Starting phenix.real_space_refine on Wed Feb 21 10:32:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd0_33744/02_2024/7yd0_33744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd0_33744/02_2024/7yd0_33744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd0_33744/02_2024/7yd0_33744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd0_33744/02_2024/7yd0_33744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd0_33744/02_2024/7yd0_33744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yd0_33744/02_2024/7yd0_33744.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.029 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 137 5.16 5 C 19426 2.51 5 N 5046 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 192": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30413 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7989 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8043 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "E" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "F" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1665 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "G" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1504 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 189} Time building chain proxies: 15.55, per 1000 atoms: 0.51 Number of scatterers: 30413 At special positions: 0 Unit cell: (143.64, 211.736, 222.376, 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 137 16.00 O 5804 8.00 N 5046 7.00 C 19426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.91 Conformation dependent library (CDL) restraints added in 5.7 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7394 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 62 sheets defined 18.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.781A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.599A pdb=" N LEU A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.772A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.558A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.519A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.598A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 857 removed outlier: 3.517A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.721A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.675A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 945 No H-bonds generated for 'chain 'A' and resid 943 through 945' Processing helix chain 'A' and resid 946 through 966 removed outlier: 3.941A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.607A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.565A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.889A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.088A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.821A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.822A pdb=" N ASN B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.552A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.519A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.972A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.505A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.506A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.988A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 905 Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.689A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.713A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.692A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.538A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.517A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.116A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.620A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.735A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.899A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.295A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.086A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.712A pdb=" N SER C1147 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.692A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU E 85 " --> pdb=" O ALA E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.688A pdb=" N ASP G 84 " --> pdb=" O GLN G 81 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU G 85 " --> pdb=" O ALA G 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.563A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.542A pdb=" N PHE A 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 7.294A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.538A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.982A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 94 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 188 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 189 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 204 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 224 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 107 removed outlier: 3.629A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 310 through 319 removed outlier: 4.856A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.635A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.407A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.983A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.716A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.716A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.320A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.786A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.648A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.989A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.666A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.655A pdb=" N ALA B 263 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 92 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 188 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 187 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 191 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 118 through 120 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.767A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.659A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.646A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.071A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.017A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.305A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 728 removed outlier: 7.305A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.069A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.266A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.616A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.570A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 63 through 67 removed outlier: 3.999A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.504A pdb=" N VAL C 90 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 192 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU C 96 " --> pdb=" O ASN C 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.504A pdb=" N VAL C 90 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 192 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 189 " --> pdb=" O LYS C 204 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 227 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 126 through 129 removed outlier: 3.618A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.545A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.551A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.795A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.625A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.461A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 728 removed outlier: 7.415A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 5.836A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.216A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.518A pdb=" N SER D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 59 through 61 removed outlier: 6.715A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 41 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 150 through 152 removed outlier: 3.784A pdb=" N TYR D 152 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.537A pdb=" N VAL E 10 " --> pdb=" O THR E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AF9, first strand: chain 'E' and resid 47 through 51 removed outlier: 5.479A pdb=" N LEU E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN E 39 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 89 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 148 through 149 Processing sheet with id=AG2, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.560A pdb=" N SER F 7 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.782A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 93 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 114 " --> pdb=" O TYR F 95 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.780A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.590A pdb=" N VAL G 10 " --> pdb=" O THR G 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AG7, first strand: chain 'G' and resid 47 through 51 removed outlier: 5.615A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR G 89 " --> pdb=" O TYR G 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 148 through 149 851 hydrogen bonds defined for protein. 2268 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: 12.79 Time building geometry restraints manager: 11.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5171 1.33 - 1.45: 8423 1.45 - 1.57: 17375 1.57 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 31139 Sorted by residual: bond pdb=" CA ALA A 27 " pdb=" C ALA A 27 " ideal model delta sigma weight residual 1.523 1.454 0.070 1.34e-02 5.57e+03 2.69e+01 bond pdb=" N ASN B 331 " pdb=" CA ASN B 331 " ideal model delta sigma weight residual 1.457 1.509 -0.051 1.29e-02 6.01e+03 1.58e+01 bond pdb=" CA TYR B 28 " pdb=" C TYR B 28 " ideal model delta sigma weight residual 1.522 1.488 0.034 1.24e-02 6.50e+03 7.50e+00 bond pdb=" C TYR B 28 " pdb=" O TYR B 28 " ideal model delta sigma weight residual 1.234 1.204 0.030 1.24e-02 6.50e+03 5.84e+00 bond pdb=" CA ALA B 27 " pdb=" CB ALA B 27 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.54e-02 4.22e+03 5.29e+00 ... (remaining 31134 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 1079 107.15 - 113.86: 17315 113.86 - 120.57: 11321 120.57 - 127.28: 12411 127.28 - 133.99: 315 Bond angle restraints: 42441 Sorted by residual: angle pdb=" N ILE B 332 " pdb=" CA ILE B 332 " pdb=" C ILE B 332 " ideal model delta sigma weight residual 108.48 117.35 -8.87 1.44e+00 4.82e-01 3.80e+01 angle pdb=" N PHE B 329 " pdb=" CA PHE B 329 " pdb=" C PHE B 329 " ideal model delta sigma weight residual 110.10 100.97 9.13 1.53e+00 4.27e-01 3.56e+01 angle pdb=" N ILE B 410 " pdb=" CA ILE B 410 " pdb=" C ILE B 410 " ideal model delta sigma weight residual 112.90 107.88 5.02 9.60e-01 1.09e+00 2.73e+01 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 112.47 123.09 -10.62 2.06e+00 2.36e-01 2.66e+01 angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.71 109.12 4.59 9.50e-01 1.11e+00 2.34e+01 ... (remaining 42436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 17706 17.11 - 34.22: 735 34.22 - 51.33: 141 51.33 - 68.44: 23 68.44 - 85.55: 9 Dihedral angle restraints: 18614 sinusoidal: 7130 harmonic: 11484 Sorted by residual: dihedral pdb=" CA PHE B 135 " pdb=" C PHE B 135 " pdb=" N CYS B 136 " pdb=" CA CYS B 136 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C PHE B 329 " pdb=" N PHE B 329 " pdb=" CA PHE B 329 " pdb=" CB PHE B 329 " ideal model delta harmonic sigma weight residual -122.60 -112.96 -9.64 0 2.50e+00 1.60e-01 1.49e+01 dihedral pdb=" SG CYS B 391 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sinusoidal sigma weight residual -73.00 -11.24 -61.76 1 2.00e+01 2.50e-03 1.26e+01 ... (remaining 18611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4398 0.072 - 0.145: 456 0.145 - 0.217: 6 0.217 - 0.290: 2 0.290 - 0.362: 1 Chirality restraints: 4863 Sorted by residual: chirality pdb=" CA PHE B 329 " pdb=" N PHE B 329 " pdb=" C PHE B 329 " pdb=" CB PHE B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" C PRO A 330 " pdb=" CB PRO A 330 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA THR B 29 " pdb=" N THR B 29 " pdb=" C THR B 29 " pdb=" CB THR B 29 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 4860 not shown) Planarity restraints: 5471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO C 330 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO A 987 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 24 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO C 25 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 25 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 25 " -0.031 5.00e-02 4.00e+02 ... (remaining 5468 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4233 2.76 - 3.29: 29294 3.29 - 3.83: 50066 3.83 - 4.36: 58495 4.36 - 4.90: 100729 Nonbonded interactions: 242817 Sorted by model distance: nonbonded pdb=" OE1 GLN A 965 " pdb=" OG SER A1003 " model vdw 2.223 2.440 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR G 5 " pdb=" OG1 THR G 23 " model vdw 2.243 2.440 nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 21 " model vdw 2.252 2.440 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.258 2.440 ... (remaining 242812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 26 through 243 or resid 262 through 1147)) selection = (chain 'C' and (resid 26 through 243 or resid 262 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.410 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 78.430 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.170 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.002 0.070 31139 Z= 0.151 Angle : 0.589 10.622 42441 Z= 0.364 Chirality : 0.040 0.362 4863 Planarity : 0.004 0.083 5471 Dihedral : 9.452 85.553 11079 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 5.95 % Allowed : 6.77 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.10), residues: 3888 helix: -2.90 (0.13), residues: 636 sheet: -2.93 (0.16), residues: 829 loop : -3.55 (0.10), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.001 0.000 HIS C1064 PHE 0.007 0.001 PHE C 318 TYR 0.007 0.001 TYR B 265 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 888 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7389 (tp40) cc_final: 0.7188 (tp40) REVERT: A 66 HIS cc_start: 0.5251 (OUTLIER) cc_final: 0.4843 (t-90) REVERT: A 97 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7037 (tmmt) REVERT: A 106 PHE cc_start: 0.7912 (m-80) cc_final: 0.7550 (m-80) REVERT: A 233 ILE cc_start: 0.3069 (OUTLIER) cc_final: 0.2787 (mm) REVERT: A 276 LEU cc_start: 0.8257 (tp) cc_final: 0.7944 (tt) REVERT: A 281 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6432 (pp20) REVERT: A 296 LEU cc_start: 0.8649 (tp) cc_final: 0.8362 (tp) REVERT: A 307 THR cc_start: 0.7855 (m) cc_final: 0.7495 (p) REVERT: A 308 VAL cc_start: 0.8388 (p) cc_final: 0.8046 (m) REVERT: A 323 THR cc_start: 0.7828 (m) cc_final: 0.6383 (p) REVERT: A 332 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7203 (tp) REVERT: A 578 ASP cc_start: 0.7648 (t0) cc_final: 0.7008 (t0) REVERT: A 587 ILE cc_start: 0.8370 (mt) cc_final: 0.8127 (mt) REVERT: A 664 ILE cc_start: 0.8295 (mt) cc_final: 0.8069 (mm) REVERT: A 725 GLU cc_start: 0.7213 (pt0) cc_final: 0.6768 (pt0) REVERT: A 734 THR cc_start: 0.8210 (t) cc_final: 0.7878 (m) REVERT: A 745 ASP cc_start: 0.5924 (m-30) cc_final: 0.5713 (m-30) REVERT: A 751 ASN cc_start: 0.7796 (m-40) cc_final: 0.7215 (m110) REVERT: A 752 LEU cc_start: 0.8319 (mm) cc_final: 0.7969 (mt) REVERT: A 762 GLN cc_start: 0.7513 (pt0) cc_final: 0.7027 (pt0) REVERT: A 773 GLU cc_start: 0.7072 (tt0) cc_final: 0.6494 (tt0) REVERT: A 776 LYS cc_start: 0.8079 (tmmt) cc_final: 0.7735 (tmmt) REVERT: A 800 PHE cc_start: 0.8071 (m-80) cc_final: 0.7723 (m-80) REVERT: A 821 LEU cc_start: 0.8211 (mm) cc_final: 0.7870 (mt) REVERT: A 825 LYS cc_start: 0.8409 (mtpm) cc_final: 0.8096 (mtpp) REVERT: A 922 LEU cc_start: 0.8865 (tp) cc_final: 0.8577 (tt) REVERT: A 933 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8220 (mtmm) REVERT: A 935 GLN cc_start: 0.8044 (tt0) cc_final: 0.7831 (tt0) REVERT: A 947 LYS cc_start: 0.8216 (mtpt) cc_final: 0.8009 (mtpp) REVERT: A 950 ASP cc_start: 0.6701 (t0) cc_final: 0.6161 (t0) REVERT: A 957 GLN cc_start: 0.7498 (pt0) cc_final: 0.7219 (pt0) REVERT: A 964 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7358 (mtmt) REVERT: A 975 SER cc_start: 0.8570 (m) cc_final: 0.7959 (t) REVERT: A 977 LEU cc_start: 0.9005 (mp) cc_final: 0.8756 (mt) REVERT: A 980 ILE cc_start: 0.8755 (mt) cc_final: 0.8527 (tt) REVERT: A 1017 GLU cc_start: 0.6378 (tm-30) cc_final: 0.5934 (tm-30) REVERT: A 1019 ARG cc_start: 0.7297 (ttm110) cc_final: 0.5865 (ttm110) REVERT: A 1028 LYS cc_start: 0.8511 (mttt) cc_final: 0.8244 (mttm) REVERT: A 1097 SER cc_start: 0.8607 (t) cc_final: 0.8299 (p) REVERT: A 1117 THR cc_start: 0.8197 (p) cc_final: 0.7823 (t) REVERT: A 1123 SER cc_start: 0.7855 (m) cc_final: 0.7652 (t) REVERT: B 29 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7858 (t) REVERT: B 54 LEU cc_start: 0.8075 (mt) cc_final: 0.7858 (mm) REVERT: B 83 VAL cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (p) REVERT: B 106 PHE cc_start: 0.7351 (m-80) cc_final: 0.7147 (m-80) REVERT: B 127 VAL cc_start: 0.8452 (t) cc_final: 0.7865 (m) REVERT: B 187 LEU cc_start: 0.7494 (tp) cc_final: 0.7243 (tt) REVERT: B 193 LYS cc_start: 0.7319 (mtmt) cc_final: 0.7094 (ttpt) REVERT: B 307 THR cc_start: 0.7695 (m) cc_final: 0.7290 (p) REVERT: B 319 ARG cc_start: 0.7104 (ttm170) cc_final: 0.6735 (ttm-80) REVERT: B 356 LYS cc_start: 0.8521 (tmmt) cc_final: 0.7924 (tmmt) REVERT: B 398 ASP cc_start: 0.5600 (t70) cc_final: 0.4939 (t0) REVERT: B 528 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8327 (mmtt) REVERT: B 535 LYS cc_start: 0.8307 (tptt) cc_final: 0.8013 (mmmm) REVERT: B 543 PHE cc_start: 0.6697 (m-10) cc_final: 0.6369 (m-80) REVERT: B 546 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8305 (tm) REVERT: B 562 PHE cc_start: 0.7200 (p90) cc_final: 0.6822 (p90) REVERT: B 603 ASN cc_start: 0.7114 (t0) cc_final: 0.6739 (t0) REVERT: B 616 ASN cc_start: 0.4918 (t0) cc_final: 0.4063 (t0) REVERT: B 659 SER cc_start: 0.8498 (m) cc_final: 0.8164 (p) REVERT: B 725 GLU cc_start: 0.7134 (tt0) cc_final: 0.6827 (tt0) REVERT: B 750 SER cc_start: 0.8425 (m) cc_final: 0.8169 (p) REVERT: B 759 PHE cc_start: 0.7311 (t80) cc_final: 0.6909 (t80) REVERT: B 765 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7260 (ttp80) REVERT: B 800 PHE cc_start: 0.7974 (m-80) cc_final: 0.7358 (m-80) REVERT: B 868 GLU cc_start: 0.7300 (tp30) cc_final: 0.6907 (tp30) REVERT: B 884 SER cc_start: 0.8794 (m) cc_final: 0.8506 (p) REVERT: B 954 HIS cc_start: 0.7120 (m-70) cc_final: 0.6764 (m90) REVERT: B 955 ASN cc_start: 0.7523 (m-40) cc_final: 0.7314 (m-40) REVERT: B 957 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7124 (tm130) REVERT: B 961 THR cc_start: 0.8167 (m) cc_final: 0.7537 (p) REVERT: B 965 GLN cc_start: 0.7321 (mt0) cc_final: 0.7067 (mt0) REVERT: B 1003 SER cc_start: 0.8340 (m) cc_final: 0.8003 (t) REVERT: B 1017 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6489 (tm-30) REVERT: B 1028 LYS cc_start: 0.8405 (mttm) cc_final: 0.7698 (mtpp) REVERT: B 1072 GLU cc_start: 0.8014 (pm20) cc_final: 0.7747 (pm20) REVERT: B 1081 ILE cc_start: 0.7822 (pt) cc_final: 0.7490 (mt) REVERT: B 1118 ASP cc_start: 0.7093 (t70) cc_final: 0.6717 (t0) REVERT: B 1123 SER cc_start: 0.8249 (t) cc_final: 0.7849 (p) REVERT: B 1141 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (tt) REVERT: C 33 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7577 (p) REVERT: C 90 VAL cc_start: 0.8670 (m) cc_final: 0.8305 (t) REVERT: C 106 PHE cc_start: 0.7862 (m-80) cc_final: 0.7637 (m-80) REVERT: C 117 LEU cc_start: 0.7983 (tp) cc_final: 0.7773 (tt) REVERT: C 128 ILE cc_start: 0.7763 (mt) cc_final: 0.7553 (mp) REVERT: C 190 PHE cc_start: 0.7996 (m-80) cc_final: 0.7760 (m-80) REVERT: C 275 PHE cc_start: 0.7929 (m-80) cc_final: 0.7674 (m-10) REVERT: C 281 GLU cc_start: 0.7169 (pp20) cc_final: 0.6638 (pp20) REVERT: C 293 LEU cc_start: 0.8484 (tp) cc_final: 0.8280 (tp) REVERT: C 408 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6663 (ppp-140) REVERT: C 542 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8087 (t0) REVERT: C 546 LEU cc_start: 0.7762 (tm) cc_final: 0.7477 (tt) REVERT: C 574 ASP cc_start: 0.6982 (t70) cc_final: 0.5971 (t0) REVERT: C 578 ASP cc_start: 0.6509 (t0) cc_final: 0.5920 (t70) REVERT: C 586 ASP cc_start: 0.7116 (t0) cc_final: 0.6614 (t0) REVERT: C 644 GLN cc_start: 0.8065 (tp40) cc_final: 0.7222 (tp40) REVERT: C 651 ILE cc_start: 0.8449 (mt) cc_final: 0.8231 (mm) REVERT: C 675 GLN cc_start: 0.6772 (mm-40) cc_final: 0.6431 (mm-40) REVERT: C 708 SER cc_start: 0.8372 (t) cc_final: 0.8112 (m) REVERT: C 712 ILE cc_start: 0.8278 (tp) cc_final: 0.8038 (tp) REVERT: C 723 THR cc_start: 0.8505 (t) cc_final: 0.8297 (p) REVERT: C 725 GLU cc_start: 0.7250 (tt0) cc_final: 0.6384 (tt0) REVERT: C 740 MET cc_start: 0.7477 (ttp) cc_final: 0.7217 (ttp) REVERT: C 764 LYS cc_start: 0.8053 (mttt) cc_final: 0.7813 (ttmm) REVERT: C 765 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7365 (ttp-110) REVERT: C 772 VAL cc_start: 0.8840 (t) cc_final: 0.8580 (m) REVERT: C 773 GLU cc_start: 0.7278 (tt0) cc_final: 0.7008 (tt0) REVERT: C 795 LYS cc_start: 0.8637 (mttt) cc_final: 0.8339 (mttm) REVERT: C 868 GLU cc_start: 0.6891 (tp30) cc_final: 0.6509 (tp30) REVERT: C 886 TRP cc_start: 0.8361 (p90) cc_final: 0.7967 (p90) REVERT: C 904 TYR cc_start: 0.7969 (m-10) cc_final: 0.7648 (m-10) REVERT: C 905 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7358 (mtt180) REVERT: C 919 ASN cc_start: 0.7978 (m-40) cc_final: 0.7686 (m-40) REVERT: C 933 LYS cc_start: 0.8295 (mtpt) cc_final: 0.8003 (ttmm) REVERT: C 977 LEU cc_start: 0.7848 (mp) cc_final: 0.6875 (mp) REVERT: C 980 ILE cc_start: 0.8845 (mt) cc_final: 0.8533 (mm) REVERT: C 981 PHE cc_start: 0.7750 (m-10) cc_final: 0.7501 (m-80) REVERT: C 1000 ARG cc_start: 0.8378 (mtt180) cc_final: 0.8127 (mtt-85) REVERT: C 1028 LYS cc_start: 0.8360 (ttmm) cc_final: 0.7768 (mttt) REVERT: C 1050 MET cc_start: 0.7659 (ptt) cc_final: 0.7288 (ptm) REVERT: C 1073 LYS cc_start: 0.7681 (tttm) cc_final: 0.7379 (mtpp) REVERT: C 1086 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7744 (mmmm) REVERT: C 1129 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8310 (m) REVERT: D 80 VAL cc_start: 0.7724 (t) cc_final: 0.7497 (p) REVERT: D 117 THR cc_start: 0.4587 (OUTLIER) cc_final: 0.4300 (t) REVERT: D 185 LEU cc_start: 0.0759 (pp) cc_final: 0.0162 (tp) REVERT: E 75 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4866 (tt) REVERT: F 145 LEU cc_start: 0.2203 (OUTLIER) cc_final: 0.1856 (pt) outliers start: 202 outliers final: 77 residues processed: 1042 average time/residue: 0.4457 time to fit residues: 725.1340 Evaluate side-chains 767 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 673 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 200 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 355 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 87 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 186 ASN A 218 GLN A 239 GLN A 334 ASN A 370 ASN A 409 GLN A 437 ASN A 564 GLN A 641 ASN A 709 ASN A 784 GLN A 853 GLN A 895 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 955 ASN A1002 GLN A1005 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 186 ASN B 245 HIS B 317 ASN B 409 GLN B 414 GLN B 422 ASN B 481 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 709 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 824 ASN B 853 GLN B 901 GLN B 907 ASN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 965 GLN B 978 ASN B1011 GLN B1054 GLN C 125 ASN C 173 GLN C 181 GLN C 280 ASN C 370 ASN C 409 GLN C 417 ASN C 540 ASN C 563 GLN C 644 GLN C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1002 GLN C1011 GLN C1106 GLN D 41 GLN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 71 ASN E 81 GLN E 111 GLN E 197 GLN F 41 GLN F 199 GLN G 39 GLN G 40 GLN G 81 GLN G 111 GLN G 197 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 31139 Z= 0.209 Angle : 0.599 11.751 42441 Z= 0.308 Chirality : 0.045 0.362 4863 Planarity : 0.005 0.070 5471 Dihedral : 6.742 75.970 4415 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.86 % Allowed : 13.37 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.12), residues: 3888 helix: -0.58 (0.19), residues: 652 sheet: -2.32 (0.16), residues: 831 loop : -3.14 (0.11), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS C 49 PHE 0.024 0.002 PHE G 142 TYR 0.024 0.001 TYR C 91 ARG 0.015 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 709 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7082 (tmmt) REVERT: A 113 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6141 (tppt) REVERT: A 189 GLU cc_start: 0.6657 (mm-30) cc_final: 0.5669 (mm-30) REVERT: A 194 ASN cc_start: 0.7024 (t0) cc_final: 0.6802 (t0) REVERT: A 233 ILE cc_start: 0.3184 (OUTLIER) cc_final: 0.2911 (mm) REVERT: A 276 LEU cc_start: 0.8299 (tp) cc_final: 0.7892 (tt) REVERT: A 307 THR cc_start: 0.7745 (m) cc_final: 0.7399 (p) REVERT: A 308 VAL cc_start: 0.8440 (p) cc_final: 0.8051 (m) REVERT: A 334 ASN cc_start: 0.7499 (t0) cc_final: 0.7054 (t0) REVERT: A 572 THR cc_start: 0.8092 (m) cc_final: 0.7276 (p) REVERT: A 578 ASP cc_start: 0.7503 (t0) cc_final: 0.7198 (t0) REVERT: A 725 GLU cc_start: 0.7076 (pt0) cc_final: 0.6432 (pt0) REVERT: A 751 ASN cc_start: 0.7624 (m-40) cc_final: 0.7098 (m110) REVERT: A 752 LEU cc_start: 0.8430 (mm) cc_final: 0.8183 (mt) REVERT: A 762 GLN cc_start: 0.7334 (pt0) cc_final: 0.7019 (pt0) REVERT: A 776 LYS cc_start: 0.8163 (tmmt) cc_final: 0.7787 (tmmt) REVERT: A 784 GLN cc_start: 0.7703 (mt0) cc_final: 0.7359 (mt0) REVERT: A 795 LYS cc_start: 0.8504 (mttm) cc_final: 0.8224 (mttm) REVERT: A 804 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7071 (mm-40) REVERT: A 825 LYS cc_start: 0.8358 (mtpm) cc_final: 0.8047 (mtpt) REVERT: A 922 LEU cc_start: 0.8798 (tp) cc_final: 0.8524 (tt) REVERT: A 933 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8178 (mtmm) REVERT: A 935 GLN cc_start: 0.8087 (tt0) cc_final: 0.7667 (tt0) REVERT: A 950 ASP cc_start: 0.6873 (t0) cc_final: 0.6400 (t0) REVERT: A 954 HIS cc_start: 0.7932 (m-70) cc_final: 0.7445 (m170) REVERT: A 961 THR cc_start: 0.8735 (p) cc_final: 0.8467 (t) REVERT: A 964 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7604 (mtmt) REVERT: A 975 SER cc_start: 0.8751 (m) cc_final: 0.8105 (t) REVERT: A 976 VAL cc_start: 0.8676 (m) cc_final: 0.8268 (p) REVERT: A 1017 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 1019 ARG cc_start: 0.7238 (ttm110) cc_final: 0.6632 (ttp80) REVERT: A 1028 LYS cc_start: 0.8389 (mttt) cc_final: 0.7676 (mtpp) REVERT: A 1031 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 1058 HIS cc_start: 0.7821 (m-70) cc_final: 0.7578 (m-70) REVERT: A 1097 SER cc_start: 0.8697 (t) cc_final: 0.8120 (p) REVERT: A 1117 THR cc_start: 0.8231 (p) cc_final: 0.7926 (t) REVERT: A 1130 ILE cc_start: 0.9001 (pt) cc_final: 0.8760 (pt) REVERT: B 54 LEU cc_start: 0.8110 (mt) cc_final: 0.7893 (mm) REVERT: B 66 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7504 (t-90) REVERT: B 83 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.6909 (p) REVERT: B 102 ARG cc_start: 0.6763 (mtm110) cc_final: 0.6206 (mtp-110) REVERT: B 127 VAL cc_start: 0.8101 (t) cc_final: 0.7368 (m) REVERT: B 193 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7299 (ttmt) REVERT: B 223 LEU cc_start: 0.7845 (mp) cc_final: 0.7550 (mt) REVERT: B 297 SER cc_start: 0.7844 (m) cc_final: 0.7444 (p) REVERT: B 307 THR cc_start: 0.7892 (m) cc_final: 0.7430 (p) REVERT: B 356 LYS cc_start: 0.8639 (tmmt) cc_final: 0.8194 (tmmt) REVERT: B 398 ASP cc_start: 0.6511 (t70) cc_final: 0.5891 (t0) REVERT: B 402 ILE cc_start: 0.6196 (OUTLIER) cc_final: 0.5793 (tp) REVERT: B 535 LYS cc_start: 0.8362 (tptt) cc_final: 0.7994 (mmmm) REVERT: B 616 ASN cc_start: 0.5630 (t0) cc_final: 0.5330 (t0) REVERT: B 659 SER cc_start: 0.8566 (m) cc_final: 0.8239 (p) REVERT: B 750 SER cc_start: 0.8319 (m) cc_final: 0.7958 (p) REVERT: B 759 PHE cc_start: 0.7239 (t80) cc_final: 0.6686 (t80) REVERT: B 800 PHE cc_start: 0.8164 (m-80) cc_final: 0.7535 (m-80) REVERT: B 868 GLU cc_start: 0.7202 (tp30) cc_final: 0.6741 (tp30) REVERT: B 884 SER cc_start: 0.8709 (m) cc_final: 0.8455 (p) REVERT: B 954 HIS cc_start: 0.7131 (m-70) cc_final: 0.6851 (m90) REVERT: B 983 ARG cc_start: 0.7559 (mtp180) cc_final: 0.7281 (mtm180) REVERT: B 1003 SER cc_start: 0.8350 (m) cc_final: 0.8005 (t) REVERT: B 1072 GLU cc_start: 0.8005 (pm20) cc_final: 0.7754 (pm20) REVERT: B 1081 ILE cc_start: 0.7938 (pt) cc_final: 0.7668 (mt) REVERT: B 1117 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7774 (p) REVERT: B 1118 ASP cc_start: 0.7375 (t70) cc_final: 0.6868 (t0) REVERT: B 1127 ASP cc_start: 0.7347 (t0) cc_final: 0.6956 (t0) REVERT: B 1141 LEU cc_start: 0.8363 (tt) cc_final: 0.8011 (tt) REVERT: C 121 ASN cc_start: 0.7943 (p0) cc_final: 0.7539 (p0) REVERT: C 128 ILE cc_start: 0.7796 (mt) cc_final: 0.7537 (mp) REVERT: C 129 LYS cc_start: 0.7451 (ttpt) cc_final: 0.6944 (ttpt) REVERT: C 164 ASN cc_start: 0.7700 (t0) cc_final: 0.7308 (t0) REVERT: C 190 PHE cc_start: 0.7742 (m-80) cc_final: 0.7465 (m-80) REVERT: C 228 ASP cc_start: 0.7495 (t70) cc_final: 0.7200 (t70) REVERT: C 275 PHE cc_start: 0.7828 (m-80) cc_final: 0.7457 (m-80) REVERT: C 329 PHE cc_start: 0.7766 (m-10) cc_final: 0.7502 (m-10) REVERT: C 408 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6951 (ppp-140) REVERT: C 546 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7138 (tp) REVERT: C 574 ASP cc_start: 0.7184 (t70) cc_final: 0.6151 (t0) REVERT: C 578 ASP cc_start: 0.6431 (t0) cc_final: 0.6016 (t70) REVERT: C 586 ASP cc_start: 0.7023 (t0) cc_final: 0.6443 (t0) REVERT: C 592 PHE cc_start: 0.8247 (p90) cc_final: 0.7938 (p90) REVERT: C 674 TYR cc_start: 0.7890 (t80) cc_final: 0.7684 (t80) REVERT: C 675 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6904 (mm-40) REVERT: C 708 SER cc_start: 0.8467 (t) cc_final: 0.8130 (m) REVERT: C 712 ILE cc_start: 0.8394 (tp) cc_final: 0.8173 (tp) REVERT: C 723 THR cc_start: 0.8517 (t) cc_final: 0.8275 (p) REVERT: C 725 GLU cc_start: 0.7114 (tt0) cc_final: 0.6845 (tt0) REVERT: C 737 ASP cc_start: 0.6830 (t0) cc_final: 0.6549 (t70) REVERT: C 773 GLU cc_start: 0.7210 (tt0) cc_final: 0.6903 (tt0) REVERT: C 776 LYS cc_start: 0.8317 (ttpm) cc_final: 0.7913 (ttpp) REVERT: C 780 GLU cc_start: 0.7174 (pt0) cc_final: 0.6844 (pt0) REVERT: C 790 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7896 (mtpt) REVERT: C 795 LYS cc_start: 0.8725 (mttt) cc_final: 0.8410 (mttm) REVERT: C 810 SER cc_start: 0.8619 (m) cc_final: 0.8019 (p) REVERT: C 854 LYS cc_start: 0.7945 (tmmt) cc_final: 0.7564 (tptp) REVERT: C 868 GLU cc_start: 0.6936 (tp30) cc_final: 0.6653 (tp30) REVERT: C 886 TRP cc_start: 0.8421 (p90) cc_final: 0.7908 (p90) REVERT: C 904 TYR cc_start: 0.7834 (m-10) cc_final: 0.7463 (m-10) REVERT: C 919 ASN cc_start: 0.7978 (m-40) cc_final: 0.7740 (m-40) REVERT: C 933 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8026 (ttmm) REVERT: C 957 GLN cc_start: 0.7455 (tm130) cc_final: 0.7036 (tm130) REVERT: C 977 LEU cc_start: 0.7654 (mp) cc_final: 0.7103 (mp) REVERT: C 980 ILE cc_start: 0.8878 (mt) cc_final: 0.8449 (mm) REVERT: C 998 THR cc_start: 0.8361 (t) cc_final: 0.8153 (t) REVERT: C 1014 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7464 (ttm-80) REVERT: C 1066 THR cc_start: 0.8439 (p) cc_final: 0.8226 (p) REVERT: C 1129 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8351 (m) REVERT: D 80 VAL cc_start: 0.8289 (t) cc_final: 0.7965 (p) REVERT: D 182 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.3873 (tt) REVERT: F 79 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5964 (pt0) REVERT: G 142 PHE cc_start: 0.4252 (OUTLIER) cc_final: 0.4006 (t80) outliers start: 199 outliers final: 118 residues processed: 841 average time/residue: 0.4208 time to fit residues: 557.8031 Evaluate side-chains 780 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 649 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Chi-restraints excluded: chain G residue 200 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 356 optimal weight: 0.1980 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 2.9990 chunk 353 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 52 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 955 ASN A 965 GLN A1048 HIS ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 563 GLN B1005 GLN B1048 HIS C 487 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1048 HIS C1101 HIS D 79 GLN ** G 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 31139 Z= 0.329 Angle : 0.634 11.839 42441 Z= 0.323 Chirality : 0.046 0.286 4863 Planarity : 0.005 0.071 5471 Dihedral : 6.490 76.708 4367 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 6.24 % Allowed : 15.26 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.12), residues: 3888 helix: 0.07 (0.20), residues: 652 sheet: -2.11 (0.16), residues: 816 loop : -2.93 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.009 0.001 HIS C1064 PHE 0.033 0.002 PHE A 190 TYR 0.026 0.002 TYR C 91 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 656 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6589 (tptp) REVERT: A 117 LEU cc_start: 0.8619 (tt) cc_final: 0.8344 (tt) REVERT: A 204 LYS cc_start: 0.8347 (tttp) cc_final: 0.7869 (ttmt) REVERT: A 233 ILE cc_start: 0.3334 (OUTLIER) cc_final: 0.3096 (mm) REVERT: A 273 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6382 (mtm180) REVERT: A 276 LEU cc_start: 0.8405 (tp) cc_final: 0.7958 (tt) REVERT: A 307 THR cc_start: 0.7639 (m) cc_final: 0.7342 (p) REVERT: A 314 GLN cc_start: 0.7475 (tp-100) cc_final: 0.7171 (tt0) REVERT: A 324 GLU cc_start: 0.6627 (mm-30) cc_final: 0.6393 (mm-30) REVERT: A 334 ASN cc_start: 0.7382 (t0) cc_final: 0.7034 (t0) REVERT: A 572 THR cc_start: 0.8188 (m) cc_final: 0.7560 (p) REVERT: A 751 ASN cc_start: 0.7822 (m-40) cc_final: 0.7340 (m110) REVERT: A 752 LEU cc_start: 0.8530 (mm) cc_final: 0.8295 (mt) REVERT: A 762 GLN cc_start: 0.7375 (pt0) cc_final: 0.7162 (pt0) REVERT: A 776 LYS cc_start: 0.8239 (tmmt) cc_final: 0.7855 (tmmt) REVERT: A 804 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7266 (mm-40) REVERT: A 825 LYS cc_start: 0.8331 (mtpm) cc_final: 0.8081 (mttm) REVERT: A 922 LEU cc_start: 0.8830 (tp) cc_final: 0.8519 (tt) REVERT: A 933 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8212 (mtmm) REVERT: A 935 GLN cc_start: 0.8199 (tt0) cc_final: 0.7983 (tt0) REVERT: A 949 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7644 (mm-40) REVERT: A 950 ASP cc_start: 0.6917 (t0) cc_final: 0.6523 (t0) REVERT: A 953 ASN cc_start: 0.8372 (m-40) cc_final: 0.8060 (m-40) REVERT: A 954 HIS cc_start: 0.7948 (m-70) cc_final: 0.7619 (m170) REVERT: A 961 THR cc_start: 0.8702 (p) cc_final: 0.8460 (t) REVERT: A 964 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7716 (mtmt) REVERT: A 975 SER cc_start: 0.8776 (m) cc_final: 0.8183 (t) REVERT: A 976 VAL cc_start: 0.8731 (m) cc_final: 0.8284 (p) REVERT: A 979 ASP cc_start: 0.7530 (m-30) cc_final: 0.7319 (m-30) REVERT: A 980 ILE cc_start: 0.8895 (mt) cc_final: 0.8427 (tp) REVERT: A 981 PHE cc_start: 0.7861 (m-10) cc_final: 0.7595 (m-10) REVERT: A 1017 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6586 (tm-30) REVERT: A 1031 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 1058 HIS cc_start: 0.7932 (m-70) cc_final: 0.7708 (m-70) REVERT: A 1117 THR cc_start: 0.8322 (p) cc_final: 0.8071 (t) REVERT: A 1128 VAL cc_start: 0.7917 (p) cc_final: 0.7706 (m) REVERT: B 66 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7493 (t-90) REVERT: B 83 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.7112 (p) REVERT: B 99 ASN cc_start: 0.7966 (p0) cc_final: 0.7742 (p0) REVERT: B 127 VAL cc_start: 0.8129 (t) cc_final: 0.7330 (m) REVERT: B 165 ASN cc_start: 0.6452 (OUTLIER) cc_final: 0.6004 (p0) REVERT: B 193 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7426 (ttmt) REVERT: B 223 LEU cc_start: 0.7996 (mp) cc_final: 0.7714 (mt) REVERT: B 267 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.7583 (m) REVERT: B 281 GLU cc_start: 0.7133 (pp20) cc_final: 0.6757 (pp20) REVERT: B 293 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8375 (tp) REVERT: B 307 THR cc_start: 0.7994 (m) cc_final: 0.7508 (p) REVERT: B 314 GLN cc_start: 0.7638 (tp40) cc_final: 0.7425 (tp40) REVERT: B 355 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8314 (ttt-90) REVERT: B 356 LYS cc_start: 0.8695 (tmmt) cc_final: 0.8252 (tmtt) REVERT: B 398 ASP cc_start: 0.6601 (t70) cc_final: 0.5816 (t0) REVERT: B 402 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6060 (tt) REVERT: B 535 LYS cc_start: 0.8380 (tptt) cc_final: 0.8034 (mmmm) REVERT: B 542 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7802 (t0) REVERT: B 551 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7806 (m) REVERT: B 659 SER cc_start: 0.8651 (m) cc_final: 0.8424 (p) REVERT: B 740 MET cc_start: 0.8101 (mtp) cc_final: 0.7876 (mtp) REVERT: B 750 SER cc_start: 0.8519 (m) cc_final: 0.8002 (p) REVERT: B 759 PHE cc_start: 0.7085 (t80) cc_final: 0.6703 (t80) REVERT: B 765 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7408 (ttp80) REVERT: B 868 GLU cc_start: 0.7197 (tp30) cc_final: 0.6737 (tp30) REVERT: B 954 HIS cc_start: 0.7227 (m-70) cc_final: 0.6854 (m90) REVERT: B 957 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 1003 SER cc_start: 0.8504 (m) cc_final: 0.8122 (t) REVERT: B 1014 ARG cc_start: 0.7545 (ttm110) cc_final: 0.7220 (ttm110) REVERT: B 1118 ASP cc_start: 0.7473 (t70) cc_final: 0.6947 (t0) REVERT: B 1127 ASP cc_start: 0.7539 (t0) cc_final: 0.7181 (t0) REVERT: B 1141 LEU cc_start: 0.8388 (tt) cc_final: 0.8043 (tt) REVERT: C 92 PHE cc_start: 0.6936 (t80) cc_final: 0.6653 (t80) REVERT: C 99 ASN cc_start: 0.7289 (t0) cc_final: 0.6882 (t0) REVERT: C 120 VAL cc_start: 0.7995 (t) cc_final: 0.7657 (p) REVERT: C 128 ILE cc_start: 0.7873 (mt) cc_final: 0.7643 (mp) REVERT: C 129 LYS cc_start: 0.7480 (ttpt) cc_final: 0.6926 (ttpt) REVERT: C 164 ASN cc_start: 0.7703 (t0) cc_final: 0.7473 (t0) REVERT: C 190 PHE cc_start: 0.7744 (m-80) cc_final: 0.7530 (m-80) REVERT: C 228 ASP cc_start: 0.7286 (t70) cc_final: 0.6971 (t70) REVERT: C 275 PHE cc_start: 0.7916 (m-80) cc_final: 0.7424 (m-10) REVERT: C 408 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7007 (ppp-140) REVERT: C 546 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7289 (tp) REVERT: C 558 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7613 (mmtp) REVERT: C 574 ASP cc_start: 0.7338 (t70) cc_final: 0.6604 (t0) REVERT: C 578 ASP cc_start: 0.6372 (t0) cc_final: 0.5970 (t70) REVERT: C 592 PHE cc_start: 0.8211 (p90) cc_final: 0.7865 (p90) REVERT: C 599 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8283 (p) REVERT: C 674 TYR cc_start: 0.8072 (t80) cc_final: 0.7831 (t80) REVERT: C 708 SER cc_start: 0.8567 (t) cc_final: 0.8164 (m) REVERT: C 712 ILE cc_start: 0.8459 (tp) cc_final: 0.8254 (tp) REVERT: C 723 THR cc_start: 0.8508 (t) cc_final: 0.8290 (p) REVERT: C 725 GLU cc_start: 0.7170 (tt0) cc_final: 0.6881 (tt0) REVERT: C 737 ASP cc_start: 0.6801 (t0) cc_final: 0.6462 (t70) REVERT: C 776 LYS cc_start: 0.8367 (ttpm) cc_final: 0.8113 (ttpp) REVERT: C 790 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7953 (mtpt) REVERT: C 795 LYS cc_start: 0.8820 (mttt) cc_final: 0.8530 (mttm) REVERT: C 810 SER cc_start: 0.8671 (m) cc_final: 0.8048 (p) REVERT: C 854 LYS cc_start: 0.7939 (tmmt) cc_final: 0.7648 (tptp) REVERT: C 868 GLU cc_start: 0.6910 (tp30) cc_final: 0.6616 (tp30) REVERT: C 884 SER cc_start: 0.8941 (m) cc_final: 0.8731 (p) REVERT: C 886 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.7852 (p90) REVERT: C 933 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8051 (ttmm) REVERT: C 957 GLN cc_start: 0.7466 (tm130) cc_final: 0.6737 (tm130) REVERT: C 977 LEU cc_start: 0.7569 (mp) cc_final: 0.6676 (mp) REVERT: C 980 ILE cc_start: 0.8777 (mt) cc_final: 0.8500 (mm) REVERT: C 981 PHE cc_start: 0.8020 (m-80) cc_final: 0.7538 (m-80) REVERT: C 1014 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7564 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7768 (mmmt) REVERT: D 80 VAL cc_start: 0.8532 (t) cc_final: 0.8155 (p) REVERT: D 182 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3449 (tt) REVERT: E 194 TYR cc_start: 0.2736 (OUTLIER) cc_final: 0.1429 (m-80) REVERT: G 142 PHE cc_start: 0.4532 (OUTLIER) cc_final: 0.4265 (t80) outliers start: 212 outliers final: 137 residues processed: 802 average time/residue: 0.4514 time to fit residues: 581.0528 Evaluate side-chains 780 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 624 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 239 optimal weight: 8.9990 chunk 357 optimal weight: 0.8980 chunk 378 optimal weight: 20.0000 chunk 186 optimal weight: 0.9990 chunk 339 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 542 ASN B 563 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31139 Z= 0.241 Angle : 0.596 8.360 42441 Z= 0.302 Chirality : 0.045 0.289 4863 Planarity : 0.005 0.075 5471 Dihedral : 6.132 74.128 4346 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 5.80 % Allowed : 16.11 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 3888 helix: 0.41 (0.20), residues: 658 sheet: -1.83 (0.17), residues: 847 loop : -2.80 (0.11), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.006 0.001 HIS B 49 PHE 0.024 0.002 PHE C 168 TYR 0.028 0.001 TYR C 91 ARG 0.006 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 638 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6514 (tptp) REVERT: A 117 LEU cc_start: 0.8591 (tt) cc_final: 0.8258 (tt) REVERT: A 233 ILE cc_start: 0.3325 (OUTLIER) cc_final: 0.3061 (mm) REVERT: A 269 TYR cc_start: 0.7100 (m-10) cc_final: 0.6889 (m-80) REVERT: A 276 LEU cc_start: 0.8379 (tp) cc_final: 0.7922 (tt) REVERT: A 307 THR cc_start: 0.7560 (m) cc_final: 0.7244 (p) REVERT: A 314 GLN cc_start: 0.7500 (tp-100) cc_final: 0.7155 (tt0) REVERT: A 324 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6340 (mm-30) REVERT: A 334 ASN cc_start: 0.7312 (t0) cc_final: 0.6979 (t0) REVERT: A 480 CYS cc_start: 0.4930 (OUTLIER) cc_final: 0.3992 (p) REVERT: A 751 ASN cc_start: 0.7755 (m-40) cc_final: 0.7378 (m110) REVERT: A 752 LEU cc_start: 0.8580 (mm) cc_final: 0.8276 (mt) REVERT: A 762 GLN cc_start: 0.7290 (pt0) cc_final: 0.7069 (pt0) REVERT: A 773 GLU cc_start: 0.7285 (tt0) cc_final: 0.6901 (tt0) REVERT: A 776 LYS cc_start: 0.8255 (tmmt) cc_final: 0.7871 (tmmt) REVERT: A 795 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8343 (mptt) REVERT: A 801 ASN cc_start: 0.5984 (OUTLIER) cc_final: 0.5576 (t0) REVERT: A 804 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7201 (mm-40) REVERT: A 825 LYS cc_start: 0.8334 (mtpm) cc_final: 0.8058 (mttm) REVERT: A 855 PHE cc_start: 0.8626 (m-80) cc_final: 0.8196 (m-80) REVERT: A 922 LEU cc_start: 0.8787 (tp) cc_final: 0.8487 (tt) REVERT: A 933 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8213 (mtmm) REVERT: A 953 ASN cc_start: 0.8266 (m-40) cc_final: 0.7318 (m-40) REVERT: A 957 GLN cc_start: 0.7397 (pt0) cc_final: 0.6936 (pm20) REVERT: A 964 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7685 (mtmt) REVERT: A 975 SER cc_start: 0.8783 (m) cc_final: 0.8179 (t) REVERT: A 976 VAL cc_start: 0.8656 (m) cc_final: 0.8251 (p) REVERT: A 979 ASP cc_start: 0.7529 (m-30) cc_final: 0.7313 (m-30) REVERT: A 980 ILE cc_start: 0.8835 (mt) cc_final: 0.8432 (tp) REVERT: A 981 PHE cc_start: 0.7798 (m-10) cc_final: 0.7578 (m-10) REVERT: A 1017 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6600 (tm-30) REVERT: A 1031 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7409 (mt-10) REVERT: A 1058 HIS cc_start: 0.7887 (m-70) cc_final: 0.7636 (m-70) REVERT: A 1117 THR cc_start: 0.8420 (p) cc_final: 0.8160 (t) REVERT: B 66 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7561 (t-90) REVERT: B 83 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7075 (p) REVERT: B 99 ASN cc_start: 0.7903 (p0) cc_final: 0.7622 (p0) REVERT: B 106 PHE cc_start: 0.7521 (m-80) cc_final: 0.7287 (m-80) REVERT: B 127 VAL cc_start: 0.8060 (t) cc_final: 0.7329 (m) REVERT: B 165 ASN cc_start: 0.6110 (OUTLIER) cc_final: 0.5574 (p0) REVERT: B 193 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7511 (ttmt) REVERT: B 212 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5825 (pp20) REVERT: B 281 GLU cc_start: 0.7037 (pp20) cc_final: 0.6563 (pp20) REVERT: B 307 THR cc_start: 0.8038 (m) cc_final: 0.7532 (p) REVERT: B 338 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: B 355 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8335 (ttt-90) REVERT: B 356 LYS cc_start: 0.8712 (tmmt) cc_final: 0.8295 (tmtt) REVERT: B 398 ASP cc_start: 0.6588 (t70) cc_final: 0.5824 (t0) REVERT: B 402 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6177 (tt) REVERT: B 465 GLU cc_start: 0.6555 (tt0) cc_final: 0.6354 (tt0) REVERT: B 535 LYS cc_start: 0.8332 (tptt) cc_final: 0.8003 (mmmm) REVERT: B 542 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8134 (t0) REVERT: B 551 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (m) REVERT: B 750 SER cc_start: 0.8344 (m) cc_final: 0.7916 (p) REVERT: B 765 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7373 (ttp80) REVERT: B 820 ASP cc_start: 0.7668 (t70) cc_final: 0.7295 (t0) REVERT: B 821 LEU cc_start: 0.8135 (mp) cc_final: 0.7806 (mp) REVERT: B 868 GLU cc_start: 0.7121 (tp30) cc_final: 0.6701 (tp30) REVERT: B 902 MET cc_start: 0.8000 (mmm) cc_final: 0.7784 (tpp) REVERT: B 935 GLN cc_start: 0.7690 (tp-100) cc_final: 0.7457 (tp-100) REVERT: B 954 HIS cc_start: 0.7197 (m-70) cc_final: 0.6843 (m90) REVERT: B 957 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7011 (tm-30) REVERT: B 1003 SER cc_start: 0.8522 (m) cc_final: 0.8116 (t) REVERT: B 1014 ARG cc_start: 0.7528 (ttm110) cc_final: 0.7194 (ttm110) REVERT: B 1017 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6778 (tm-30) REVERT: B 1118 ASP cc_start: 0.7535 (t70) cc_final: 0.6941 (t0) REVERT: B 1127 ASP cc_start: 0.7611 (t0) cc_final: 0.7235 (t0) REVERT: B 1141 LEU cc_start: 0.8366 (tt) cc_final: 0.8008 (tt) REVERT: C 92 PHE cc_start: 0.6987 (t80) cc_final: 0.6769 (t80) REVERT: C 96 GLU cc_start: 0.6422 (pt0) cc_final: 0.6187 (pt0) REVERT: C 99 ASN cc_start: 0.7291 (t0) cc_final: 0.7065 (t0) REVERT: C 128 ILE cc_start: 0.7906 (mt) cc_final: 0.7649 (mp) REVERT: C 129 LYS cc_start: 0.7505 (ttpt) cc_final: 0.6912 (ttpt) REVERT: C 164 ASN cc_start: 0.7693 (t0) cc_final: 0.7472 (t0) REVERT: C 190 PHE cc_start: 0.7742 (m-80) cc_final: 0.7489 (m-80) REVERT: C 228 ASP cc_start: 0.7321 (t70) cc_final: 0.7003 (t70) REVERT: C 275 PHE cc_start: 0.7927 (m-80) cc_final: 0.7400 (m-10) REVERT: C 297 SER cc_start: 0.7628 (m) cc_final: 0.7253 (p) REVERT: C 408 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7114 (ppp-140) REVERT: C 536 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7941 (p0) REVERT: C 546 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7132 (tt) REVERT: C 558 LYS cc_start: 0.7951 (mmtp) cc_final: 0.7600 (mmtp) REVERT: C 574 ASP cc_start: 0.7367 (t70) cc_final: 0.6630 (t0) REVERT: C 592 PHE cc_start: 0.8210 (p90) cc_final: 0.7997 (p90) REVERT: C 599 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8340 (p) REVERT: C 615 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8055 (m) REVERT: C 674 TYR cc_start: 0.7915 (t80) cc_final: 0.7627 (t80) REVERT: C 708 SER cc_start: 0.8508 (t) cc_final: 0.8092 (m) REVERT: C 711 SER cc_start: 0.7685 (m) cc_final: 0.7447 (p) REVERT: C 723 THR cc_start: 0.8515 (t) cc_final: 0.8286 (p) REVERT: C 725 GLU cc_start: 0.7169 (tt0) cc_final: 0.6881 (tt0) REVERT: C 737 ASP cc_start: 0.6628 (t0) cc_final: 0.6315 (t70) REVERT: C 790 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7952 (mtpt) REVERT: C 795 LYS cc_start: 0.8791 (mttt) cc_final: 0.8486 (mttm) REVERT: C 810 SER cc_start: 0.8665 (m) cc_final: 0.8015 (p) REVERT: C 854 LYS cc_start: 0.7852 (tmmt) cc_final: 0.7642 (tptp) REVERT: C 868 GLU cc_start: 0.6851 (tp30) cc_final: 0.6552 (tp30) REVERT: C 886 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.7785 (p90) REVERT: C 902 MET cc_start: 0.7882 (tpp) cc_final: 0.7521 (mmm) REVERT: C 933 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8053 (ttmm) REVERT: C 957 GLN cc_start: 0.7437 (tm130) cc_final: 0.6683 (tm130) REVERT: C 977 LEU cc_start: 0.7536 (mp) cc_final: 0.6919 (mp) REVERT: C 980 ILE cc_start: 0.8767 (mt) cc_final: 0.8447 (mm) REVERT: C 981 PHE cc_start: 0.8046 (m-80) cc_final: 0.7685 (m-80) REVERT: C 1002 GLN cc_start: 0.7814 (tp40) cc_final: 0.6856 (tm-30) REVERT: C 1014 ARG cc_start: 0.7790 (tpp80) cc_final: 0.7525 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7774 (mmmt) REVERT: D 182 LEU cc_start: 0.4344 (OUTLIER) cc_final: 0.3663 (tt) REVERT: E 194 TYR cc_start: 0.2493 (OUTLIER) cc_final: 0.1228 (m-80) REVERT: F 182 LEU cc_start: 0.7795 (tp) cc_final: 0.7102 (tt) REVERT: G 142 PHE cc_start: 0.4759 (OUTLIER) cc_final: 0.4331 (t80) REVERT: G 183 LEU cc_start: -0.4998 (OUTLIER) cc_final: -0.5299 (tp) outliers start: 197 outliers final: 136 residues processed: 770 average time/residue: 0.4599 time to fit residues: 568.7786 Evaluate side-chains 782 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 624 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.3980 chunk 215 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 282 optimal weight: 0.0980 chunk 156 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 690 GLN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 505 HIS B 542 ASN B1048 HIS ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31139 Z= 0.217 Angle : 0.587 12.763 42441 Z= 0.293 Chirality : 0.044 0.272 4863 Planarity : 0.004 0.078 5471 Dihedral : 6.071 73.562 4344 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.77 % Allowed : 17.41 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.13), residues: 3888 helix: 0.62 (0.21), residues: 648 sheet: -1.68 (0.17), residues: 832 loop : -2.65 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.010 0.001 HIS B 505 PHE 0.030 0.001 PHE A 190 TYR 0.023 0.001 TYR C 91 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 633 time to evaluate : 3.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6514 (tptp) REVERT: A 117 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8236 (tt) REVERT: A 233 ILE cc_start: 0.3350 (OUTLIER) cc_final: 0.3074 (mm) REVERT: A 269 TYR cc_start: 0.7058 (m-10) cc_final: 0.6846 (m-80) REVERT: A 276 LEU cc_start: 0.8394 (tp) cc_final: 0.7861 (tt) REVERT: A 307 THR cc_start: 0.7527 (m) cc_final: 0.7186 (p) REVERT: A 314 GLN cc_start: 0.7503 (tp-100) cc_final: 0.7157 (tt0) REVERT: A 324 GLU cc_start: 0.6588 (mm-30) cc_final: 0.6349 (mm-30) REVERT: A 334 ASN cc_start: 0.7260 (t0) cc_final: 0.6953 (t0) REVERT: A 663 ASP cc_start: 0.6940 (m-30) cc_final: 0.6739 (m-30) REVERT: A 708 SER cc_start: 0.8201 (m) cc_final: 0.7984 (p) REVERT: A 752 LEU cc_start: 0.8598 (mm) cc_final: 0.8364 (mt) REVERT: A 762 GLN cc_start: 0.7306 (pt0) cc_final: 0.7027 (pt0) REVERT: A 776 LYS cc_start: 0.8276 (tmmt) cc_final: 0.7878 (tmmt) REVERT: A 801 ASN cc_start: 0.5796 (OUTLIER) cc_final: 0.5402 (t0) REVERT: A 825 LYS cc_start: 0.8321 (mtpm) cc_final: 0.8037 (mttm) REVERT: A 855 PHE cc_start: 0.8585 (m-80) cc_final: 0.8199 (m-80) REVERT: A 922 LEU cc_start: 0.8778 (tp) cc_final: 0.8483 (tt) REVERT: A 933 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8237 (mtmm) REVERT: A 953 ASN cc_start: 0.8267 (m-40) cc_final: 0.7535 (m110) REVERT: A 957 GLN cc_start: 0.7410 (pt0) cc_final: 0.7056 (pm20) REVERT: A 964 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7684 (mtmt) REVERT: A 975 SER cc_start: 0.8771 (m) cc_final: 0.8179 (t) REVERT: A 976 VAL cc_start: 0.8616 (m) cc_final: 0.8379 (m) REVERT: A 979 ASP cc_start: 0.7568 (m-30) cc_final: 0.7290 (m-30) REVERT: A 980 ILE cc_start: 0.8671 (mt) cc_final: 0.8313 (tp) REVERT: A 981 PHE cc_start: 0.7786 (m-10) cc_final: 0.7561 (m-10) REVERT: A 1017 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6615 (tm-30) REVERT: A 1031 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 1117 THR cc_start: 0.8436 (p) cc_final: 0.8185 (t) REVERT: B 66 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7545 (t-90) REVERT: B 83 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.7060 (p) REVERT: B 99 ASN cc_start: 0.7928 (p0) cc_final: 0.7615 (p0) REVERT: B 127 VAL cc_start: 0.8059 (t) cc_final: 0.7317 (m) REVERT: B 165 ASN cc_start: 0.6155 (OUTLIER) cc_final: 0.5589 (p0) REVERT: B 193 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7580 (ttmt) REVERT: B 212 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5814 (pp20) REVERT: B 223 LEU cc_start: 0.7914 (mp) cc_final: 0.7632 (mt) REVERT: B 281 GLU cc_start: 0.7024 (pp20) cc_final: 0.6588 (pp20) REVERT: B 307 THR cc_start: 0.8047 (m) cc_final: 0.7538 (p) REVERT: B 338 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.6039 (m-80) REVERT: B 355 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8350 (ttt-90) REVERT: B 356 LYS cc_start: 0.8681 (tmmt) cc_final: 0.8289 (tmtt) REVERT: B 398 ASP cc_start: 0.6581 (t70) cc_final: 0.5895 (t0) REVERT: B 535 LYS cc_start: 0.8333 (tptt) cc_final: 0.8040 (mmmm) REVERT: B 542 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8209 (t0) REVERT: B 551 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7849 (m) REVERT: B 643 PHE cc_start: 0.7815 (t80) cc_final: 0.7559 (t80) REVERT: B 739 THR cc_start: 0.8376 (m) cc_final: 0.8160 (m) REVERT: B 750 SER cc_start: 0.8350 (m) cc_final: 0.7927 (p) REVERT: B 755 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 765 ARG cc_start: 0.7617 (ttp80) cc_final: 0.7335 (ttp80) REVERT: B 820 ASP cc_start: 0.7646 (t70) cc_final: 0.7318 (t0) REVERT: B 821 LEU cc_start: 0.8074 (mp) cc_final: 0.7849 (tt) REVERT: B 868 GLU cc_start: 0.7111 (tp30) cc_final: 0.6711 (tp30) REVERT: B 902 MET cc_start: 0.8063 (mmm) cc_final: 0.7747 (mmm) REVERT: B 954 HIS cc_start: 0.7201 (m-70) cc_final: 0.6878 (m90) REVERT: B 957 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7029 (tm-30) REVERT: B 1003 SER cc_start: 0.8504 (m) cc_final: 0.8107 (t) REVERT: B 1014 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7214 (ttm110) REVERT: B 1118 ASP cc_start: 0.7523 (t70) cc_final: 0.6899 (t0) REVERT: B 1127 ASP cc_start: 0.7642 (t0) cc_final: 0.7276 (t0) REVERT: B 1141 LEU cc_start: 0.8347 (tt) cc_final: 0.7990 (tt) REVERT: C 96 GLU cc_start: 0.6513 (pt0) cc_final: 0.6214 (pt0) REVERT: C 99 ASN cc_start: 0.7256 (t0) cc_final: 0.7021 (t0) REVERT: C 128 ILE cc_start: 0.7980 (mt) cc_final: 0.7690 (mp) REVERT: C 129 LYS cc_start: 0.7442 (ttpt) cc_final: 0.6821 (tppt) REVERT: C 164 ASN cc_start: 0.7746 (t0) cc_final: 0.7511 (t0) REVERT: C 190 PHE cc_start: 0.7637 (m-80) cc_final: 0.7389 (m-80) REVERT: C 228 ASP cc_start: 0.7320 (t70) cc_final: 0.7031 (t70) REVERT: C 275 PHE cc_start: 0.7931 (m-80) cc_final: 0.7406 (m-10) REVERT: C 297 SER cc_start: 0.7611 (m) cc_final: 0.7229 (p) REVERT: C 327 VAL cc_start: 0.8092 (t) cc_final: 0.7851 (m) REVERT: C 408 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7045 (ppp-140) REVERT: C 536 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8266 (p0) REVERT: C 546 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7181 (tt) REVERT: C 558 LYS cc_start: 0.7928 (mmtp) cc_final: 0.7555 (mmtp) REVERT: C 574 ASP cc_start: 0.7326 (t70) cc_final: 0.6583 (t0) REVERT: C 592 PHE cc_start: 0.8130 (p90) cc_final: 0.7862 (p90) REVERT: C 599 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8299 (p) REVERT: C 674 TYR cc_start: 0.7883 (t80) cc_final: 0.7663 (t80) REVERT: C 708 SER cc_start: 0.8494 (t) cc_final: 0.8094 (p) REVERT: C 711 SER cc_start: 0.7708 (m) cc_final: 0.7503 (p) REVERT: C 723 THR cc_start: 0.8515 (t) cc_final: 0.8291 (p) REVERT: C 725 GLU cc_start: 0.7191 (tt0) cc_final: 0.6909 (tt0) REVERT: C 737 ASP cc_start: 0.6610 (t0) cc_final: 0.6321 (t70) REVERT: C 790 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7914 (ttmm) REVERT: C 795 LYS cc_start: 0.8776 (mttt) cc_final: 0.8478 (mttm) REVERT: C 810 SER cc_start: 0.8674 (m) cc_final: 0.8013 (p) REVERT: C 811 LYS cc_start: 0.8676 (tttp) cc_final: 0.8318 (tttm) REVERT: C 854 LYS cc_start: 0.7895 (tmmt) cc_final: 0.7617 (tptp) REVERT: C 868 GLU cc_start: 0.6862 (tp30) cc_final: 0.6599 (tp30) REVERT: C 886 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7765 (p90) REVERT: C 933 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8065 (ttmm) REVERT: C 957 GLN cc_start: 0.7435 (tm130) cc_final: 0.6708 (tm130) REVERT: C 977 LEU cc_start: 0.7542 (mp) cc_final: 0.6877 (mp) REVERT: C 980 ILE cc_start: 0.8737 (mt) cc_final: 0.8424 (mm) REVERT: C 981 PHE cc_start: 0.8058 (m-80) cc_final: 0.7716 (m-80) REVERT: C 1002 GLN cc_start: 0.7804 (tp40) cc_final: 0.6870 (tm-30) REVERT: C 1014 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7508 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7669 (mmmt) REVERT: D 182 LEU cc_start: 0.4418 (mp) cc_final: 0.3726 (tt) REVERT: E 194 TYR cc_start: 0.2550 (OUTLIER) cc_final: 0.1199 (m-80) REVERT: F 182 LEU cc_start: 0.7949 (tp) cc_final: 0.7361 (tt) REVERT: G 183 LEU cc_start: -0.5025 (OUTLIER) cc_final: -0.5378 (tp) outliers start: 196 outliers final: 144 residues processed: 771 average time/residue: 0.4485 time to fit residues: 552.1502 Evaluate side-chains 777 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 615 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 379 optimal weight: 50.0000 chunk 314 optimal weight: 0.0570 chunk 175 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 784 GLN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 542 ASN C 540 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31139 Z= 0.206 Angle : 0.586 11.906 42441 Z= 0.291 Chirality : 0.044 0.278 4863 Planarity : 0.004 0.075 5471 Dihedral : 6.111 72.922 4344 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.16 % Allowed : 17.38 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.13), residues: 3888 helix: 0.72 (0.21), residues: 649 sheet: -1.66 (0.17), residues: 797 loop : -2.57 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.001 HIS B1048 PHE 0.031 0.001 PHE A 190 TYR 0.029 0.001 TYR C 91 ARG 0.006 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 628 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6491 (tptp) REVERT: A 117 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8226 (tt) REVERT: A 233 ILE cc_start: 0.3341 (OUTLIER) cc_final: 0.3062 (mm) REVERT: A 269 TYR cc_start: 0.7040 (m-10) cc_final: 0.6830 (m-80) REVERT: A 276 LEU cc_start: 0.8414 (tp) cc_final: 0.7856 (tt) REVERT: A 314 GLN cc_start: 0.7499 (tp-100) cc_final: 0.7164 (tt0) REVERT: A 324 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6318 (mm-30) REVERT: A 334 ASN cc_start: 0.7250 (t0) cc_final: 0.6955 (t0) REVERT: A 480 CYS cc_start: 0.4867 (OUTLIER) cc_final: 0.4060 (p) REVERT: A 708 SER cc_start: 0.8174 (m) cc_final: 0.7950 (p) REVERT: A 717 ASN cc_start: 0.5945 (t0) cc_final: 0.5538 (t0) REVERT: A 752 LEU cc_start: 0.8513 (mm) cc_final: 0.8251 (mt) REVERT: A 762 GLN cc_start: 0.7242 (pt0) cc_final: 0.6930 (pt0) REVERT: A 776 LYS cc_start: 0.8271 (tmmt) cc_final: 0.7893 (tmmt) REVERT: A 790 LYS cc_start: 0.7892 (mtpt) cc_final: 0.7659 (mtpt) REVERT: A 801 ASN cc_start: 0.5800 (OUTLIER) cc_final: 0.5396 (t0) REVERT: A 825 LYS cc_start: 0.8334 (mtpm) cc_final: 0.8036 (mttm) REVERT: A 855 PHE cc_start: 0.8575 (m-80) cc_final: 0.8186 (m-80) REVERT: A 922 LEU cc_start: 0.8744 (tp) cc_final: 0.8474 (tt) REVERT: A 933 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8219 (mtmm) REVERT: A 953 ASN cc_start: 0.8291 (m-40) cc_final: 0.7589 (m-40) REVERT: A 957 GLN cc_start: 0.7416 (pt0) cc_final: 0.7120 (pm20) REVERT: A 964 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7699 (mtmt) REVERT: A 975 SER cc_start: 0.8756 (m) cc_final: 0.8163 (t) REVERT: A 976 VAL cc_start: 0.8627 (m) cc_final: 0.8325 (m) REVERT: A 980 ILE cc_start: 0.8667 (mt) cc_final: 0.8302 (tp) REVERT: A 981 PHE cc_start: 0.7786 (m-10) cc_final: 0.7548 (m-10) REVERT: A 1017 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6618 (tm-30) REVERT: A 1031 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 1117 THR cc_start: 0.8429 (p) cc_final: 0.8169 (t) REVERT: B 66 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7527 (t-90) REVERT: B 83 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7085 (p) REVERT: B 99 ASN cc_start: 0.7918 (p0) cc_final: 0.7573 (p0) REVERT: B 127 VAL cc_start: 0.8077 (t) cc_final: 0.7339 (m) REVERT: B 165 ASN cc_start: 0.6152 (OUTLIER) cc_final: 0.5586 (p0) REVERT: B 193 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7515 (ttmt) REVERT: B 212 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5830 (pp20) REVERT: B 223 LEU cc_start: 0.7929 (mp) cc_final: 0.7654 (mt) REVERT: B 224 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: B 307 THR cc_start: 0.8063 (m) cc_final: 0.7539 (p) REVERT: B 338 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.6006 (m-80) REVERT: B 355 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8355 (ttt-90) REVERT: B 356 LYS cc_start: 0.8683 (tmmt) cc_final: 0.8297 (tmtt) REVERT: B 398 ASP cc_start: 0.6537 (t70) cc_final: 0.5846 (t0) REVERT: B 402 ILE cc_start: 0.6744 (OUTLIER) cc_final: 0.6352 (tt) REVERT: B 535 LYS cc_start: 0.8304 (tptt) cc_final: 0.8030 (mmmm) REVERT: B 539 VAL cc_start: 0.8053 (m) cc_final: 0.7807 (m) REVERT: B 543 PHE cc_start: 0.7324 (m-10) cc_final: 0.6998 (m-80) REVERT: B 574 ASP cc_start: 0.7386 (t70) cc_final: 0.7100 (t0) REVERT: B 643 PHE cc_start: 0.7852 (t80) cc_final: 0.7576 (t80) REVERT: B 750 SER cc_start: 0.8324 (m) cc_final: 0.7956 (p) REVERT: B 755 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 820 ASP cc_start: 0.7640 (t70) cc_final: 0.7294 (t0) REVERT: B 868 GLU cc_start: 0.7110 (tp30) cc_final: 0.6718 (tp30) REVERT: B 902 MET cc_start: 0.8031 (mmm) cc_final: 0.7710 (mmm) REVERT: B 921 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7739 (mtpp) REVERT: B 954 HIS cc_start: 0.7206 (m-70) cc_final: 0.6874 (m90) REVERT: B 957 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 1003 SER cc_start: 0.8505 (m) cc_final: 0.8142 (t) REVERT: B 1014 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7222 (ttm110) REVERT: B 1019 ARG cc_start: 0.7541 (ttp-110) cc_final: 0.7339 (ttp80) REVERT: B 1118 ASP cc_start: 0.7513 (t70) cc_final: 0.6885 (t0) REVERT: B 1127 ASP cc_start: 0.7662 (t0) cc_final: 0.7304 (t0) REVERT: B 1141 LEU cc_start: 0.8334 (tt) cc_final: 0.7961 (tt) REVERT: C 96 GLU cc_start: 0.6524 (pt0) cc_final: 0.6224 (pt0) REVERT: C 99 ASN cc_start: 0.7260 (t0) cc_final: 0.6979 (t0) REVERT: C 120 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7708 (p) REVERT: C 128 ILE cc_start: 0.7930 (mt) cc_final: 0.7705 (mp) REVERT: C 164 ASN cc_start: 0.7706 (t0) cc_final: 0.7461 (t0) REVERT: C 170 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.5666 (m-10) REVERT: C 190 PHE cc_start: 0.7623 (m-80) cc_final: 0.7374 (m-80) REVERT: C 228 ASP cc_start: 0.7368 (t70) cc_final: 0.7064 (t70) REVERT: C 275 PHE cc_start: 0.7932 (m-80) cc_final: 0.7407 (m-10) REVERT: C 297 SER cc_start: 0.7648 (m) cc_final: 0.7278 (p) REVERT: C 327 VAL cc_start: 0.8094 (t) cc_final: 0.7849 (m) REVERT: C 356 LYS cc_start: 0.7579 (tmmt) cc_final: 0.7283 (ttpt) REVERT: C 408 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7019 (ppp-140) REVERT: C 536 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8182 (p0) REVERT: C 546 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7187 (tt) REVERT: C 558 LYS cc_start: 0.7908 (mmtp) cc_final: 0.7537 (mmtp) REVERT: C 574 ASP cc_start: 0.7326 (t70) cc_final: 0.6629 (t0) REVERT: C 599 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8298 (p) REVERT: C 602 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.7955 (p) REVERT: C 708 SER cc_start: 0.8379 (t) cc_final: 0.7984 (p) REVERT: C 723 THR cc_start: 0.8516 (t) cc_final: 0.8296 (p) REVERT: C 725 GLU cc_start: 0.7189 (tt0) cc_final: 0.6914 (tt0) REVERT: C 737 ASP cc_start: 0.6722 (t0) cc_final: 0.6426 (t70) REVERT: C 790 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7909 (ttmm) REVERT: C 795 LYS cc_start: 0.8776 (mttt) cc_final: 0.8459 (mttm) REVERT: C 810 SER cc_start: 0.8668 (m) cc_final: 0.7995 (p) REVERT: C 854 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7609 (tptp) REVERT: C 868 GLU cc_start: 0.6831 (tp30) cc_final: 0.6559 (tp30) REVERT: C 886 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7757 (p90) REVERT: C 904 TYR cc_start: 0.7817 (m-10) cc_final: 0.7599 (m-10) REVERT: C 933 LYS cc_start: 0.8333 (mtpt) cc_final: 0.8053 (ttmm) REVERT: C 945 LEU cc_start: 0.8605 (mm) cc_final: 0.8397 (mp) REVERT: C 957 GLN cc_start: 0.7438 (tm130) cc_final: 0.6881 (tm130) REVERT: C 977 LEU cc_start: 0.7541 (mp) cc_final: 0.6807 (mp) REVERT: C 980 ILE cc_start: 0.8738 (mt) cc_final: 0.8413 (mm) REVERT: C 981 PHE cc_start: 0.8064 (m-80) cc_final: 0.7711 (m-80) REVERT: C 1002 GLN cc_start: 0.7823 (tp40) cc_final: 0.6878 (tm-30) REVERT: C 1014 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7518 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7662 (mmmt) REVERT: D 182 LEU cc_start: 0.4442 (OUTLIER) cc_final: 0.3850 (tt) REVERT: E 194 TYR cc_start: 0.2723 (OUTLIER) cc_final: 0.1320 (m-80) REVERT: F 182 LEU cc_start: 0.7910 (tp) cc_final: 0.7351 (tt) REVERT: G 183 LEU cc_start: -0.5056 (OUTLIER) cc_final: -0.5401 (tp) outliers start: 209 outliers final: 139 residues processed: 767 average time/residue: 0.4243 time to fit residues: 516.4992 Evaluate side-chains 775 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 612 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 276 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 319 optimal weight: 10.0000 chunk 211 optimal weight: 0.0060 chunk 377 optimal weight: 7.9990 chunk 236 optimal weight: 0.0570 chunk 230 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 66 HIS A 205 HIS A 690 GLN A 784 GLN A 913 GLN A 935 GLN A1002 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 895 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31139 Z= 0.165 Angle : 0.578 12.380 42441 Z= 0.284 Chirality : 0.044 0.252 4863 Planarity : 0.004 0.074 5471 Dihedral : 6.042 72.299 4344 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.60 % Allowed : 18.09 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.13), residues: 3888 helix: 0.87 (0.21), residues: 648 sheet: -1.46 (0.17), residues: 839 loop : -2.50 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.006 0.001 HIS A 205 PHE 0.032 0.001 PHE A 190 TYR 0.027 0.001 TYR C 91 ARG 0.006 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 624 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6468 (tptp) REVERT: A 117 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 233 ILE cc_start: 0.3337 (OUTLIER) cc_final: 0.3053 (mm) REVERT: A 276 LEU cc_start: 0.8412 (tp) cc_final: 0.7853 (tt) REVERT: A 314 GLN cc_start: 0.7500 (tp-100) cc_final: 0.6973 (tt0) REVERT: A 324 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6331 (mm-30) REVERT: A 334 ASN cc_start: 0.7210 (t0) cc_final: 0.6934 (t0) REVERT: A 480 CYS cc_start: 0.4840 (OUTLIER) cc_final: 0.3990 (p) REVERT: A 542 ASN cc_start: 0.8317 (t0) cc_final: 0.7763 (t0) REVERT: A 708 SER cc_start: 0.8114 (m) cc_final: 0.7886 (p) REVERT: A 717 ASN cc_start: 0.6008 (t0) cc_final: 0.5606 (t0) REVERT: A 752 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8311 (mt) REVERT: A 776 LYS cc_start: 0.8275 (tmmt) cc_final: 0.7631 (tmmt) REVERT: A 780 GLU cc_start: 0.7120 (pt0) cc_final: 0.6700 (pt0) REVERT: A 801 ASN cc_start: 0.5806 (OUTLIER) cc_final: 0.5406 (t0) REVERT: A 825 LYS cc_start: 0.8313 (mtpm) cc_final: 0.8024 (mttm) REVERT: A 855 PHE cc_start: 0.8507 (m-80) cc_final: 0.8115 (m-80) REVERT: A 922 LEU cc_start: 0.8741 (tp) cc_final: 0.8457 (tt) REVERT: A 933 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8259 (mtmm) REVERT: A 953 ASN cc_start: 0.8263 (m-40) cc_final: 0.7991 (m-40) REVERT: A 964 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7665 (mtmt) REVERT: A 975 SER cc_start: 0.8716 (m) cc_final: 0.8118 (t) REVERT: A 976 VAL cc_start: 0.8571 (m) cc_final: 0.8192 (p) REVERT: A 979 ASP cc_start: 0.7519 (m-30) cc_final: 0.7300 (m-30) REVERT: A 980 ILE cc_start: 0.8627 (mt) cc_final: 0.8315 (tt) REVERT: A 981 PHE cc_start: 0.7779 (m-10) cc_final: 0.7568 (m-10) REVERT: A 1017 GLU cc_start: 0.6981 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 1031 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 1117 THR cc_start: 0.8399 (p) cc_final: 0.8143 (t) REVERT: B 34 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7475 (mtt-85) REVERT: B 66 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7537 (t-90) REVERT: B 83 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.7071 (p) REVERT: B 99 ASN cc_start: 0.7884 (p0) cc_final: 0.7556 (p0) REVERT: B 127 VAL cc_start: 0.8094 (t) cc_final: 0.7339 (m) REVERT: B 165 ASN cc_start: 0.6093 (OUTLIER) cc_final: 0.5487 (p0) REVERT: B 193 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7562 (ttmt) REVERT: B 212 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5910 (pp20) REVERT: B 223 LEU cc_start: 0.7904 (mp) cc_final: 0.7628 (mt) REVERT: B 224 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 298 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7121 (mm-30) REVERT: B 307 THR cc_start: 0.8060 (m) cc_final: 0.7545 (p) REVERT: B 338 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: B 355 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8342 (ttt-90) REVERT: B 356 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8313 (tmtt) REVERT: B 398 ASP cc_start: 0.6545 (t70) cc_final: 0.5848 (t0) REVERT: B 402 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6383 (tt) REVERT: B 535 LYS cc_start: 0.8310 (tptt) cc_final: 0.8040 (mmmm) REVERT: B 539 VAL cc_start: 0.8008 (m) cc_final: 0.7775 (m) REVERT: B 543 PHE cc_start: 0.7352 (m-10) cc_final: 0.7043 (m-80) REVERT: B 574 ASP cc_start: 0.7401 (t70) cc_final: 0.7064 (t0) REVERT: B 643 PHE cc_start: 0.7858 (t80) cc_final: 0.7642 (t80) REVERT: B 750 SER cc_start: 0.8278 (m) cc_final: 0.7906 (p) REVERT: B 755 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 777 ASN cc_start: 0.7697 (m-40) cc_final: 0.7406 (m110) REVERT: B 820 ASP cc_start: 0.7567 (t70) cc_final: 0.7248 (t0) REVERT: B 868 GLU cc_start: 0.7101 (tp30) cc_final: 0.6717 (tp30) REVERT: B 902 MET cc_start: 0.7975 (mmm) cc_final: 0.7693 (mmm) REVERT: B 921 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7674 (mtpp) REVERT: B 954 HIS cc_start: 0.7189 (m-70) cc_final: 0.6834 (m90) REVERT: B 957 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 1003 SER cc_start: 0.8487 (m) cc_final: 0.8146 (t) REVERT: B 1014 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7219 (ttm110) REVERT: B 1019 ARG cc_start: 0.7457 (ttp-110) cc_final: 0.7165 (ttp-110) REVERT: B 1118 ASP cc_start: 0.7483 (t70) cc_final: 0.6867 (t0) REVERT: B 1127 ASP cc_start: 0.7674 (t0) cc_final: 0.7316 (t0) REVERT: B 1141 LEU cc_start: 0.8297 (tt) cc_final: 0.7933 (tt) REVERT: C 96 GLU cc_start: 0.6586 (pt0) cc_final: 0.6285 (pt0) REVERT: C 99 ASN cc_start: 0.7251 (t0) cc_final: 0.6977 (t0) REVERT: C 120 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7669 (p) REVERT: C 128 ILE cc_start: 0.7938 (mt) cc_final: 0.7726 (mp) REVERT: C 164 ASN cc_start: 0.7706 (t0) cc_final: 0.7433 (t0) REVERT: C 170 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: C 190 PHE cc_start: 0.7606 (m-80) cc_final: 0.7395 (m-80) REVERT: C 194 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7889 (p0) REVERT: C 228 ASP cc_start: 0.7334 (t70) cc_final: 0.7111 (t70) REVERT: C 275 PHE cc_start: 0.7917 (m-80) cc_final: 0.7379 (m-10) REVERT: C 297 SER cc_start: 0.7607 (m) cc_final: 0.7217 (p) REVERT: C 327 VAL cc_start: 0.8077 (t) cc_final: 0.7830 (m) REVERT: C 408 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6987 (ppp-140) REVERT: C 536 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8214 (p0) REVERT: C 546 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7179 (tt) REVERT: C 558 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7517 (mmtp) REVERT: C 574 ASP cc_start: 0.7353 (t70) cc_final: 0.6570 (t0) REVERT: C 599 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8366 (p) REVERT: C 708 SER cc_start: 0.8165 (t) cc_final: 0.7890 (p) REVERT: C 723 THR cc_start: 0.8523 (t) cc_final: 0.8303 (p) REVERT: C 725 GLU cc_start: 0.7193 (tt0) cc_final: 0.6918 (tt0) REVERT: C 737 ASP cc_start: 0.6675 (t0) cc_final: 0.6424 (t70) REVERT: C 790 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7943 (mtpt) REVERT: C 795 LYS cc_start: 0.8787 (mttt) cc_final: 0.8433 (mttm) REVERT: C 810 SER cc_start: 0.8698 (m) cc_final: 0.8060 (p) REVERT: C 854 LYS cc_start: 0.7772 (tmmt) cc_final: 0.7517 (tptp) REVERT: C 868 GLU cc_start: 0.6844 (tp30) cc_final: 0.6618 (tp30) REVERT: C 886 TRP cc_start: 0.8320 (p90) cc_final: 0.7745 (p90) REVERT: C 904 TYR cc_start: 0.7739 (m-10) cc_final: 0.7504 (m-10) REVERT: C 933 LYS cc_start: 0.8283 (mtpt) cc_final: 0.8031 (ttmm) REVERT: C 945 LEU cc_start: 0.8606 (mm) cc_final: 0.8402 (mp) REVERT: C 957 GLN cc_start: 0.7390 (tm130) cc_final: 0.7070 (tm130) REVERT: C 977 LEU cc_start: 0.7525 (mp) cc_final: 0.6782 (mp) REVERT: C 980 ILE cc_start: 0.8739 (mt) cc_final: 0.8429 (mm) REVERT: C 981 PHE cc_start: 0.8042 (m-80) cc_final: 0.7683 (m-80) REVERT: C 1002 GLN cc_start: 0.7753 (tp40) cc_final: 0.6840 (tm-30) REVERT: C 1014 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7447 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7637 (mmmt) REVERT: D 182 LEU cc_start: 0.4377 (OUTLIER) cc_final: 0.3809 (tt) REVERT: E 194 TYR cc_start: 0.2859 (OUTLIER) cc_final: 0.1388 (m-80) REVERT: F 182 LEU cc_start: 0.7933 (tp) cc_final: 0.7364 (tt) REVERT: G 183 LEU cc_start: -0.5079 (OUTLIER) cc_final: -0.5421 (tp) outliers start: 190 outliers final: 139 residues processed: 747 average time/residue: 0.4237 time to fit residues: 500.8570 Evaluate side-chains 775 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 611 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 240 optimal weight: 0.1980 chunk 257 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 296 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 690 GLN A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 450 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31139 Z= 0.232 Angle : 0.596 12.050 42441 Z= 0.294 Chirality : 0.044 0.225 4863 Planarity : 0.004 0.075 5471 Dihedral : 6.089 71.686 4343 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.60 % Allowed : 18.62 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 3888 helix: 0.89 (0.21), residues: 647 sheet: -1.50 (0.17), residues: 808 loop : -2.44 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 49 HIS 0.005 0.001 HIS C1064 PHE 0.033 0.001 PHE A 190 TYR 0.026 0.001 TYR C 91 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 626 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6511 (tptp) REVERT: A 117 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 233 ILE cc_start: 0.3430 (OUTLIER) cc_final: 0.3179 (mm) REVERT: A 269 TYR cc_start: 0.7123 (m-80) cc_final: 0.6638 (m-80) REVERT: A 276 LEU cc_start: 0.8438 (tp) cc_final: 0.8031 (tt) REVERT: A 314 GLN cc_start: 0.7497 (tp-100) cc_final: 0.7220 (tt0) REVERT: A 324 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6360 (mm-30) REVERT: A 334 ASN cc_start: 0.7191 (t0) cc_final: 0.6931 (t0) REVERT: A 542 ASN cc_start: 0.8361 (t0) cc_final: 0.7796 (t0) REVERT: A 708 SER cc_start: 0.8122 (m) cc_final: 0.7913 (p) REVERT: A 717 ASN cc_start: 0.5820 (t0) cc_final: 0.5394 (t0) REVERT: A 762 GLN cc_start: 0.7353 (pt0) cc_final: 0.7006 (pt0) REVERT: A 776 LYS cc_start: 0.8270 (tmmt) cc_final: 0.7643 (tmmt) REVERT: A 780 GLU cc_start: 0.7098 (pt0) cc_final: 0.6693 (pt0) REVERT: A 790 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7708 (mtpt) REVERT: A 801 ASN cc_start: 0.5668 (OUTLIER) cc_final: 0.5215 (t0) REVERT: A 825 LYS cc_start: 0.8302 (mtpm) cc_final: 0.8015 (mttm) REVERT: A 855 PHE cc_start: 0.8559 (m-80) cc_final: 0.8240 (m-80) REVERT: A 922 LEU cc_start: 0.8774 (tp) cc_final: 0.8483 (tt) REVERT: A 933 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8220 (mtmm) REVERT: A 964 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7712 (mtmt) REVERT: A 975 SER cc_start: 0.8712 (m) cc_final: 0.8130 (t) REVERT: A 976 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 979 ASP cc_start: 0.7541 (m-30) cc_final: 0.7318 (m-30) REVERT: A 980 ILE cc_start: 0.8615 (mt) cc_final: 0.8323 (tt) REVERT: A 981 PHE cc_start: 0.7782 (m-10) cc_final: 0.7573 (m-10) REVERT: A 1017 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6665 (tm-30) REVERT: A 1031 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 1110 TYR cc_start: 0.8257 (t80) cc_final: 0.7653 (t80) REVERT: A 1117 THR cc_start: 0.8427 (p) cc_final: 0.8171 (t) REVERT: B 34 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7685 (mtt-85) REVERT: B 66 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7469 (t-90) REVERT: B 83 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7133 (p) REVERT: B 99 ASN cc_start: 0.7936 (p0) cc_final: 0.7592 (p0) REVERT: B 127 VAL cc_start: 0.8112 (t) cc_final: 0.7382 (m) REVERT: B 193 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7466 (ttmt) REVERT: B 223 LEU cc_start: 0.7917 (mp) cc_final: 0.7650 (mt) REVERT: B 307 THR cc_start: 0.8091 (m) cc_final: 0.7570 (p) REVERT: B 355 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8380 (ttt-90) REVERT: B 398 ASP cc_start: 0.6505 (t70) cc_final: 0.5882 (t0) REVERT: B 402 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6360 (tt) REVERT: B 535 LYS cc_start: 0.8276 (tptt) cc_final: 0.8008 (mmmm) REVERT: B 539 VAL cc_start: 0.8018 (m) cc_final: 0.7778 (m) REVERT: B 543 PHE cc_start: 0.7385 (m-10) cc_final: 0.7100 (m-80) REVERT: B 547 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8231 (ttmm) REVERT: B 643 PHE cc_start: 0.7967 (t80) cc_final: 0.7688 (t80) REVERT: B 739 THR cc_start: 0.8218 (m) cc_final: 0.8005 (m) REVERT: B 750 SER cc_start: 0.8270 (m) cc_final: 0.7880 (p) REVERT: B 755 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 820 ASP cc_start: 0.7579 (t70) cc_final: 0.7292 (t0) REVERT: B 868 GLU cc_start: 0.7124 (tp30) cc_final: 0.6743 (tp30) REVERT: B 902 MET cc_start: 0.7986 (mmm) cc_final: 0.7684 (mmm) REVERT: B 954 HIS cc_start: 0.7225 (m-70) cc_final: 0.6855 (m90) REVERT: B 957 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7132 (tm-30) REVERT: B 1003 SER cc_start: 0.8506 (m) cc_final: 0.8141 (t) REVERT: B 1014 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7235 (ttm110) REVERT: B 1019 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7297 (ttp80) REVERT: B 1118 ASP cc_start: 0.7496 (t70) cc_final: 0.6910 (t0) REVERT: B 1127 ASP cc_start: 0.7693 (t0) cc_final: 0.7354 (t0) REVERT: B 1141 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7896 (tt) REVERT: C 96 GLU cc_start: 0.6656 (pt0) cc_final: 0.6289 (pt0) REVERT: C 99 ASN cc_start: 0.7359 (t0) cc_final: 0.7016 (t0) REVERT: C 120 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7683 (p) REVERT: C 128 ILE cc_start: 0.7932 (mt) cc_final: 0.7693 (mp) REVERT: C 164 ASN cc_start: 0.7721 (t0) cc_final: 0.7445 (t0) REVERT: C 170 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5873 (m-80) REVERT: C 228 ASP cc_start: 0.7343 (t70) cc_final: 0.7086 (t70) REVERT: C 237 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7134 (mtp85) REVERT: C 275 PHE cc_start: 0.7944 (m-80) cc_final: 0.7413 (m-10) REVERT: C 297 SER cc_start: 0.7685 (m) cc_final: 0.7235 (p) REVERT: C 327 VAL cc_start: 0.8090 (t) cc_final: 0.7853 (m) REVERT: C 408 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6880 (ppp-140) REVERT: C 536 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8255 (p0) REVERT: C 546 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7270 (tt) REVERT: C 558 LYS cc_start: 0.7902 (mmtp) cc_final: 0.7482 (mmtp) REVERT: C 574 ASP cc_start: 0.7365 (t70) cc_final: 0.6611 (t0) REVERT: C 599 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8322 (p) REVERT: C 602 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.7977 (p) REVERT: C 619 GLU cc_start: 0.6838 (tt0) cc_final: 0.6612 (tt0) REVERT: C 723 THR cc_start: 0.8525 (t) cc_final: 0.8304 (p) REVERT: C 725 GLU cc_start: 0.7169 (tt0) cc_final: 0.6901 (tt0) REVERT: C 737 ASP cc_start: 0.6733 (t0) cc_final: 0.6433 (t70) REVERT: C 764 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8227 (ttpp) REVERT: C 790 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7959 (mtpt) REVERT: C 795 LYS cc_start: 0.8793 (mttt) cc_final: 0.8452 (mttm) REVERT: C 810 SER cc_start: 0.8750 (m) cc_final: 0.8026 (p) REVERT: C 854 LYS cc_start: 0.7860 (tmmt) cc_final: 0.7593 (tptp) REVERT: C 868 GLU cc_start: 0.6855 (tp30) cc_final: 0.6596 (tp30) REVERT: C 886 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7761 (p90) REVERT: C 904 TYR cc_start: 0.7809 (m-10) cc_final: 0.7564 (m-10) REVERT: C 933 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8055 (ttmm) REVERT: C 945 LEU cc_start: 0.8613 (mm) cc_final: 0.8407 (mp) REVERT: C 957 GLN cc_start: 0.7438 (tm130) cc_final: 0.7091 (tm130) REVERT: C 966 LEU cc_start: 0.8510 (mt) cc_final: 0.8189 (mt) REVERT: C 977 LEU cc_start: 0.7538 (mp) cc_final: 0.6763 (mp) REVERT: C 980 ILE cc_start: 0.8763 (mt) cc_final: 0.8435 (mm) REVERT: C 981 PHE cc_start: 0.8067 (m-80) cc_final: 0.7709 (m-80) REVERT: C 1002 GLN cc_start: 0.7773 (tp40) cc_final: 0.6838 (tm-30) REVERT: C 1014 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7532 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7749 (mmmt) REVERT: D 182 LEU cc_start: 0.4476 (OUTLIER) cc_final: 0.3878 (tt) REVERT: E 47 LYS cc_start: 0.3373 (OUTLIER) cc_final: 0.2170 (ttmm) REVERT: E 194 TYR cc_start: 0.2981 (OUTLIER) cc_final: 0.1496 (m-80) REVERT: F 182 LEU cc_start: 0.7980 (tp) cc_final: 0.7431 (tt) REVERT: G 183 LEU cc_start: -0.4745 (OUTLIER) cc_final: -0.5025 (tp) outliers start: 190 outliers final: 141 residues processed: 748 average time/residue: 0.4252 time to fit residues: 502.1942 Evaluate side-chains 779 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 615 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 4.9990 chunk 361 optimal weight: 2.9990 chunk 330 optimal weight: 20.0000 chunk 352 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 276 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 350 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 52 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 360 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN G 173 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.211 31139 Z= 0.763 Angle : 0.868 12.694 42441 Z= 0.454 Chirality : 0.056 0.308 4863 Planarity : 0.006 0.079 5471 Dihedral : 7.028 70.770 4339 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.17 % Favored : 87.81 % Rotamer: Outliers : 5.45 % Allowed : 19.29 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.12), residues: 3888 helix: -0.09 (0.20), residues: 649 sheet: -1.78 (0.17), residues: 827 loop : -2.69 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 64 HIS 0.020 0.002 HIS B1064 PHE 0.048 0.003 PHE C 168 TYR 0.038 0.003 TYR C 279 ARG 0.014 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 642 time to evaluate : 3.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7421 (mmm-85) REVERT: A 113 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6558 (tttp) REVERT: A 117 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 227 VAL cc_start: 0.8404 (m) cc_final: 0.8199 (t) REVERT: A 233 ILE cc_start: 0.3792 (OUTLIER) cc_final: 0.3505 (mm) REVERT: A 276 LEU cc_start: 0.8531 (tp) cc_final: 0.8115 (tt) REVERT: A 307 THR cc_start: 0.7789 (m) cc_final: 0.7434 (p) REVERT: A 314 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 324 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6394 (mm-30) REVERT: A 334 ASN cc_start: 0.7281 (t0) cc_final: 0.7026 (t0) REVERT: A 342 PHE cc_start: 0.7420 (m-80) cc_final: 0.7014 (m-80) REVERT: A 437 ASN cc_start: 0.5597 (OUTLIER) cc_final: 0.5112 (p0) REVERT: A 690 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7368 (mm110) REVERT: A 762 GLN cc_start: 0.7597 (pt0) cc_final: 0.7204 (pt0) REVERT: A 776 LYS cc_start: 0.8310 (tmmt) cc_final: 0.8069 (tptp) REVERT: A 790 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7781 (mtpt) REVERT: A 801 ASN cc_start: 0.5425 (OUTLIER) cc_final: 0.5211 (t0) REVERT: A 804 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7363 (mm110) REVERT: A 825 LYS cc_start: 0.8398 (mtpm) cc_final: 0.8100 (mttm) REVERT: A 858 LEU cc_start: 0.8663 (mt) cc_final: 0.8443 (mt) REVERT: A 878 LEU cc_start: 0.8509 (mt) cc_final: 0.8153 (mp) REVERT: A 922 LEU cc_start: 0.8905 (tp) cc_final: 0.8669 (tt) REVERT: A 933 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8302 (mtmm) REVERT: A 935 GLN cc_start: 0.8475 (tt0) cc_final: 0.7850 (mt0) REVERT: A 936 ASP cc_start: 0.8031 (m-30) cc_final: 0.7819 (m-30) REVERT: A 950 ASP cc_start: 0.7388 (t0) cc_final: 0.6957 (t0) REVERT: A 964 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7874 (mtmt) REVERT: A 975 SER cc_start: 0.8740 (m) cc_final: 0.8176 (t) REVERT: A 976 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8446 (p) REVERT: A 981 PHE cc_start: 0.7883 (m-10) cc_final: 0.7657 (m-10) REVERT: A 1017 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 1031 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 1107 ARG cc_start: 0.7787 (mpt180) cc_final: 0.7079 (mpt180) REVERT: A 1110 TYR cc_start: 0.8258 (t80) cc_final: 0.7634 (t80) REVERT: A 1117 THR cc_start: 0.8524 (p) cc_final: 0.8312 (t) REVERT: B 66 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7961 (t-90) REVERT: B 83 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7441 (p) REVERT: B 102 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6631 (mtp-110) REVERT: B 119 ILE cc_start: 0.8145 (mt) cc_final: 0.7936 (mp) REVERT: B 193 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7560 (ttmt) REVERT: B 212 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6008 (pp20) REVERT: B 223 LEU cc_start: 0.8109 (mp) cc_final: 0.7740 (mt) REVERT: B 265 TYR cc_start: 0.8385 (p90) cc_final: 0.8179 (p90) REVERT: B 308 VAL cc_start: 0.8549 (t) cc_final: 0.8275 (m) REVERT: B 338 PHE cc_start: 0.7133 (t80) cc_final: 0.6749 (t80) REVERT: B 356 LYS cc_start: 0.8685 (tmmt) cc_final: 0.8289 (tmtt) REVERT: B 398 ASP cc_start: 0.6394 (t70) cc_final: 0.5876 (t0) REVERT: B 528 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8285 (mmtt) REVERT: B 535 LYS cc_start: 0.8470 (tptt) cc_final: 0.8217 (mmmm) REVERT: B 542 ASN cc_start: 0.8557 (t0) cc_final: 0.8268 (t0) REVERT: B 547 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8281 (ttmm) REVERT: B 619 GLU cc_start: 0.7026 (tt0) cc_final: 0.6671 (tt0) REVERT: B 710 ASN cc_start: 0.8484 (p0) cc_final: 0.8245 (p0) REVERT: B 750 SER cc_start: 0.8452 (m) cc_final: 0.8001 (p) REVERT: B 755 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 765 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7437 (ttp80) REVERT: B 795 LYS cc_start: 0.7986 (mttt) cc_final: 0.7736 (mttp) REVERT: B 820 ASP cc_start: 0.7845 (t70) cc_final: 0.7460 (t0) REVERT: B 824 ASN cc_start: 0.8086 (m-40) cc_final: 0.7817 (m-40) REVERT: B 868 GLU cc_start: 0.7276 (tp30) cc_final: 0.6859 (tp30) REVERT: B 902 MET cc_start: 0.8108 (mmm) cc_final: 0.7833 (tpp) REVERT: B 954 HIS cc_start: 0.7339 (m-70) cc_final: 0.6971 (m90) REVERT: B 957 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7219 (tm-30) REVERT: B 983 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7818 (mtm180) REVERT: B 1003 SER cc_start: 0.8511 (m) cc_final: 0.8115 (t) REVERT: B 1017 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6773 (tm-30) REVERT: B 1086 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8109 (mtmt) REVERT: B 1118 ASP cc_start: 0.7565 (t70) cc_final: 0.6971 (t0) REVERT: B 1127 ASP cc_start: 0.7813 (t0) cc_final: 0.7582 (t0) REVERT: B 1141 LEU cc_start: 0.8340 (tt) cc_final: 0.7841 (tt) REVERT: C 96 GLU cc_start: 0.6771 (pt0) cc_final: 0.6332 (pt0) REVERT: C 99 ASN cc_start: 0.7706 (t0) cc_final: 0.7147 (t0) REVERT: C 106 PHE cc_start: 0.8072 (m-80) cc_final: 0.7763 (m-10) REVERT: C 110 LEU cc_start: 0.8155 (mt) cc_final: 0.7640 (mt) REVERT: C 120 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7907 (p) REVERT: C 121 ASN cc_start: 0.8155 (p0) cc_final: 0.7717 (p0) REVERT: C 128 ILE cc_start: 0.8122 (mt) cc_final: 0.7876 (mp) REVERT: C 129 LYS cc_start: 0.7604 (ttpt) cc_final: 0.6950 (tppt) REVERT: C 228 ASP cc_start: 0.7405 (t70) cc_final: 0.7091 (t0) REVERT: C 237 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.6928 (mtp-110) REVERT: C 275 PHE cc_start: 0.8286 (m-80) cc_final: 0.7448 (m-10) REVERT: C 408 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6974 (ppp-140) REVERT: C 536 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7996 (p0) REVERT: C 558 LYS cc_start: 0.8055 (mmtp) cc_final: 0.7623 (mmtp) REVERT: C 574 ASP cc_start: 0.7732 (t70) cc_final: 0.6845 (t0) REVERT: C 581 THR cc_start: 0.8431 (m) cc_final: 0.8126 (p) REVERT: C 599 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8409 (p) REVERT: C 602 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8101 (p) REVERT: C 619 GLU cc_start: 0.7291 (tt0) cc_final: 0.7026 (tt0) REVERT: C 702 GLU cc_start: 0.7263 (mp0) cc_final: 0.6988 (mp0) REVERT: C 710 ASN cc_start: 0.7826 (p0) cc_final: 0.7476 (p0) REVERT: C 723 THR cc_start: 0.8562 (t) cc_final: 0.8340 (p) REVERT: C 725 GLU cc_start: 0.7210 (tt0) cc_final: 0.6965 (tt0) REVERT: C 737 ASP cc_start: 0.7259 (t0) cc_final: 0.6978 (t70) REVERT: C 776 LYS cc_start: 0.8403 (ttpm) cc_final: 0.8184 (ttpp) REVERT: C 790 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7979 (ttmm) REVERT: C 795 LYS cc_start: 0.8811 (mttt) cc_final: 0.8489 (mttm) REVERT: C 810 SER cc_start: 0.8734 (m) cc_final: 0.8018 (p) REVERT: C 854 LYS cc_start: 0.8254 (tmmt) cc_final: 0.7925 (tptp) REVERT: C 868 GLU cc_start: 0.6913 (tp30) cc_final: 0.6605 (tp30) REVERT: C 886 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.8085 (p90) REVERT: C 933 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8130 (ttmm) REVERT: C 945 LEU cc_start: 0.8657 (mm) cc_final: 0.8444 (mp) REVERT: C 977 LEU cc_start: 0.7678 (mp) cc_final: 0.7277 (mp) REVERT: C 980 ILE cc_start: 0.8758 (mt) cc_final: 0.8413 (mm) REVERT: C 981 PHE cc_start: 0.8205 (m-80) cc_final: 0.7961 (m-80) REVERT: C 1014 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7655 (ttm-80) REVERT: C 1086 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7972 (mmmt) REVERT: C 1137 VAL cc_start: 0.8640 (t) cc_final: 0.8258 (m) REVERT: E 47 LYS cc_start: 0.3948 (OUTLIER) cc_final: 0.2172 (ttmm) REVERT: E 194 TYR cc_start: 0.2981 (OUTLIER) cc_final: 0.1491 (m-80) REVERT: G 183 LEU cc_start: -0.4708 (OUTLIER) cc_final: -0.4990 (tp) outliers start: 185 outliers final: 133 residues processed: 764 average time/residue: 0.4441 time to fit residues: 535.7094 Evaluate side-chains 767 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 613 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Chi-restraints excluded: chain G residue 194 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.6980 chunk 372 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 0.0970 chunk 258 optimal weight: 1.9990 chunk 390 optimal weight: 0.3980 chunk 359 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 52 GLN A 61 ASN A 690 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 370 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 978 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 186 ASN C 895 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31139 Z= 0.204 Angle : 0.656 12.011 42441 Z= 0.327 Chirality : 0.046 0.248 4863 Planarity : 0.005 0.074 5471 Dihedral : 6.503 70.093 4335 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.39 % Allowed : 21.21 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.13), residues: 3888 helix: 0.47 (0.21), residues: 663 sheet: -1.47 (0.17), residues: 844 loop : -2.51 (0.12), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.004 0.001 HIS A1048 PHE 0.049 0.002 PHE B 168 TYR 0.033 0.001 TYR A 265 ARG 0.007 0.000 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 639 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6377 (tttp) REVERT: A 117 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 193 LYS cc_start: 0.7689 (ptpp) cc_final: 0.7408 (ptpp) REVERT: A 233 ILE cc_start: 0.3619 (OUTLIER) cc_final: 0.3330 (mm) REVERT: A 269 TYR cc_start: 0.7389 (m-10) cc_final: 0.7104 (m-80) REVERT: A 276 LEU cc_start: 0.8400 (tp) cc_final: 0.7858 (tt) REVERT: A 314 GLN cc_start: 0.7477 (tp-100) cc_final: 0.7163 (tt0) REVERT: A 324 GLU cc_start: 0.6530 (mm-30) cc_final: 0.6252 (mm-30) REVERT: A 342 PHE cc_start: 0.7275 (m-80) cc_final: 0.6969 (m-80) REVERT: A 690 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7106 (mm110) REVERT: A 762 GLN cc_start: 0.7355 (pt0) cc_final: 0.6952 (pt0) REVERT: A 776 LYS cc_start: 0.8251 (tmmt) cc_final: 0.8012 (tptp) REVERT: A 790 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7657 (mtpt) REVERT: A 801 ASN cc_start: 0.5323 (OUTLIER) cc_final: 0.4985 (t0) REVERT: A 804 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7359 (mm110) REVERT: A 825 LYS cc_start: 0.8372 (mtpm) cc_final: 0.8082 (mttm) REVERT: A 855 PHE cc_start: 0.8523 (m-80) cc_final: 0.8218 (m-80) REVERT: A 922 LEU cc_start: 0.8790 (tp) cc_final: 0.8505 (tt) REVERT: A 933 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8269 (mtmm) REVERT: A 950 ASP cc_start: 0.7285 (t0) cc_final: 0.6912 (t0) REVERT: A 964 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7736 (mtmt) REVERT: A 975 SER cc_start: 0.8691 (m) cc_final: 0.8100 (t) REVERT: A 976 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 980 ILE cc_start: 0.8668 (mt) cc_final: 0.8363 (tt) REVERT: A 1017 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6621 (tm-30) REVERT: A 1058 HIS cc_start: 0.7920 (m-70) cc_final: 0.7625 (m-70) REVERT: A 1117 THR cc_start: 0.8440 (p) cc_final: 0.8197 (t) REVERT: B 66 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7604 (t-90) REVERT: B 81 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6583 (p0) REVERT: B 83 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7462 (p) REVERT: B 193 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7510 (ttmt) REVERT: B 212 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6169 (pp20) REVERT: B 265 TYR cc_start: 0.8345 (p90) cc_final: 0.8091 (p90) REVERT: B 338 PHE cc_start: 0.6618 (t80) cc_final: 0.6348 (t80) REVERT: B 356 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8331 (tmmt) REVERT: B 398 ASP cc_start: 0.6568 (t70) cc_final: 0.5866 (t0) REVERT: B 402 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6512 (tt) REVERT: B 535 LYS cc_start: 0.8395 (tptt) cc_final: 0.8040 (mmmm) REVERT: B 542 ASN cc_start: 0.8457 (t0) cc_final: 0.8199 (t0) REVERT: B 547 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8202 (ttmm) REVERT: B 574 ASP cc_start: 0.7554 (t70) cc_final: 0.6956 (t0) REVERT: B 619 GLU cc_start: 0.6664 (tt0) cc_final: 0.6396 (tt0) REVERT: B 750 SER cc_start: 0.8266 (m) cc_final: 0.7929 (p) REVERT: B 755 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 795 LYS cc_start: 0.7788 (mttt) cc_final: 0.7533 (mttp) REVERT: B 820 ASP cc_start: 0.7368 (t70) cc_final: 0.7048 (t0) REVERT: B 868 GLU cc_start: 0.7200 (tp30) cc_final: 0.6802 (tp30) REVERT: B 902 MET cc_start: 0.8035 (mmm) cc_final: 0.7718 (mmm) REVERT: B 957 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7135 (tm-30) REVERT: B 988 GLU cc_start: 0.6844 (tp30) cc_final: 0.6441 (tp30) REVERT: B 1003 SER cc_start: 0.8428 (m) cc_final: 0.8011 (t) REVERT: B 1017 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6724 (tm-30) REVERT: B 1118 ASP cc_start: 0.7389 (t70) cc_final: 0.6830 (t0) REVERT: B 1127 ASP cc_start: 0.7705 (t0) cc_final: 0.7495 (t0) REVERT: C 96 GLU cc_start: 0.6643 (pt0) cc_final: 0.6232 (pt0) REVERT: C 99 ASN cc_start: 0.7556 (t0) cc_final: 0.7068 (t0) REVERT: C 120 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7754 (p) REVERT: C 128 ILE cc_start: 0.7911 (mt) cc_final: 0.7655 (mp) REVERT: C 164 ASN cc_start: 0.7113 (t0) cc_final: 0.6820 (t0) REVERT: C 228 ASP cc_start: 0.7346 (t70) cc_final: 0.7112 (t0) REVERT: C 237 ARG cc_start: 0.7560 (mtp-110) cc_final: 0.7166 (mtp85) REVERT: C 297 SER cc_start: 0.7751 (m) cc_final: 0.7248 (p) REVERT: C 327 VAL cc_start: 0.7980 (t) cc_final: 0.7778 (m) REVERT: C 356 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8112 (ttpp) REVERT: C 408 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6858 (ppp-140) REVERT: C 508 TYR cc_start: 0.6611 (m-80) cc_final: 0.5782 (m-80) REVERT: C 536 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8168 (p0) REVERT: C 558 LYS cc_start: 0.7944 (mmtp) cc_final: 0.7427 (mmtp) REVERT: C 574 ASP cc_start: 0.7456 (t70) cc_final: 0.6537 (t0) REVERT: C 599 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8364 (p) REVERT: C 602 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8020 (p) REVERT: C 619 GLU cc_start: 0.7007 (tt0) cc_final: 0.6769 (tt0) REVERT: C 702 GLU cc_start: 0.7147 (mp0) cc_final: 0.6855 (mp0) REVERT: C 710 ASN cc_start: 0.7613 (p0) cc_final: 0.7135 (p0) REVERT: C 725 GLU cc_start: 0.7178 (tt0) cc_final: 0.6925 (tt0) REVERT: C 737 ASP cc_start: 0.6984 (t0) cc_final: 0.6669 (t70) REVERT: C 776 LYS cc_start: 0.8329 (ttpm) cc_final: 0.8014 (ttpp) REVERT: C 790 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7917 (ttmm) REVERT: C 795 LYS cc_start: 0.8675 (mttt) cc_final: 0.8389 (mttm) REVERT: C 854 LYS cc_start: 0.7963 (tmmt) cc_final: 0.7665 (tptp) REVERT: C 868 GLU cc_start: 0.6808 (tp30) cc_final: 0.6547 (tp30) REVERT: C 904 TYR cc_start: 0.7786 (m-10) cc_final: 0.7531 (m-10) REVERT: C 933 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8040 (ttmm) REVERT: C 945 LEU cc_start: 0.8652 (mm) cc_final: 0.8431 (mp) REVERT: C 957 GLN cc_start: 0.7453 (tm130) cc_final: 0.7085 (tm130) REVERT: C 980 ILE cc_start: 0.8719 (mt) cc_final: 0.8396 (mm) REVERT: C 981 PHE cc_start: 0.8113 (m-80) cc_final: 0.7718 (m-80) REVERT: C 1002 GLN cc_start: 0.7876 (tp40) cc_final: 0.6869 (tm-30) REVERT: C 1086 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7732 (mmmt) REVERT: D 182 LEU cc_start: 0.4490 (OUTLIER) cc_final: 0.4035 (tp) REVERT: E 47 LYS cc_start: 0.3746 (OUTLIER) cc_final: 0.2443 (ttmm) REVERT: E 194 TYR cc_start: 0.3006 (OUTLIER) cc_final: 0.1503 (m-80) REVERT: F 182 LEU cc_start: 0.7935 (tp) cc_final: 0.7459 (tt) REVERT: G 183 LEU cc_start: -0.4521 (OUTLIER) cc_final: -0.4807 (tp) outliers start: 149 outliers final: 115 residues processed: 744 average time/residue: 0.4346 time to fit residues: 509.8055 Evaluate side-chains 758 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 622 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 194 TYR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.0000 chunk 331 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 86 optimal weight: 0.4980 chunk 311 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 57 optimal weight: 0.0770 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 218 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 710 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 186 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.189035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138537 restraints weight = 56324.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142251 restraints weight = 25880.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143048 restraints weight = 16148.658| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31139 Z= 0.174 Angle : 0.623 12.422 42441 Z= 0.310 Chirality : 0.045 0.230 4863 Planarity : 0.005 0.076 5471 Dihedral : 6.286 69.465 4334 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.39 % Allowed : 21.68 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.13), residues: 3888 helix: 0.79 (0.21), residues: 655 sheet: -1.36 (0.18), residues: 814 loop : -2.40 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.003 0.001 HIS A1048 PHE 0.035 0.001 PHE A 190 TYR 0.031 0.001 TYR A 265 ARG 0.005 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9170.17 seconds wall clock time: 165 minutes 58.83 seconds (9958.83 seconds total)