluate side-chains 459 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 369 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 994 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 290 optimal weight: 0.9980 chunk 200 optimal weight: 0.3980 chunk 300 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN A1134 ASN B 115 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1036 GLN E1134 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN G 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.185590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.152720 restraints weight = 45753.481| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.56 r_work: 0.3735 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30591 Z= 0.138 Angle : 0.649 12.101 41757 Z= 0.323 Chirality : 0.048 0.505 4768 Planarity : 0.004 0.047 5329 Dihedral : 6.409 58.427 4806 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 3.02 % Allowed : 12.52 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3735 helix: 1.44 (0.20), residues: 606 sheet: -0.19 (0.15), residues: 1008 loop : -0.64 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 78 TYR 0.019 0.002 TYR D 52 PHE 0.017 0.001 PHE A 168 TRP 0.035 0.002 TRP H 97 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00306 (30507) covalent geometry : angle 0.61107 (41556) SS BOND : bond 0.00374 ( 48) SS BOND : angle 1.79030 ( 96) hydrogen bonds : bond 0.04338 ( 1098) hydrogen bonds : angle 6.08726 ( 3060) Misc. bond : bond 0.00503 ( 1) link_BETA1-4 : bond 0.00714 ( 1) link_BETA1-4 : angle 1.16878 ( 3) link_BETA1-6 : bond 0.00174 ( 1) link_BETA1-6 : angle 1.22476 ( 3) link_NAG-ASN : bond 0.00565 ( 33) link_NAG-ASN : angle 4.18117 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 411 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0668 (mmt) cc_final: -0.1216 (tmm) REVERT: A 160 TYR cc_start: 0.6049 (p90) cc_final: 0.5837 (p90) REVERT: A 326 ILE cc_start: 0.8638 (mm) cc_final: 0.8287 (pt) REVERT: A 347 PHE cc_start: 0.7845 (m-10) cc_final: 0.7519 (m-80) REVERT: A 396 TYR cc_start: 0.8689 (m-80) cc_final: 0.8080 (m-80) REVERT: A 498 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7754 (tm130) REVERT: A 529 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7794 (tptt) REVERT: A 697 MET cc_start: 0.7645 (ptm) cc_final: 0.6859 (ttt) REVERT: A 794 ILE cc_start: 0.8683 (mm) cc_final: 0.8411 (tt) REVERT: A 796 ASP cc_start: 0.6599 (t0) cc_final: 0.5933 (p0) REVERT: B 32 PHE cc_start: 0.7569 (m-80) cc_final: 0.7265 (m-10) REVERT: B 177 MET cc_start: 0.2526 (mpp) cc_final: 0.2080 (mpp) REVERT: B 238 PHE cc_start: 0.3174 (OUTLIER) cc_final: 0.2583 (p90) REVERT: B 326 ILE cc_start: 0.8500 (mm) cc_final: 0.8275 (pt) REVERT: B 529 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7863 (tptt) REVERT: B 796 ASP cc_start: 0.6245 (t0) cc_final: 0.5632 (p0) REVERT: B 900 MET cc_start: 0.5788 (OUTLIER) cc_final: 0.5336 (mtp) REVERT: B 902 MET cc_start: 0.8329 (tpt) cc_final: 0.7839 (tpt) REVERT: B 994 ASP cc_start: 0.8492 (t0) cc_final: 0.8079 (t0) REVERT: D 6 GLN cc_start: 0.5710 (pt0) cc_final: 0.5149 (pt0) REVERT: D 94 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8334 (ptt-90) REVERT: D 103 TRP cc_start: 0.8274 (m100) cc_final: 0.7263 (m100) REVERT: E 32 PHE cc_start: 0.7590 (m-80) cc_final: 0.7336 (m-10) REVERT: E 332 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7815 (mm) REVERT: E 345 THR cc_start: 0.8009 (t) cc_final: 0.7793 (t) REVERT: E 529 LYS cc_start: 0.8128 (ptmt) cc_final: 0.7745 (tttp) REVERT: E 796 ASP cc_start: 0.6229 (t0) cc_final: 0.5614 (p0) REVERT: F 46 GLU cc_start: 0.6332 (mp0) cc_final: 0.6103 (mp0) REVERT: H 46 GLU cc_start: 0.6733 (mp0) cc_final: 0.6450 (mp0) REVERT: H 86 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6173 (t0) REVERT: H 89 MET cc_start: 0.7137 (tpt) cc_final: 0.6913 (tpt) REVERT: C 46 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.6706 (t80) REVERT: G 6 GLN cc_start: 0.7459 (mt0) cc_final: 0.6861 (mt0) REVERT: G 68 THR cc_start: 0.7953 (p) cc_final: 0.7589 (t) REVERT: L 46 PHE cc_start: 0.8201 (t80) cc_final: 0.7980 (t80) REVERT: L 55 SER cc_start: 0.6211 (m) cc_final: 0.5879 (p) REVERT: L 82 GLU cc_start: 0.3314 (mm-30) cc_final: 0.2937 (pp20) outliers start: 97 outliers final: 70 residues processed: 469 average time/residue: 0.1658 time to fit residues: 129.4975 Evaluate side-chains 456 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 379 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 170 optimal weight: 5.9990 chunk 329 optimal weight: 0.0870 chunk 107 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 178 optimal weight: 0.1980 chunk 335 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 185 optimal weight: 0.0980 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 317 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1036 GLN A1108 ASN B 137 ASN B 493 GLN B1036 GLN E 137 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN C 36 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.187670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153993 restraints weight = 45378.005| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.41 r_work: 0.3773 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30591 Z= 0.117 Angle : 0.611 11.246 41757 Z= 0.305 Chirality : 0.047 0.458 4768 Planarity : 0.004 0.039 5329 Dihedral : 6.102 59.432 4806 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 3.21 % Allowed : 13.08 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 3735 helix: 1.68 (0.20), residues: 606 sheet: -0.11 (0.15), residues: 999 loop : -0.64 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.018 0.001 TYR B1047 PHE 0.019 0.001 PHE G 46 TRP 0.025 0.002 TRP F 103 HIS 0.005 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (30507) covalent geometry : angle 0.57894 (41556) SS BOND : bond 0.00339 ( 48) SS BOND : angle 1.67101 ( 96) hydrogen bonds : bond 0.04038 ( 1098) hydrogen bonds : angle 5.86424 ( 3060) Misc. bond : bond 0.00389 ( 1) link_BETA1-4 : bond 0.00561 ( 1) link_BETA1-4 : angle 1.00246 ( 3) link_BETA1-6 : bond 0.00277 ( 1) link_BETA1-6 : angle 1.27560 ( 3) link_NAG-ASN : bond 0.00531 ( 33) link_NAG-ASN : angle 3.74304 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 400 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8368 (ptp90) cc_final: 0.8083 (mtt180) REVERT: A 153 MET cc_start: 0.0731 (mmt) cc_final: -0.1158 (tmm) REVERT: A 187 LYS cc_start: 0.6598 (mmtt) cc_final: 0.6342 (mmtp) REVERT: A 271 GLN cc_start: 0.6359 (mp10) cc_final: 0.5924 (mp10) REVERT: A 326 ILE cc_start: 0.8635 (mm) cc_final: 0.8334 (pt) REVERT: A 347 PHE cc_start: 0.7752 (m-10) cc_final: 0.7470 (m-80) REVERT: A 396 TYR cc_start: 0.8657 (m-80) cc_final: 0.8228 (m-80) REVERT: A 498 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7440 (tm130) REVERT: A 529 LYS cc_start: 0.8256 (ptmt) cc_final: 0.7974 (pttm) REVERT: A 697 MET cc_start: 0.7653 (ptm) cc_final: 0.6830 (ttt) REVERT: A 796 ASP cc_start: 0.6507 (t0) cc_final: 0.6030 (p0) REVERT: B 32 PHE cc_start: 0.7613 (m-80) cc_final: 0.7336 (m-10) REVERT: B 177 MET cc_start: 0.2194 (mpp) cc_final: 0.1912 (mpp) REVERT: B 529 LYS cc_start: 0.8217 (ptmt) cc_final: 0.7867 (tttp) REVERT: B 650 LEU cc_start: 0.7105 (tp) cc_final: 0.6731 (tp) REVERT: B 796 ASP cc_start: 0.6228 (t0) cc_final: 0.5686 (p0) REVERT: B 900 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5222 (mtp) REVERT: B 902 MET cc_start: 0.8257 (tpt) cc_final: 0.7840 (tpt) REVERT: B 994 ASP cc_start: 0.8453 (t0) cc_final: 0.8026 (t0) REVERT: B 1050 MET cc_start: 0.7349 (ptm) cc_final: 0.7145 (ptm) REVERT: D 6 GLN cc_start: 0.5731 (pt0) cc_final: 0.5205 (pt0) REVERT: D 94 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8394 (ptt-90) REVERT: E 32 PHE cc_start: 0.7631 (m-80) cc_final: 0.7392 (m-10) REVERT: E 153 MET cc_start: 0.0630 (mmt) cc_final: -0.0933 (tmm) REVERT: E 332 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7795 (mm) REVERT: E 529 LYS cc_start: 0.8144 (ptmt) cc_final: 0.7784 (tttp) REVERT: E 697 MET cc_start: 0.7744 (ptm) cc_final: 0.6868 (ttt) REVERT: E 796 ASP cc_start: 0.6233 (t0) cc_final: 0.5640 (p0) REVERT: F 46 GLU cc_start: 0.6191 (mp0) cc_final: 0.5945 (mp0) REVERT: H 69 ILE cc_start: 0.8476 (mt) cc_final: 0.8221 (mt) REVERT: H 86 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.6092 (t0) REVERT: C 46 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.6620 (t80) REVERT: G 38 LEU cc_start: 0.8188 (mp) cc_final: 0.7893 (mt) REVERT: G 68 THR cc_start: 0.7999 (p) cc_final: 0.7662 (t) REVERT: L 55 SER cc_start: 0.6160 (m) cc_final: 0.5930 (p) REVERT: L 82 GLU cc_start: 0.3273 (mm-30) cc_final: 0.2965 (pp20) outliers start: 103 outliers final: 67 residues processed: 456 average time/residue: 0.1714 time to fit residues: 129.3520 Evaluate side-chains 443 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 370 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 224 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 191 optimal weight: 4.9990 chunk 97 optimal weight: 0.0970 chunk 290 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1108 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 606 ASN E 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.183722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.149539 restraints weight = 45508.334| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.41 r_work: 0.3714 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30591 Z= 0.178 Angle : 0.646 10.679 41757 Z= 0.325 Chirality : 0.048 0.450 4768 Planarity : 0.004 0.040 5329 Dihedral : 6.110 59.128 4806 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 3.43 % Allowed : 13.12 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 3735 helix: 1.50 (0.20), residues: 609 sheet: -0.16 (0.16), residues: 963 loop : -0.72 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 38 TYR 0.019 0.002 TYR H 100G PHE 0.037 0.002 PHE G 46 TRP 0.057 0.002 TRP F 97 HIS 0.005 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00416 (30507) covalent geometry : angle 0.61343 (41556) SS BOND : bond 0.00399 ( 48) SS BOND : angle 1.77673 ( 96) hydrogen bonds : bond 0.04225 ( 1098) hydrogen bonds : angle 5.88091 ( 3060) Misc. bond : bond 0.01307 ( 1) link_BETA1-4 : bond 0.00617 ( 1) link_BETA1-4 : angle 1.09481 ( 3) link_BETA1-6 : bond 0.00413 ( 1) link_BETA1-6 : angle 1.28795 ( 3) link_NAG-ASN : bond 0.00581 ( 33) link_NAG-ASN : angle 3.87727 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 385 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0547 (mmt) cc_final: -0.1260 (tmm) REVERT: A 187 LYS cc_start: 0.6564 (mmtt) cc_final: 0.6257 (mmtp) REVERT: A 326 ILE cc_start: 0.8643 (mm) cc_final: 0.8339 (pt) REVERT: A 357 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7813 (ptm-80) REVERT: A 396 TYR cc_start: 0.8722 (m-80) cc_final: 0.8235 (m-80) REVERT: A 498 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7574 (tm130) REVERT: A 529 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8073 (pttm) REVERT: A 794 ILE cc_start: 0.8680 (mm) cc_final: 0.8417 (tt) REVERT: A 796 ASP cc_start: 0.6778 (t0) cc_final: 0.6263 (p0) REVERT: B 32 PHE cc_start: 0.7629 (m-80) cc_final: 0.7367 (m-10) REVERT: B 153 MET cc_start: 0.1043 (mmt) cc_final: -0.0961 (tmm) REVERT: B 177 MET cc_start: 0.2261 (mpp) cc_final: 0.1990 (mpp) REVERT: B 238 PHE cc_start: 0.3601 (OUTLIER) cc_final: 0.2793 (p90) REVERT: B 317 ASN cc_start: 0.7546 (m-40) cc_final: 0.6772 (m110) REVERT: B 453 TYR cc_start: 0.8647 (p90) cc_final: 0.8320 (p90) REVERT: B 506 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: B 529 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7916 (tttp) REVERT: B 650 LEU cc_start: 0.7240 (tp) cc_final: 0.6798 (tp) REVERT: B 796 ASP cc_start: 0.6286 (t0) cc_final: 0.5931 (p0) REVERT: B 900 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5431 (mtp) REVERT: B 994 ASP cc_start: 0.8516 (t0) cc_final: 0.8092 (t0) REVERT: D 94 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8378 (ptt-90) REVERT: E 32 PHE cc_start: 0.7617 (m-80) cc_final: 0.7410 (m-10) REVERT: E 153 MET cc_start: 0.0511 (mmt) cc_final: -0.1039 (tmm) REVERT: E 332 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7968 (mm) REVERT: E 529 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7829 (tptt) REVERT: E 737 ASP cc_start: 0.7962 (m-30) cc_final: 0.7588 (t0) REVERT: E 796 ASP cc_start: 0.6426 (t0) cc_final: 0.5979 (p0) REVERT: E 1050 MET cc_start: 0.7458 (ptt) cc_final: 0.7232 (ptt) REVERT: F 46 GLU cc_start: 0.6348 (mp0) cc_final: 0.6051 (mp0) REVERT: H 86 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.6157 (t0) REVERT: C 46 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6867 (t80) REVERT: G 68 THR cc_start: 0.8043 (p) cc_final: 0.7697 (t) REVERT: L 55 SER cc_start: 0.6143 (m) cc_final: 0.5931 (p) REVERT: L 82 GLU cc_start: 0.3656 (mm-30) cc_final: 0.3171 (pp20) outliers start: 110 outliers final: 81 residues processed: 442 average time/residue: 0.1760 time to fit residues: 128.0106 Evaluate side-chains 456 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 367 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 320 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 chunk 178 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 294 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN E 317 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 907 ASN E1108 ASN C 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.186271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.153009 restraints weight = 45397.826| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.36 r_work: 0.3759 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30591 Z= 0.127 Angle : 0.613 10.508 41757 Z= 0.308 Chirality : 0.046 0.430 4768 Planarity : 0.004 0.037 5329 Dihedral : 5.912 58.930 4806 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.71 % Rotamer: Outliers : 2.83 % Allowed : 14.42 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 3735 helix: 1.67 (0.20), residues: 606 sheet: -0.14 (0.15), residues: 999 loop : -0.73 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 38 TYR 0.018 0.001 TYR E 266 PHE 0.037 0.001 PHE G 46 TRP 0.026 0.002 TRP F 33 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00289 (30507) covalent geometry : angle 0.58287 (41556) SS BOND : bond 0.00358 ( 48) SS BOND : angle 1.57581 ( 96) hydrogen bonds : bond 0.03983 ( 1098) hydrogen bonds : angle 5.77674 ( 3060) Misc. bond : bond 0.00407 ( 1) link_BETA1-4 : bond 0.00579 ( 1) link_BETA1-4 : angle 1.08235 ( 3) link_BETA1-6 : bond 0.00328 ( 1) link_BETA1-6 : angle 1.30072 ( 3) link_NAG-ASN : bond 0.00535 ( 33) link_NAG-ASN : angle 3.64109 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 394 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0589 (mmt) cc_final: -0.1302 (tmm) REVERT: A 187 LYS cc_start: 0.6446 (mmtt) cc_final: 0.6223 (mmtp) REVERT: A 317 ASN cc_start: 0.7752 (m-40) cc_final: 0.6941 (m110) REVERT: A 326 ILE cc_start: 0.8634 (mm) cc_final: 0.8386 (pt) REVERT: A 347 PHE cc_start: 0.7749 (m-10) cc_final: 0.7437 (m-80) REVERT: A 357 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7773 (ptm-80) REVERT: A 396 TYR cc_start: 0.8704 (m-80) cc_final: 0.8273 (m-80) REVERT: A 498 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7397 (tm130) REVERT: A 529 LYS cc_start: 0.8354 (ptmt) cc_final: 0.7965 (tptt) REVERT: A 794 ILE cc_start: 0.8660 (mm) cc_final: 0.8423 (tt) REVERT: A 796 ASP cc_start: 0.6697 (t0) cc_final: 0.6204 (p0) REVERT: B 32 PHE cc_start: 0.7646 (m-80) cc_final: 0.7372 (m-10) REVERT: B 153 MET cc_start: 0.0987 (mmt) cc_final: -0.1071 (tmm) REVERT: B 177 MET cc_start: 0.2031 (mpp) cc_final: 0.1828 (mpp) REVERT: B 237 ARG cc_start: 0.6575 (tmm-80) cc_final: 0.6059 (tmm-80) REVERT: B 453 TYR cc_start: 0.8606 (p90) cc_final: 0.8274 (p90) REVERT: B 529 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7935 (tttp) REVERT: B 650 LEU cc_start: 0.7083 (tp) cc_final: 0.6620 (tp) REVERT: B 737 ASP cc_start: 0.8031 (m-30) cc_final: 0.7625 (t0) REVERT: B 796 ASP cc_start: 0.6196 (t0) cc_final: 0.5917 (p0) REVERT: B 900 MET cc_start: 0.5686 (OUTLIER) cc_final: 0.5160 (mtp) REVERT: B 994 ASP cc_start: 0.8464 (t0) cc_final: 0.8021 (t0) REVERT: D 94 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8339 (ptt-90) REVERT: D 103 TRP cc_start: 0.8279 (m100) cc_final: 0.7562 (m100) REVERT: E 32 PHE cc_start: 0.7630 (m-80) cc_final: 0.7394 (m-10) REVERT: E 153 MET cc_start: 0.0586 (mmt) cc_final: -0.1027 (tmm) REVERT: E 529 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7847 (tptt) REVERT: E 697 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6887 (ttt) REVERT: E 796 ASP cc_start: 0.6382 (t0) cc_final: 0.5943 (p0) REVERT: E 873 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.7055 (t80) REVERT: F 46 GLU cc_start: 0.6220 (mp0) cc_final: 0.5938 (mp0) REVERT: C 46 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.6938 (t80) REVERT: G 38 LEU cc_start: 0.8172 (mp) cc_final: 0.7947 (mt) REVERT: G 68 THR cc_start: 0.7994 (p) cc_final: 0.7690 (t) REVERT: L 55 SER cc_start: 0.6283 (m) cc_final: 0.6054 (p) REVERT: L 82 GLU cc_start: 0.3409 (mm-30) cc_final: 0.3144 (pp20) outliers start: 91 outliers final: 73 residues processed: 435 average time/residue: 0.1796 time to fit residues: 126.5877 Evaluate side-chains 454 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 375 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1108 ASN Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 49 ARG Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 265 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 317 optimal weight: 0.8980 chunk 303 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 325 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1108 ASN D 6 GLN E 317 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.186549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152791 restraints weight = 45070.881| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.55 r_work: 0.3723 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30591 Z= 0.146 Angle : 0.622 10.820 41757 Z= 0.313 Chirality : 0.047 0.427 4768 Planarity : 0.004 0.051 5329 Dihedral : 5.852 59.181 4806 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.71 % Allowed : 14.86 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 3735 helix: 1.62 (0.20), residues: 606 sheet: 0.06 (0.17), residues: 906 loop : -0.76 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 646 TYR 0.016 0.001 TYR H 100G PHE 0.027 0.001 PHE G 46 TRP 0.036 0.002 TRP F 97 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00339 (30507) covalent geometry : angle 0.59367 (41556) SS BOND : bond 0.00353 ( 48) SS BOND : angle 1.57906 ( 96) hydrogen bonds : bond 0.04024 ( 1098) hydrogen bonds : angle 5.80200 ( 3060) Misc. bond : bond 0.00346 ( 1) link_BETA1-4 : bond 0.00564 ( 1) link_BETA1-4 : angle 1.00427 ( 3) link_BETA1-6 : bond 0.00559 ( 1) link_BETA1-6 : angle 1.26759 ( 3) link_NAG-ASN : bond 0.00536 ( 33) link_NAG-ASN : angle 3.59859 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 382 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0466 (mmt) cc_final: -0.1384 (tmm) REVERT: A 187 LYS cc_start: 0.6549 (mmtt) cc_final: 0.6315 (mmtp) REVERT: A 317 ASN cc_start: 0.7761 (m-40) cc_final: 0.6968 (m110) REVERT: A 326 ILE cc_start: 0.8632 (mm) cc_final: 0.8383 (pt) REVERT: A 347 PHE cc_start: 0.7858 (m-10) cc_final: 0.7561 (m-80) REVERT: A 357 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7843 (ptm-80) REVERT: A 396 TYR cc_start: 0.8746 (m-80) cc_final: 0.8323 (m-80) REVERT: A 498 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7398 (tm130) REVERT: A 529 LYS cc_start: 0.8399 (ptmt) cc_final: 0.7974 (tptt) REVERT: A 796 ASP cc_start: 0.6774 (t0) cc_final: 0.6161 (p0) REVERT: A 1050 MET cc_start: 0.7576 (ptt) cc_final: 0.7300 (ptt) REVERT: B 32 PHE cc_start: 0.7604 (m-80) cc_final: 0.7351 (m-10) REVERT: B 153 MET cc_start: 0.0892 (mmt) cc_final: -0.1060 (tmm) REVERT: B 177 MET cc_start: 0.2097 (mpp) cc_final: 0.1867 (mpp) REVERT: B 237 ARG cc_start: 0.6615 (tmm-80) cc_final: 0.6091 (tmm-80) REVERT: B 238 PHE cc_start: 0.3632 (OUTLIER) cc_final: 0.2815 (p90) REVERT: B 317 ASN cc_start: 0.7580 (m-40) cc_final: 0.6839 (m110) REVERT: B 453 TYR cc_start: 0.8611 (p90) cc_final: 0.8268 (p90) REVERT: B 529 LYS cc_start: 0.8363 (ptmt) cc_final: 0.7932 (tttp) REVERT: B 650 LEU cc_start: 0.7156 (tp) cc_final: 0.6663 (tp) REVERT: B 737 ASP cc_start: 0.8058 (m-30) cc_final: 0.7635 (t0) REVERT: B 796 ASP cc_start: 0.6349 (t0) cc_final: 0.5920 (p0) REVERT: B 900 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.5280 (mtp) REVERT: B 994 ASP cc_start: 0.8521 (t0) cc_final: 0.8061 (t0) REVERT: D 94 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8406 (ptt-90) REVERT: D 103 TRP cc_start: 0.8278 (m100) cc_final: 0.7461 (m100) REVERT: E 32 PHE cc_start: 0.7619 (m-80) cc_final: 0.7411 (m-10) REVERT: E 153 MET cc_start: 0.0495 (mmt) cc_final: -0.1078 (tmm) REVERT: E 389 ASP cc_start: 0.8390 (t0) cc_final: 0.7961 (t0) REVERT: E 529 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7854 (tptt) REVERT: E 697 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6932 (ttt) REVERT: E 737 ASP cc_start: 0.7990 (m-30) cc_final: 0.7657 (t0) REVERT: E 796 ASP cc_start: 0.6475 (t0) cc_final: 0.5925 (p0) REVERT: F 46 GLU cc_start: 0.6308 (mp0) cc_final: 0.5990 (mp0) REVERT: C 46 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.6919 (t80) REVERT: G 68 THR cc_start: 0.8051 (p) cc_final: 0.7695 (t) REVERT: L 46 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7765 (t80) REVERT: L 82 GLU cc_start: 0.3623 (mm-30) cc_final: 0.3093 (pp20) outliers start: 87 outliers final: 72 residues processed: 421 average time/residue: 0.1764 time to fit residues: 120.9681 Evaluate side-chains 448 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 369 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 49 ARG Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 46 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 116 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 311 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 189 optimal weight: 0.0170 chunk 18 optimal weight: 0.5980 chunk 119 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1108 ASN D 6 GLN E 317 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1108 ASN C 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.188264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.155807 restraints weight = 44420.334| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.32 r_work: 0.3797 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30591 Z= 0.137 Angle : 0.622 10.412 41757 Z= 0.311 Chirality : 0.047 0.419 4768 Planarity : 0.004 0.038 5329 Dihedral : 5.811 58.993 4805 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 2.77 % Allowed : 14.83 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3735 helix: 1.60 (0.20), residues: 606 sheet: 0.09 (0.16), residues: 909 loop : -0.76 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 646 TYR 0.022 0.001 TYR D 52 PHE 0.022 0.001 PHE A 906 TRP 0.058 0.002 TRP F 97 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00316 (30507) covalent geometry : angle 0.59365 (41556) SS BOND : bond 0.00342 ( 48) SS BOND : angle 1.55367 ( 96) hydrogen bonds : bond 0.03971 ( 1098) hydrogen bonds : angle 5.77001 ( 3060) Misc. bond : bond 0.00332 ( 1) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 1.04117 ( 3) link_BETA1-6 : bond 0.00413 ( 1) link_BETA1-6 : angle 1.23310 ( 3) link_NAG-ASN : bond 0.00518 ( 33) link_NAG-ASN : angle 3.60055 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 384 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0413 (mmt) cc_final: -0.1450 (tmm) REVERT: A 317 ASN cc_start: 0.7622 (m-40) cc_final: 0.6731 (m110) REVERT: A 347 PHE cc_start: 0.7706 (m-10) cc_final: 0.7380 (m-80) REVERT: A 357 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7757 (ptm-80) REVERT: A 396 TYR cc_start: 0.8707 (m-80) cc_final: 0.8353 (m-80) REVERT: A 498 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7489 (tm130) REVERT: A 529 LYS cc_start: 0.8418 (ptmt) cc_final: 0.8058 (tptt) REVERT: A 697 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6689 (ttt) REVERT: A 796 ASP cc_start: 0.6690 (t0) cc_final: 0.6417 (p0) REVERT: A 873 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6850 (t80) REVERT: B 153 MET cc_start: 0.1065 (mmt) cc_final: -0.1098 (tmm) REVERT: B 317 ASN cc_start: 0.7380 (m-40) cc_final: 0.6570 (m110) REVERT: B 389 ASP cc_start: 0.8167 (t0) cc_final: 0.7821 (t0) REVERT: B 529 LYS cc_start: 0.8356 (ptmt) cc_final: 0.8055 (tptt) REVERT: B 650 LEU cc_start: 0.7144 (tp) cc_final: 0.6693 (tp) REVERT: B 737 ASP cc_start: 0.7849 (m-30) cc_final: 0.7567 (t0) REVERT: B 900 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5306 (mtp) REVERT: B 994 ASP cc_start: 0.8432 (t0) cc_final: 0.8019 (t0) REVERT: D 6 GLN cc_start: 0.5421 (pt0) cc_final: 0.5203 (pt0) REVERT: D 94 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8336 (ptt-90) REVERT: D 103 TRP cc_start: 0.8226 (m100) cc_final: 0.7583 (m100) REVERT: E 153 MET cc_start: 0.0699 (mmt) cc_final: -0.1047 (tmm) REVERT: E 389 ASP cc_start: 0.8288 (t0) cc_final: 0.7890 (t0) REVERT: E 529 LYS cc_start: 0.8293 (ptmt) cc_final: 0.8010 (tptt) REVERT: E 697 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6798 (ttt) REVERT: E 796 ASP cc_start: 0.6428 (t0) cc_final: 0.6089 (p0) REVERT: E 873 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.7108 (t80) REVERT: F 46 GLU cc_start: 0.6271 (mp0) cc_final: 0.6022 (mp0) REVERT: H 46 GLU cc_start: 0.6244 (mp0) cc_final: 0.5963 (mp0) REVERT: C 46 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7144 (t80) REVERT: G 68 THR cc_start: 0.8052 (p) cc_final: 0.7750 (t) REVERT: G 82 GLU cc_start: 0.3731 (mm-30) cc_final: 0.3165 (pp20) REVERT: L 46 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7654 (t80) REVERT: L 82 GLU cc_start: 0.3668 (mm-30) cc_final: 0.3157 (pp20) outliers start: 89 outliers final: 73 residues processed: 426 average time/residue: 0.1815 time to fit residues: 125.7469 Evaluate side-chains 448 residues out of total 3294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 366 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 LYS Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1108 ASN Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 49 ARG Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 46 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 227 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 302 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN E 317 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.188164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155847 restraints weight = 44817.516| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.29 r_work: 0.3828 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.319 30591 Z= 0.266 Angle : 0.868 65.900 41757 Z= 0.527 Chirality : 0.047 0.481 4768 Planarity : 0.007 0.270 5329 Dihedral : 5.827 58.991 4805 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 2.65 % Allowed : 15.08 % Favored : 82.27 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3735 helix: 1.59 (0.20), residues: 606 sheet: 0.09 (0.17), residues: 909 loop : -0.76 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.066 0.002 TYR E 369 PHE 0.018 0.001 PHE A 906 TRP 0.054 0.002 TRP F 97 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00537 (30507) covalent geometry : angle 0.84795 (41556) SS BOND : bond 0.00403 ( 48) SS BOND : angle 1.81734 ( 96) hydrogen bonds : bond 0.04000 ( 1098) hydrogen bonds : angle 5.77727 ( 3060) Misc. bond : bond 0.00334 ( 1) link_BETA1-4 : bond 0.00471 ( 1) link_BETA1-4 : angle 1.01334 ( 3) link_BETA1-6 : bond 0.00366 ( 1) link_BETA1-6 : angle 1.23229 ( 3) link_NAG-ASN : bond 0.00529 ( 33) link_NAG-ASN : angle 3.60160 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8376.46 seconds wall clock time: 143 minutes 48.85 seconds (8628.85 seconds total)