Starting phenix.real_space_refine on Fri Aug 9 00:17:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xlv_38460/08_2024/8xlv_38460.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xlv_38460/08_2024/8xlv_38460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xlv_38460/08_2024/8xlv_38460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xlv_38460/08_2024/8xlv_38460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xlv_38460/08_2024/8xlv_38460.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xlv_38460/08_2024/8xlv_38460.cif" } resolution = 3.07 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= 0.001 sd= 0.027 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 108 5.16 5 C 15478 2.51 5 N 3965 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24219 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7924 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 6 Chain: "B" Number of atoms: 7867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7867 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 54, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7924 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.56, per 1000 atoms: 0.64 Number of scatterers: 24219 At special positions: 0 Unit cell: (135.807, 131.124, 174.609, 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 108 16.00 O 4668 8.00 N 3965 7.00 C 15478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 648 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 759 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 748 " distance=2.03 Simple disulfide: pdb=" SG CYS A1031 " - pdb=" SG CYS A1042 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1125 " 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 480 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS B 737 " - pdb=" SG CYS B 759 " distance=2.03 Simple disulfide: pdb=" SG CYS B 742 " - pdb=" SG CYS B 748 " distance=2.03 Simple disulfide: pdb=" SG CYS B1031 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1125 " 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 524 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 537 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 661 " - pdb=" SG CYS C 670 " distance=2.03 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 759 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 748 " distance=2.03 Simple disulfide: pdb=" SG CYS C1031 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1125 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1201 " - " ASN A 615 " " NAG A1202 " - " ASN A 708 " " NAG A1203 " - " ASN A 716 " " NAG A1204 " - " ASN A1073 " " NAG A1205 " - " ASN A1097 " " NAG A1206 " - " ASN A1133 " " NAG A1207 " - " ASN A 234 " " NAG A1208 " - " ASN A 354 " " NAG A1209 " - " ASN A 343 " " NAG B1201 " - " ASN B 615 " " NAG B1202 " - " ASN B 708 " " NAG B1203 " - " ASN B 716 " " NAG B1204 " - " ASN B1073 " " NAG B1205 " - " ASN B1097 " " NAG B1206 " - " ASN B1133 " " NAG B1207 " - " ASN B 282 " " NAG B1208 " - " ASN B 354 " " NAG B1209 " - " ASN B 343 " " NAG C1201 " - " ASN C 615 " " NAG C1202 " - " ASN C 708 " " NAG C1203 " - " ASN C 716 " " NAG C1204 " - " ASN C1073 " " NAG C1205 " - " ASN C1097 " " NAG C1206 " - " ASN C1133 " " NAG D 1 " - " ASN A 800 " " NAG E 1 " - " ASN B 800 " " NAG F 1 " - " ASN C 800 " " NAG G 1 " - " ASN C 331 " " NAG H 1 " - " ASN C 343 " " NAG I 1 " - " ASN C 354 " Time building additional restraints: 9.52 Conformation dependent library (CDL) restraints added in 4.4 seconds 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5666 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 45 sheets defined 25.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 removed outlier: 5.151A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.741A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 736 through 742 Processing helix chain 'A' and resid 745 through 754 removed outlier: 3.577A pdb=" N LEU A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.734A pdb=" N LYS A 813 " --> pdb=" O LYS A 810 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 814 " --> pdb=" O PRO A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 814' Processing helix chain 'A' and resid 815 through 825 Processing helix chain 'A' and resid 865 through 883 Processing helix chain 'A' and resid 885 through 889 Processing helix chain 'A' and resid 896 through 907 removed outlier: 3.526A pdb=" N ALA A 902 " --> pdb=" O PRO A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.701A pdb=" N TYR A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 939 removed outlier: 3.631A pdb=" N ILE A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 934 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 935 " --> pdb=" O GLY A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.607A pdb=" N ILE A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1031 removed outlier: 4.365A pdb=" N VAL A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 5.061A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.536A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 Processing helix chain 'B' and resid 736 through 742 Processing helix chain 'B' and resid 745 through 754 removed outlier: 3.781A pdb=" N GLN B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 Processing helix chain 'B' and resid 810 through 814 removed outlier: 3.752A pdb=" N LYS B 813 " --> pdb=" O LYS B 810 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG B 814 " --> pdb=" O PRO B 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 814' Processing helix chain 'B' and resid 815 through 825 Processing helix chain 'B' and resid 865 through 883 Processing helix chain 'B' and resid 885 through 889 Processing helix chain 'B' and resid 896 through 907 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.639A pdb=" N TYR B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 940 Processing helix chain 'B' and resid 944 through 964 Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 975 through 981 removed outlier: 3.514A pdb=" N ILE B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1031 removed outlier: 4.334A pdb=" N VAL B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1117 No H-bonds generated for 'chain 'B' and resid 1115 through 1117' Processing helix chain 'C' and resid 295 through 303 removed outlier: 5.114A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.776A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.944A pdb=" N GLU C 406 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 615 through 625 Processing helix chain 'C' and resid 736 through 742 Processing helix chain 'C' and resid 745 through 754 removed outlier: 3.808A pdb=" N GLN C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 Processing helix chain 'C' and resid 810 through 814 removed outlier: 3.634A pdb=" N LYS C 813 " --> pdb=" O LYS C 810 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 814 " --> pdb=" O PRO C 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 810 through 814' Processing helix chain 'C' and resid 815 through 825 Processing helix chain 'C' and resid 865 through 883 Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.616A pdb=" N GLY C 888 " --> pdb=" O TRP C 885 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY C 890 " --> pdb=" O PHE C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 912 through 918 Processing helix chain 'C' and resid 918 through 940 removed outlier: 3.550A pdb=" N GLY C 931 " --> pdb=" O ASN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 964 Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 975 through 981 removed outlier: 3.502A pdb=" N ILE C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.839A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.133A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.581A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.557A pdb=" N THR A 598 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 659 removed outlier: 6.149A pdb=" N GLU A 653 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR A 695 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL A 655 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 666 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 671 " --> pdb=" O PRO A 664 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 727 removed outlier: 7.032A pdb=" N VAL A1064 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 727 Processing sheet with id=AB6, first strand: chain 'A' and resid 732 through 735 removed outlier: 4.424A pdb=" N LYS A 732 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 removed outlier: 6.096A pdb=" N ILE A 787 " --> pdb=" O ASN C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1119 through 1124 removed outlier: 3.674A pdb=" N SER A1122 " --> pdb=" O ALA A1086 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA A1086 " --> pdb=" O SER A1122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.033A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.971A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.920A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.567A pdb=" N THR B 315 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL B 594 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 317 " --> pdb=" O GLY B 592 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY B 592 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY B 593 " --> pdb=" O GLN B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.556A pdb=" N THR B 552 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 374 through 379 removed outlier: 6.826A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 6.548A pdb=" N PHE B 564 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 653 through 659 removed outlier: 6.237A pdb=" N GLU B 653 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 695 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL B 655 " --> pdb=" O THR B 695 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.582A pdb=" N LYS C 789 " --> pdb=" O ASN B 702 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 712 removed outlier: 3.584A pdb=" N THR B1075 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN B1105 " --> pdb=" O GLU B1110 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU B1110 " --> pdb=" O GLN B1105 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 727 removed outlier: 7.065A pdb=" N GLY B1058 " --> pdb=" O SER B1054 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER B1054 " --> pdb=" O GLY B1058 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B1060 " --> pdb=" O PRO B1052 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B1062 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER B1050 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B1064 " --> pdb=" O LEU B1048 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 732 through 735 removed outlier: 4.444A pdb=" N LYS B 732 " --> pdb=" O LEU B 860 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1080 through 1081 removed outlier: 4.715A pdb=" N ALA B1086 " --> pdb=" O SER B1122 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.652A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 5.326A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.549A pdb=" N THR C 598 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 315 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL C 594 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN C 317 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY C 592 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 609 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE1, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.778A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR C 430 " --> pdb=" O PHE C 514 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 552 through 553 Processing sheet with id=AE5, first strand: chain 'C' and resid 653 through 659 removed outlier: 6.253A pdb=" N GLU C 653 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR C 695 " --> pdb=" O GLU C 653 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL C 655 " --> pdb=" O THR C 695 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA C 671 " --> pdb=" O PRO C 664 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.542A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER C1054 " --> pdb=" O GLY C1058 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C1060 " --> pdb=" O PRO C1052 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C1062 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER C1050 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1064 " --> pdb=" O LEU C1048 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.542A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 Processing sheet with id=AE9, first strand: chain 'C' and resid 1080 through 1081 removed outlier: 5.123A pdb=" N GLY C1123 " --> pdb=" O ALA C1086 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C1088 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL C1121 " --> pdb=" O PHE C1088 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.43 Time building geometry restraints manager: 10.30 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: 4589 1.33 - 1.45: 6505 1.45 - 1.57: 13566 1.57 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 24795 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N HIS A 518 " pdb=" CA HIS A 518 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.24e-02 6.50e+03 9.34e+00 bond pdb=" N ASN A 280 " pdb=" CA ASN A 280 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.25e-02 6.40e+03 8.09e+00 bond pdb=" N ASN C 280 " pdb=" CA ASN C 280 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.56e+00 bond pdb=" N ALA A 519 " pdb=" CA ALA A 519 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.49e+00 ... (remaining 24790 not shown) Histogram of bond angle deviations from ideal: 95.86 - 103.54: 315 103.54 - 111.22: 10191 111.22 - 118.90: 9627 118.90 - 126.57: 13316 126.57 - 134.25: 296 Bond angle restraints: 33745 Sorted by residual: angle pdb=" N TYR C 279 " pdb=" CA TYR C 279 " pdb=" CB TYR C 279 " ideal model delta sigma weight residual 109.97 95.86 14.11 1.47e+00 4.63e-01 9.21e+01 angle pdb=" C TYR C 279 " pdb=" CA TYR C 279 " pdb=" CB TYR C 279 " ideal model delta sigma weight residual 109.65 119.31 -9.66 1.71e+00 3.42e-01 3.19e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 108.39 5.14 9.80e-01 1.04e+00 2.75e+01 angle pdb=" N GLY A 613 " pdb=" CA GLY A 613 " pdb=" C GLY A 613 " ideal model delta sigma weight residual 114.16 124.32 -10.16 2.00e+00 2.50e-01 2.58e+01 angle pdb=" CA TYR C 279 " pdb=" CB TYR C 279 " pdb=" CG TYR C 279 " ideal model delta sigma weight residual 113.90 123.04 -9.14 1.80e+00 3.09e-01 2.58e+01 ... (remaining 33740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13886 17.83 - 35.66: 1068 35.66 - 53.49: 173 53.49 - 71.32: 63 71.32 - 89.14: 26 Dihedral angle restraints: 15216 sinusoidal: 6406 harmonic: 8810 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 487 " pdb=" CB CYS C 487 " ideal model delta sinusoidal sigma weight residual 93.00 -177.91 -89.09 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 487 " pdb=" CB CYS B 487 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 487 " pdb=" CB CYS A 487 " ideal model delta sinusoidal sigma weight residual 93.00 152.33 -59.33 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 15213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 3891 0.173 - 0.347: 11 0.347 - 0.520: 5 0.520 - 0.694: 2 0.694 - 0.867: 3 Chirality restraints: 3912 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.85e+01 ... (remaining 3909 not shown) Planarity restraints: 4339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.308 2.00e-02 2.50e+03 2.66e-01 8.84e+02 pdb=" C7 NAG H 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.472 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.304 2.00e-02 2.50e+03 2.63e-01 8.65e+02 pdb=" C7 NAG G 1 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.467 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.299 2.00e-02 2.50e+03 2.58e-01 8.32e+02 pdb=" C7 NAG I 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.457 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.073 2.00e-02 2.50e+03 ... (remaining 4336 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2100 2.74 - 3.28: 24958 3.28 - 3.82: 40523 3.82 - 4.36: 48313 4.36 - 4.90: 82407 Nonbonded interactions: 198301 Sorted by model distance: nonbonded pdb=" NZ LYS B 528 " pdb=" O SER B 529 " model vdw 2.202 3.120 nonbonded pdb=" O ALA A 878 " pdb=" OG1 THR A 882 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN B1073 " pdb=" NE2 GLN C 894 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR B 911 " pdb=" NE2 GLN B1105 " model vdw 2.216 3.120 nonbonded pdb=" OG1 THR C 911 " pdb=" OE1 GLN C1105 " model vdw 2.227 3.040 ... (remaining 198296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 515 or resid 524 through 1139 or resid 1201 thr \ ough 1206)) selection = (chain 'B' and (resid 26 through 1139 or resid 1201 through 1206)) selection = (chain 'C' and (resid 26 through 515 or resid 524 through 1139 or resid 1201 thr \ ough 1206)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 68.670 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.120 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 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 : 0.003 0.039 24795 Z= 0.224 Angle : 0.668 14.106 33745 Z= 0.381 Chirality : 0.055 0.867 3912 Planarity : 0.010 0.266 4309 Dihedral : 13.414 89.145 9439 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.78 % Favored : 91.95 % Rotamer: Outliers : 0.15 % Allowed : 0.53 % Favored : 99.32 % Cbeta Deviations : 0.04 % 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: -1.74 (0.15), residues: 2981 helix: 0.68 (0.20), residues: 697 sheet: -1.03 (0.20), residues: 632 loop : -2.10 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 885 HIS 0.009 0.001 HIS C 339 PHE 0.021 0.001 PHE C 905 TYR 0.041 0.001 TYR C 279 ARG 0.007 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 698 time to evaluate : 2.621 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 33 THR cc_start: 0.7594 (p) cc_final: 0.7343 (p) REVERT: A 42 VAL cc_start: 0.8125 (t) cc_final: 0.7848 (t) REVERT: A 48 LEU cc_start: 0.8047 (mp) cc_final: 0.7725 (mt) REVERT: A 62 VAL cc_start: 0.7068 (t) cc_final: 0.6712 (m) REVERT: A 128 ILE cc_start: 0.6767 (mt) cc_final: 0.6407 (mp) REVERT: A 192 PHE cc_start: 0.7915 (m-80) cc_final: 0.7434 (m-80) REVERT: A 285 ILE cc_start: 0.7433 (mt) cc_final: 0.7145 (mt) REVERT: A 293 LEU cc_start: 0.7475 (mp) cc_final: 0.6815 (pp) REVERT: A 382 VAL cc_start: 0.3709 (t) cc_final: 0.3261 (p) REVERT: A 384 PRO cc_start: 0.6175 (Cg_endo) cc_final: 0.5817 (Cg_exo) REVERT: A 536 LYS cc_start: 0.6997 (mtpp) cc_final: 0.6604 (mtpt) REVERT: A 591 PHE cc_start: 0.7914 (p90) cc_final: 0.7598 (p90) REVERT: A 640 ASN cc_start: 0.7513 (m110) cc_final: 0.7246 (m-40) REVERT: A 645 ARG cc_start: 0.7725 (mtm180) cc_final: 0.7493 (mtm180) REVERT: A 654 TYR cc_start: 0.7763 (t80) cc_final: 0.7545 (t80) REVERT: A 658 SER cc_start: 0.8210 (m) cc_final: 0.7781 (p) REVERT: A 662 ASP cc_start: 0.7309 (t70) cc_final: 0.6973 (t70) REVERT: A 702 ASN cc_start: 0.7694 (t0) cc_final: 0.7276 (t0) REVERT: A 724 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 736 ASP cc_start: 0.7401 (t0) cc_final: 0.7099 (t0) REVERT: A 739 MET cc_start: 0.7371 (ttm) cc_final: 0.6974 (tpp) REVERT: A 747 GLU cc_start: 0.6927 (mp0) cc_final: 0.6477 (mp0) REVERT: A 763 LYS cc_start: 0.7402 (ttpp) cc_final: 0.7074 (mtpp) REVERT: A 789 LYS cc_start: 0.8124 (mttp) cc_final: 0.7610 (mmtp) REVERT: A 813 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7411 (mmtm) REVERT: A 903 TYR cc_start: 0.5702 (t80) cc_final: 0.5129 (t80) REVERT: A 944 LEU cc_start: 0.8007 (mt) cc_final: 0.7789 (mp) REVERT: A 968 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7794 (mttm) REVERT: A 973 SER cc_start: 0.8271 (t) cc_final: 0.7976 (m) REVERT: A 978 ASP cc_start: 0.6959 (t0) cc_final: 0.6729 (t0) REVERT: A 992 ILE cc_start: 0.7584 (mm) cc_final: 0.7302 (mt) REVERT: A 1046 TYR cc_start: 0.8083 (m-80) cc_final: 0.7870 (m-10) REVERT: A 1072 LYS cc_start: 0.7654 (tptp) cc_final: 0.7188 (tppp) REVERT: A 1083 ASP cc_start: 0.6981 (t0) cc_final: 0.6765 (m-30) REVERT: A 1088 PHE cc_start: 0.7955 (m-80) cc_final: 0.7545 (m-80) REVERT: A 1091 GLU cc_start: 0.6868 (pm20) cc_final: 0.6627 (pm20) REVERT: B 30 ASN cc_start: 0.7478 (p0) cc_final: 0.7247 (p0) REVERT: B 88 ASP cc_start: 0.6874 (p0) cc_final: 0.6429 (p0) REVERT: B 90 VAL cc_start: 0.7203 (m) cc_final: 0.6943 (t) REVERT: B 168 PHE cc_start: 0.8354 (t80) cc_final: 0.7982 (t80) REVERT: B 278 LYS cc_start: 0.7978 (tttt) cc_final: 0.7467 (tttp) REVERT: B 309 GLU cc_start: 0.7517 (mp0) cc_final: 0.7069 (mp0) REVERT: B 313 TYR cc_start: 0.7577 (m-80) cc_final: 0.6921 (m-80) REVERT: B 317 ASN cc_start: 0.7398 (m-40) cc_final: 0.7166 (m-40) REVERT: B 319 ARG cc_start: 0.7377 (ptp-110) cc_final: 0.7094 (ptm160) REVERT: B 324 GLU cc_start: 0.5839 (mp0) cc_final: 0.5279 (mp0) REVERT: B 555 ASN cc_start: 0.7252 (p0) cc_final: 0.6958 (p0) REVERT: B 556 LYS cc_start: 0.7845 (mptt) cc_final: 0.7493 (mttt) REVERT: B 563 GLN cc_start: 0.7323 (mm110) cc_final: 0.6967 (mm-40) REVERT: B 583 ILE cc_start: 0.5434 (tp) cc_final: 0.5160 (mt) REVERT: B 591 PHE cc_start: 0.7825 (p90) cc_final: 0.7623 (p90) REVERT: B 653 GLU cc_start: 0.7781 (pm20) cc_final: 0.7370 (pm20) REVERT: B 657 ASN cc_start: 0.8114 (m-40) cc_final: 0.7859 (m-40) REVERT: B 658 SER cc_start: 0.8385 (m) cc_final: 0.8016 (t) REVERT: B 696 MET cc_start: 0.7569 (ttp) cc_final: 0.7177 (ttm) REVERT: B 707 SER cc_start: 0.8068 (m) cc_final: 0.7632 (p) REVERT: B 709 ASN cc_start: 0.8031 (p0) cc_final: 0.7702 (p0) REVERT: B 724 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6678 (tm-30) REVERT: B 736 ASP cc_start: 0.7233 (t0) cc_final: 0.7020 (t0) REVERT: B 739 MET cc_start: 0.7361 (ttm) cc_final: 0.6886 (ttm) REVERT: B 772 GLU cc_start: 0.6877 (tt0) cc_final: 0.6519 (tt0) REVERT: B 775 LYS cc_start: 0.7462 (ttpt) cc_final: 0.7220 (tttm) REVERT: B 778 GLN cc_start: 0.7565 (tp40) cc_final: 0.7057 (tm-30) REVERT: B 785 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7335 (mmtm) REVERT: B 789 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7606 (mtpp) REVERT: B 866 ASP cc_start: 0.6757 (p0) cc_final: 0.6248 (p0) REVERT: B 867 GLU cc_start: 0.6707 (mp0) cc_final: 0.6160 (mp0) REVERT: B 918 ASN cc_start: 0.7407 (m110) cc_final: 0.7146 (m110) REVERT: B 948 GLN cc_start: 0.7573 (tp40) cc_final: 0.7346 (mm-40) REVERT: B 952 ASN cc_start: 0.7697 (m-40) cc_final: 0.7477 (m-40) REVERT: B 964 GLN cc_start: 0.7640 (mt0) cc_final: 0.7271 (mt0) REVERT: B 989 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6494 (mt-10) REVERT: B 1040 ASP cc_start: 0.7585 (m-30) cc_final: 0.7317 (m-30) REVERT: B 1112 GLN cc_start: 0.7588 (mt0) cc_final: 0.7074 (mm-40) REVERT: B 1134 ASN cc_start: 0.7115 (t0) cc_final: 0.6693 (m-40) REVERT: B 1135 THR cc_start: 0.7910 (m) cc_final: 0.7048 (m) REVERT: C 30 ASN cc_start: 0.6853 (p0) cc_final: 0.6583 (p0) REVERT: C 191 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7165 (mt-10) REVERT: C 269 TYR cc_start: 0.7818 (m-80) cc_final: 0.7112 (m-10) REVERT: C 278 LYS cc_start: 0.7005 (ttpm) cc_final: 0.6740 (ttpm) REVERT: C 279 TYR cc_start: 0.7213 (m-80) cc_final: 0.6838 (m-80) REVERT: C 317 ASN cc_start: 0.8251 (m-40) cc_final: 0.7977 (m-40) REVERT: C 436 TRP cc_start: 0.5300 (p90) cc_final: 0.4552 (p90) REVERT: C 510 VAL cc_start: 0.6651 (t) cc_final: 0.6271 (m) REVERT: C 528 LYS cc_start: 0.7550 (tptp) cc_final: 0.7047 (tptp) REVERT: C 529 SER cc_start: 0.7611 (t) cc_final: 0.7333 (m) REVERT: C 540 PHE cc_start: 0.6359 (p90) cc_final: 0.6141 (p90) REVERT: C 548 THR cc_start: 0.7714 (p) cc_final: 0.7500 (m) REVERT: C 555 ASN cc_start: 0.7520 (p0) cc_final: 0.6654 (p0) REVERT: C 557 LYS cc_start: 0.7943 (mptt) cc_final: 0.7380 (mptt) REVERT: C 573 ASP cc_start: 0.6924 (m-30) cc_final: 0.6623 (m-30) REVERT: C 590 SER cc_start: 0.8320 (m) cc_final: 0.8101 (p) REVERT: C 618 GLU cc_start: 0.7030 (tp30) cc_final: 0.6729 (tp30) REVERT: C 645 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7432 (mtm180) REVERT: C 674 GLN cc_start: 0.7119 (pp30) cc_final: 0.6808 (pp30) REVERT: C 702 ASN cc_start: 0.7613 (t0) cc_final: 0.7288 (t0) REVERT: C 707 SER cc_start: 0.7828 (m) cc_final: 0.7567 (t) REVERT: C 724 GLU cc_start: 0.7674 (tm-30) cc_final: 0.6983 (tm-30) REVERT: C 749 SER cc_start: 0.7201 (t) cc_final: 0.6842 (m) REVERT: C 778 GLN cc_start: 0.7706 (tp40) cc_final: 0.7322 (tp40) REVERT: C 779 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 789 LYS cc_start: 0.8146 (mppt) cc_final: 0.7918 (mppt) REVERT: C 868 MET cc_start: 0.7677 (mtt) cc_final: 0.7431 (mtt) REVERT: C 934 GLN cc_start: 0.8060 (mt0) cc_final: 0.7809 (mt0) REVERT: C 1072 LYS cc_start: 0.7637 (tptp) cc_final: 0.7151 (tptp) REVERT: C 1083 ASP cc_start: 0.7228 (t0) cc_final: 0.6986 (m-30) REVERT: C 1124 ASN cc_start: 0.7281 (p0) cc_final: 0.6869 (p0) outliers start: 4 outliers final: 1 residues processed: 700 average time/residue: 0.3682 time to fit residues: 393.9062 Evaluate side-chains 584 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 583 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 0.9990 chunk 228 optimal weight: 0.4980 chunk 127 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 236 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 314 GLN A 409 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN A 612 GLN A 709 ASN A 761 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN A1009 GLN B 125 ASN B 612 GLN B 754 GLN B 855 ASN B 954 ASN C 134 GLN C 339 HIS C 543 ASN C 612 GLN C 643 GLN C 709 ASN C 783 GLN C1057 HIS C1105 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 24795 Z= 0.237 Angle : 0.629 11.032 33745 Z= 0.324 Chirality : 0.047 0.368 3912 Planarity : 0.005 0.062 4309 Dihedral : 6.971 59.230 3998 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 2.41 % Allowed : 9.10 % Favored : 88.49 % 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: -1.48 (0.15), residues: 2981 helix: 1.10 (0.20), residues: 701 sheet: -0.86 (0.20), residues: 644 loop : -2.06 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 885 HIS 0.008 0.001 HIS C 339 PHE 0.027 0.002 PHE A 758 TYR 0.024 0.001 TYR C 706 ARG 0.006 0.001 ARG B1090 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 593 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.4404 (pm20) cc_final: 0.3384 (pt0) REVERT: A 28 TYR cc_start: 0.6860 (m-80) cc_final: 0.6083 (m-80) REVERT: A 48 LEU cc_start: 0.8083 (mp) cc_final: 0.7757 (mt) REVERT: A 62 VAL cc_start: 0.7141 (t) cc_final: 0.6784 (m) REVERT: A 116 SER cc_start: 0.5662 (m) cc_final: 0.5042 (p) REVERT: A 127 PHE cc_start: 0.5477 (m-80) cc_final: 0.5145 (m-10) REVERT: A 128 ILE cc_start: 0.6884 (mt) cc_final: 0.6465 (mp) REVERT: A 190 ARG cc_start: 0.6881 (mpt-90) cc_final: 0.6590 (mmt90) REVERT: A 220 PHE cc_start: 0.7637 (t80) cc_final: 0.7261 (t80) REVERT: A 273 ARG cc_start: 0.7183 (ttm170) cc_final: 0.6845 (tpp-160) REVERT: A 285 ILE cc_start: 0.7293 (mt) cc_final: 0.7030 (mt) REVERT: A 287 ASP cc_start: 0.7093 (t0) cc_final: 0.6595 (m-30) REVERT: A 384 PRO cc_start: 0.5957 (Cg_endo) cc_final: 0.5737 (Cg_exo) REVERT: A 409 GLN cc_start: 0.6983 (tp40) cc_final: 0.6635 (tp-100) REVERT: A 429 PHE cc_start: 0.5779 (t80) cc_final: 0.5503 (t80) REVERT: A 452 TRP cc_start: 0.7399 (m-10) cc_final: 0.7144 (m100) REVERT: A 536 LYS cc_start: 0.6310 (mtpp) cc_final: 0.6103 (mtmt) REVERT: A 591 PHE cc_start: 0.7863 (p90) cc_final: 0.7474 (p90) REVERT: A 645 ARG cc_start: 0.7746 (mtm180) cc_final: 0.7527 (mtm180) REVERT: A 658 SER cc_start: 0.8250 (m) cc_final: 0.7814 (p) REVERT: A 662 ASP cc_start: 0.7323 (t70) cc_final: 0.6933 (t70) REVERT: A 702 ASN cc_start: 0.7603 (t0) cc_final: 0.7327 (t0) REVERT: A 724 GLU cc_start: 0.7597 (tm-30) cc_final: 0.6821 (tm-30) REVERT: A 729 SER cc_start: 0.8436 (m) cc_final: 0.8184 (t) REVERT: A 736 ASP cc_start: 0.7316 (t0) cc_final: 0.6915 (t0) REVERT: A 739 MET cc_start: 0.7321 (ttm) cc_final: 0.6980 (tpp) REVERT: A 747 GLU cc_start: 0.7146 (mp0) cc_final: 0.6667 (mp0) REVERT: A 763 LYS cc_start: 0.7475 (ttpp) cc_final: 0.7145 (mtpp) REVERT: A 789 LYS cc_start: 0.8161 (mttp) cc_final: 0.7696 (mmtp) REVERT: A 810 LYS cc_start: 0.7118 (ptpt) cc_final: 0.6705 (ptpt) REVERT: A 813 LYS cc_start: 0.7844 (mmtm) cc_final: 0.7519 (mmtm) REVERT: A 858 THR cc_start: 0.7797 (t) cc_final: 0.7509 (p) REVERT: A 868 MET cc_start: 0.7434 (mtt) cc_final: 0.7185 (mtm) REVERT: A 948 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6661 (mm-40) REVERT: A 966 SER cc_start: 0.7859 (t) cc_final: 0.7640 (p) REVERT: A 968 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8067 (mttm) REVERT: A 978 ASP cc_start: 0.7100 (t0) cc_final: 0.6843 (t0) REVERT: A 1046 TYR cc_start: 0.8169 (m-80) cc_final: 0.7956 (m-10) REVERT: A 1072 LYS cc_start: 0.7771 (tptp) cc_final: 0.7324 (tppp) REVERT: A 1083 ASP cc_start: 0.7038 (t0) cc_final: 0.6726 (m-30) REVERT: A 1088 PHE cc_start: 0.8026 (m-80) cc_final: 0.7738 (m-80) REVERT: A 1090 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.7554 (mtt90) REVERT: A 1091 GLU cc_start: 0.7000 (pm20) cc_final: 0.6428 (pm20) REVERT: A 1106 ARG cc_start: 0.6918 (ptp-170) cc_final: 0.6652 (ptp-170) REVERT: A 1110 GLU cc_start: 0.7783 (tt0) cc_final: 0.7490 (tt0) REVERT: A 1134 ASN cc_start: 0.7345 (t0) cc_final: 0.7088 (m-40) REVERT: B 30 ASN cc_start: 0.7619 (p0) cc_final: 0.7379 (p0) REVERT: B 87 ASN cc_start: 0.6476 (m-40) cc_final: 0.6126 (p0) REVERT: B 88 ASP cc_start: 0.6922 (p0) cc_final: 0.6446 (p0) REVERT: B 153 MET cc_start: 0.5828 (ttp) cc_final: 0.5561 (ppp) REVERT: B 168 PHE cc_start: 0.8316 (t80) cc_final: 0.7943 (t80) REVERT: B 278 LYS cc_start: 0.7988 (tttt) cc_final: 0.7465 (tttp) REVERT: B 309 GLU cc_start: 0.7601 (mp0) cc_final: 0.7099 (mp0) REVERT: B 313 TYR cc_start: 0.7666 (m-80) cc_final: 0.6916 (m-80) REVERT: B 317 ASN cc_start: 0.7552 (m-40) cc_final: 0.7194 (m-40) REVERT: B 319 ARG cc_start: 0.7377 (ptp-110) cc_final: 0.7172 (ptm160) REVERT: B 321 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7296 (mm-40) REVERT: B 324 GLU cc_start: 0.6424 (mp0) cc_final: 0.5957 (mp0) REVERT: B 531 ASN cc_start: 0.7806 (t0) cc_final: 0.7479 (m-40) REVERT: B 548 THR cc_start: 0.8144 (p) cc_final: 0.7806 (m) REVERT: B 556 LYS cc_start: 0.7830 (mptt) cc_final: 0.7463 (mttt) REVERT: B 563 GLN cc_start: 0.7602 (mm110) cc_final: 0.7280 (mm-40) REVERT: B 583 ILE cc_start: 0.5479 (tp) cc_final: 0.5254 (mt) REVERT: B 591 PHE cc_start: 0.7953 (p90) cc_final: 0.7521 (p90) REVERT: B 618 GLU cc_start: 0.7344 (tp30) cc_final: 0.7008 (tp30) REVERT: B 627 GLN cc_start: 0.7187 (mt0) cc_final: 0.6760 (mt0) REVERT: B 653 GLU cc_start: 0.7897 (pm20) cc_final: 0.7447 (pm20) REVERT: B 657 ASN cc_start: 0.8119 (m-40) cc_final: 0.7847 (m-40) REVERT: B 658 SER cc_start: 0.8422 (m) cc_final: 0.8031 (t) REVERT: B 696 MET cc_start: 0.7504 (ttp) cc_final: 0.7123 (ptp) REVERT: B 724 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6632 (tm-30) REVERT: B 772 GLU cc_start: 0.6899 (tt0) cc_final: 0.6322 (tt0) REVERT: B 775 LYS cc_start: 0.7487 (ttpt) cc_final: 0.7239 (tttm) REVERT: B 778 GLN cc_start: 0.7507 (tp40) cc_final: 0.6977 (tm-30) REVERT: B 785 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7338 (mmtm) REVERT: B 789 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7690 (ttmm) REVERT: B 855 ASN cc_start: 0.8083 (m-40) cc_final: 0.7880 (m-40) REVERT: B 866 ASP cc_start: 0.6730 (p0) cc_final: 0.6096 (p0) REVERT: B 867 GLU cc_start: 0.6750 (mp0) cc_final: 0.6242 (mp0) REVERT: B 918 ASN cc_start: 0.7396 (m110) cc_final: 0.7154 (m110) REVERT: B 948 GLN cc_start: 0.7591 (tp40) cc_final: 0.7371 (tp-100) REVERT: B 952 ASN cc_start: 0.7765 (m-40) cc_final: 0.7546 (m-40) REVERT: B 959 ASN cc_start: 0.7432 (m-40) cc_final: 0.7201 (t0) REVERT: B 964 GLN cc_start: 0.7665 (mt0) cc_final: 0.7294 (mt0) REVERT: B 968 LYS cc_start: 0.8328 (mtmm) cc_final: 0.7945 (mttm) REVERT: B 989 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6541 (mt-10) REVERT: B 1037 LYS cc_start: 0.8115 (mttm) cc_final: 0.7808 (mttm) REVERT: B 1040 ASP cc_start: 0.7680 (m-30) cc_final: 0.7453 (m-30) REVERT: B 1070 GLN cc_start: 0.7487 (mt0) cc_final: 0.7244 (mt0) REVERT: B 1090 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7127 (ttt-90) REVERT: B 1106 ARG cc_start: 0.6943 (mtp180) cc_final: 0.6649 (mtp180) REVERT: B 1112 GLN cc_start: 0.7554 (mt0) cc_final: 0.7093 (mm-40) REVERT: B 1134 ASN cc_start: 0.7198 (t0) cc_final: 0.6647 (m-40) REVERT: B 1135 THR cc_start: 0.7907 (m) cc_final: 0.7099 (m) REVERT: C 269 TYR cc_start: 0.7974 (m-80) cc_final: 0.7209 (m-10) REVERT: C 278 LYS cc_start: 0.7215 (ttpm) cc_final: 0.6868 (ttpm) REVERT: C 317 ASN cc_start: 0.8253 (m-40) cc_final: 0.7887 (m-40) REVERT: C 338 PHE cc_start: 0.7379 (m-10) cc_final: 0.7153 (m-10) REVERT: C 356 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7510 (p) REVERT: C 357 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7122 (ttm110) REVERT: C 436 TRP cc_start: 0.5307 (p90) cc_final: 0.4549 (p90) REVERT: C 510 VAL cc_start: 0.6729 (t) cc_final: 0.6344 (m) REVERT: C 528 LYS cc_start: 0.7579 (tptp) cc_final: 0.7074 (tptp) REVERT: C 529 SER cc_start: 0.7856 (t) cc_final: 0.7304 (m) REVERT: C 555 ASN cc_start: 0.7536 (p0) cc_final: 0.6628 (p0) REVERT: C 557 LYS cc_start: 0.8008 (mptt) cc_final: 0.7401 (mptt) REVERT: C 573 ASP cc_start: 0.7002 (m-30) cc_final: 0.6690 (m-30) REVERT: C 618 GLU cc_start: 0.7005 (tp30) cc_final: 0.6734 (tp30) REVERT: C 645 ARG cc_start: 0.7728 (mtm180) cc_final: 0.7463 (mtm180) REVERT: C 674 GLN cc_start: 0.7114 (pp30) cc_final: 0.6809 (pp30) REVERT: C 702 ASN cc_start: 0.7654 (t0) cc_final: 0.7382 (t0) REVERT: C 720 SER cc_start: 0.8471 (t) cc_final: 0.7968 (p) REVERT: C 746 THR cc_start: 0.6743 (p) cc_final: 0.6280 (m) REVERT: C 749 SER cc_start: 0.7220 (t) cc_final: 0.6908 (m) REVERT: C 755 TYR cc_start: 0.8480 (m-80) cc_final: 0.8089 (m-80) REVERT: C 772 GLU cc_start: 0.7261 (tt0) cc_final: 0.6922 (tt0) REVERT: C 779 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7561 (mt-10) REVERT: C 803 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7793 (mm-40) REVERT: C 868 MET cc_start: 0.7793 (mtt) cc_final: 0.7580 (mtt) REVERT: C 910 VAL cc_start: 0.7675 (t) cc_final: 0.7448 (t) REVERT: C 934 GLN cc_start: 0.7760 (mt0) cc_final: 0.7542 (mt0) REVERT: C 982 ARG cc_start: 0.6916 (ttp80) cc_final: 0.6657 (mtp-110) REVERT: C 1044 LYS cc_start: 0.8200 (tptp) cc_final: 0.7857 (tptp) REVERT: C 1072 LYS cc_start: 0.7742 (tptp) cc_final: 0.7220 (tptp) REVERT: C 1083 ASP cc_start: 0.7276 (t0) cc_final: 0.6811 (t0) REVERT: C 1124 ASN cc_start: 0.7159 (p0) cc_final: 0.6892 (p0) REVERT: C 1135 THR cc_start: 0.7079 (m) cc_final: 0.6864 (p) outliers start: 64 outliers final: 37 residues processed: 615 average time/residue: 0.3786 time to fit residues: 358.8586 Evaluate side-chains 599 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 560 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 274 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 ASN A 894 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 709 ASN C 709 ASN C 918 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 24795 Z= 0.294 Angle : 0.607 10.268 33745 Z= 0.317 Chirality : 0.047 0.358 3912 Planarity : 0.005 0.092 4309 Dihedral : 6.606 59.530 3998 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.15 % Rotamer: Outliers : 2.52 % Allowed : 12.04 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.52 (0.15), residues: 2981 helix: 0.96 (0.19), residues: 708 sheet: -0.81 (0.20), residues: 661 loop : -2.08 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.004 0.001 HIS C1082 PHE 0.027 0.002 PHE C 540 TYR 0.019 0.001 TYR A1066 ARG 0.005 0.000 ARG A 982 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 608 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6840 (m-80) cc_final: 0.6137 (m-80) REVERT: A 48 LEU cc_start: 0.8108 (mp) cc_final: 0.7814 (mt) REVERT: A 62 VAL cc_start: 0.7216 (t) cc_final: 0.6902 (m) REVERT: A 87 ASN cc_start: 0.7111 (m-40) cc_final: 0.6880 (m110) REVERT: A 116 SER cc_start: 0.6095 (m) cc_final: 0.5476 (p) REVERT: A 127 PHE cc_start: 0.5642 (m-80) cc_final: 0.5226 (m-10) REVERT: A 128 ILE cc_start: 0.6877 (mt) cc_final: 0.6491 (mp) REVERT: A 190 ARG cc_start: 0.6971 (mpt-90) cc_final: 0.6555 (mpp80) REVERT: A 206 LYS cc_start: 0.7659 (tptm) cc_final: 0.7386 (tptm) REVERT: A 220 PHE cc_start: 0.7800 (t80) cc_final: 0.7448 (t80) REVERT: A 285 ILE cc_start: 0.7343 (mt) cc_final: 0.7023 (mt) REVERT: A 384 PRO cc_start: 0.6222 (Cg_endo) cc_final: 0.5991 (Cg_exo) REVERT: A 409 GLN cc_start: 0.7103 (tp40) cc_final: 0.6675 (tp-100) REVERT: A 452 TRP cc_start: 0.7431 (m-10) cc_final: 0.7194 (m100) REVERT: A 563 GLN cc_start: 0.7200 (mp10) cc_final: 0.6843 (mp10) REVERT: A 564 PHE cc_start: 0.6331 (m-10) cc_final: 0.6109 (m-10) REVERT: A 591 PHE cc_start: 0.7876 (p90) cc_final: 0.7393 (p90) REVERT: A 595 SER cc_start: 0.8715 (m) cc_final: 0.8362 (p) REVERT: A 645 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7552 (mtm180) REVERT: A 658 SER cc_start: 0.8276 (m) cc_final: 0.7836 (p) REVERT: A 662 ASP cc_start: 0.7392 (t70) cc_final: 0.6995 (t70) REVERT: A 724 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 736 ASP cc_start: 0.7285 (t0) cc_final: 0.6917 (t0) REVERT: A 739 MET cc_start: 0.7320 (ttm) cc_final: 0.7012 (tpp) REVERT: A 747 GLU cc_start: 0.7174 (mp0) cc_final: 0.6723 (mp0) REVERT: A 763 LYS cc_start: 0.7482 (ttpp) cc_final: 0.7271 (mtpp) REVERT: A 789 LYS cc_start: 0.8245 (mttp) cc_final: 0.7782 (mmtp) REVERT: A 813 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7509 (mmtm) REVERT: A 858 THR cc_start: 0.7869 (t) cc_final: 0.7569 (p) REVERT: A 948 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7042 (mm-40) REVERT: A 966 SER cc_start: 0.7985 (t) cc_final: 0.7753 (p) REVERT: A 968 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7793 (mttm) REVERT: A 978 ASP cc_start: 0.7160 (t0) cc_final: 0.6889 (t0) REVERT: A 1033 LEU cc_start: 0.8067 (mp) cc_final: 0.7785 (mp) REVERT: A 1072 LYS cc_start: 0.7773 (tptp) cc_final: 0.7302 (tppp) REVERT: A 1083 ASP cc_start: 0.7048 (t70) cc_final: 0.6838 (m-30) REVERT: A 1090 ARG cc_start: 0.7875 (mtt-85) cc_final: 0.7458 (mtt90) REVERT: A 1091 GLU cc_start: 0.7003 (pm20) cc_final: 0.6550 (pm20) REVERT: A 1110 GLU cc_start: 0.7784 (tt0) cc_final: 0.7520 (tt0) REVERT: A 1134 ASN cc_start: 0.7445 (t0) cc_final: 0.7124 (m-40) REVERT: B 30 ASN cc_start: 0.7693 (p0) cc_final: 0.7448 (p0) REVERT: B 45 SER cc_start: 0.7412 (p) cc_final: 0.6948 (t) REVERT: B 87 ASN cc_start: 0.6701 (m-40) cc_final: 0.6434 (p0) REVERT: B 88 ASP cc_start: 0.6993 (p0) cc_final: 0.6778 (p0) REVERT: B 168 PHE cc_start: 0.8343 (t80) cc_final: 0.8007 (t80) REVERT: B 278 LYS cc_start: 0.7979 (tttt) cc_final: 0.7738 (tttt) REVERT: B 281 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6880 (mm-30) REVERT: B 309 GLU cc_start: 0.7611 (mp0) cc_final: 0.7077 (mp0) REVERT: B 313 TYR cc_start: 0.7680 (m-80) cc_final: 0.6917 (m-80) REVERT: B 317 ASN cc_start: 0.7626 (m-40) cc_final: 0.7258 (m-40) REVERT: B 319 ARG cc_start: 0.7421 (ptp-110) cc_final: 0.7162 (ptm160) REVERT: B 321 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7196 (mm110) REVERT: B 324 GLU cc_start: 0.6647 (mp0) cc_final: 0.5973 (mp0) REVERT: B 531 ASN cc_start: 0.7823 (t0) cc_final: 0.7493 (m-40) REVERT: B 548 THR cc_start: 0.8128 (p) cc_final: 0.7832 (m) REVERT: B 556 LYS cc_start: 0.7831 (mptt) cc_final: 0.7363 (mptt) REVERT: B 563 GLN cc_start: 0.7665 (mm110) cc_final: 0.7328 (mm-40) REVERT: B 577 ASP cc_start: 0.7745 (m-30) cc_final: 0.7267 (m-30) REVERT: B 582 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5729 (tm-30) REVERT: B 583 ILE cc_start: 0.5930 (tp) cc_final: 0.5430 (mt) REVERT: B 591 PHE cc_start: 0.7972 (p90) cc_final: 0.7545 (p90) REVERT: B 618 GLU cc_start: 0.7331 (tp30) cc_final: 0.6979 (tp30) REVERT: B 627 GLN cc_start: 0.7225 (mt0) cc_final: 0.6750 (mt0) REVERT: B 653 GLU cc_start: 0.7953 (pm20) cc_final: 0.7493 (pm20) REVERT: B 657 ASN cc_start: 0.8105 (m-40) cc_final: 0.7844 (m-40) REVERT: B 696 MET cc_start: 0.7524 (ttp) cc_final: 0.7210 (ptp) REVERT: B 724 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6870 (tm-30) REVERT: B 772 GLU cc_start: 0.6938 (tt0) cc_final: 0.6528 (tt0) REVERT: B 778 GLN cc_start: 0.7475 (tp40) cc_final: 0.6848 (tm-30) REVERT: B 785 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7366 (mmtm) REVERT: B 789 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7713 (mtpp) REVERT: B 866 ASP cc_start: 0.6815 (p0) cc_final: 0.6022 (p0) REVERT: B 867 GLU cc_start: 0.6825 (mp0) cc_final: 0.6172 (mp0) REVERT: B 881 ILE cc_start: 0.8149 (pt) cc_final: 0.7797 (mt) REVERT: B 918 ASN cc_start: 0.7425 (m110) cc_final: 0.7197 (m110) REVERT: B 948 GLN cc_start: 0.7599 (tp40) cc_final: 0.7374 (tp-100) REVERT: B 952 ASN cc_start: 0.7766 (m-40) cc_final: 0.7553 (m-40) REVERT: B 959 ASN cc_start: 0.7429 (m-40) cc_final: 0.7189 (t0) REVERT: B 964 GLN cc_start: 0.7733 (mt0) cc_final: 0.7305 (mt0) REVERT: B 968 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7829 (mttp) REVERT: B 978 ASP cc_start: 0.7239 (t0) cc_final: 0.6811 (t0) REVERT: B 982 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7252 (ttm170) REVERT: B 989 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6759 (mt-10) REVERT: B 1027 LYS cc_start: 0.7527 (mttm) cc_final: 0.7017 (mttm) REVERT: B 1040 ASP cc_start: 0.7806 (m-30) cc_final: 0.7542 (m-30) REVERT: B 1070 GLN cc_start: 0.7693 (mt0) cc_final: 0.7473 (mt0) REVERT: B 1112 GLN cc_start: 0.7516 (mt0) cc_final: 0.7067 (mm-40) REVERT: B 1134 ASN cc_start: 0.7366 (t0) cc_final: 0.6962 (m-40) REVERT: B 1135 THR cc_start: 0.7958 (m) cc_final: 0.7216 (m) REVERT: C 45 SER cc_start: 0.8105 (p) cc_final: 0.7602 (t) REVERT: C 55 PHE cc_start: 0.7700 (m-80) cc_final: 0.7291 (m-80) REVERT: C 269 TYR cc_start: 0.7986 (m-80) cc_final: 0.7361 (m-10) REVERT: C 278 LYS cc_start: 0.7274 (ttpm) cc_final: 0.6890 (ttpm) REVERT: C 314 GLN cc_start: 0.8344 (tp40) cc_final: 0.8019 (tp40) REVERT: C 328 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7052 (tpt-90) REVERT: C 356 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7591 (p) REVERT: C 357 ARG cc_start: 0.7500 (ttm110) cc_final: 0.7174 (ttm110) REVERT: C 409 GLN cc_start: 0.7488 (mt0) cc_final: 0.6719 (mp10) REVERT: C 418 ILE cc_start: 0.6174 (mm) cc_final: 0.5512 (mm) REVERT: C 436 TRP cc_start: 0.5247 (p90) cc_final: 0.4597 (p90) REVERT: C 453 TYR cc_start: 0.6483 (p90) cc_final: 0.5920 (p90) REVERT: C 510 VAL cc_start: 0.6688 (t) cc_final: 0.6289 (m) REVERT: C 527 LYS cc_start: 0.7775 (ttmm) cc_final: 0.7569 (ttmm) REVERT: C 528 LYS cc_start: 0.7583 (tptp) cc_final: 0.7083 (tptp) REVERT: C 529 SER cc_start: 0.7874 (t) cc_final: 0.7243 (m) REVERT: C 543 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7402 (m110) REVERT: C 555 ASN cc_start: 0.7515 (p0) cc_final: 0.6714 (p0) REVERT: C 557 LYS cc_start: 0.8049 (mptt) cc_final: 0.7640 (mptt) REVERT: C 605 ASN cc_start: 0.8728 (m-40) cc_final: 0.8522 (m-40) REVERT: C 645 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7457 (mtm180) REVERT: C 674 GLN cc_start: 0.7091 (pp30) cc_final: 0.6759 (pp30) REVERT: C 702 ASN cc_start: 0.7650 (t0) cc_final: 0.7383 (t0) REVERT: C 720 SER cc_start: 0.8414 (t) cc_final: 0.7949 (p) REVERT: C 746 THR cc_start: 0.6946 (p) cc_final: 0.6582 (m) REVERT: C 749 SER cc_start: 0.7218 (t) cc_final: 0.6880 (m) REVERT: C 755 TYR cc_start: 0.8532 (m-80) cc_final: 0.8198 (m-80) REVERT: C 772 GLU cc_start: 0.7270 (tt0) cc_final: 0.6912 (tt0) REVERT: C 779 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 803 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7702 (mm-40) REVERT: C 868 MET cc_start: 0.7816 (mtt) cc_final: 0.7611 (mtt) REVERT: C 910 VAL cc_start: 0.7766 (t) cc_final: 0.7504 (p) REVERT: C 934 GLN cc_start: 0.7715 (mt0) cc_final: 0.7272 (mt0) REVERT: C 982 ARG cc_start: 0.6905 (ttp80) cc_final: 0.6645 (mtp-110) REVERT: C 1044 LYS cc_start: 0.8190 (tptp) cc_final: 0.7770 (tptp) REVERT: C 1072 LYS cc_start: 0.7758 (tptp) cc_final: 0.7175 (tptp) REVERT: C 1083 ASP cc_start: 0.7280 (t0) cc_final: 0.6854 (t0) REVERT: C 1124 ASN cc_start: 0.7081 (p0) cc_final: 0.6830 (p0) REVERT: C 1134 ASN cc_start: 0.6794 (t0) cc_final: 0.5852 (m110) REVERT: C 1135 THR cc_start: 0.7198 (m) cc_final: 0.6496 (p) outliers start: 67 outliers final: 42 residues processed: 639 average time/residue: 0.3941 time to fit residues: 383.9528 Evaluate side-chains 626 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 581 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 165 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 321 GLN A 563 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN A1107 ASN B 674 GLN B 709 ASN B 900 GLN C 317 ASN C 709 ASN C1087 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24795 Z= 0.239 Angle : 0.572 9.374 33745 Z= 0.297 Chirality : 0.045 0.349 3912 Planarity : 0.004 0.058 4309 Dihedral : 6.427 59.546 3998 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.25 % Favored : 92.62 % Rotamer: Outliers : 2.56 % Allowed : 14.48 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.15), residues: 2981 helix: 1.01 (0.19), residues: 709 sheet: -0.78 (0.20), residues: 652 loop : -2.02 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS C1082 PHE 0.019 0.001 PHE B 135 TYR 0.017 0.001 TYR B1066 ARG 0.009 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 593 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6809 (m-80) cc_final: 0.6118 (m-80) REVERT: A 48 LEU cc_start: 0.8121 (mp) cc_final: 0.7819 (mt) REVERT: A 62 VAL cc_start: 0.7235 (t) cc_final: 0.6961 (m) REVERT: A 116 SER cc_start: 0.6184 (m) cc_final: 0.5573 (p) REVERT: A 127 PHE cc_start: 0.5626 (m-80) cc_final: 0.5197 (m-10) REVERT: A 128 ILE cc_start: 0.6873 (mt) cc_final: 0.6485 (mp) REVERT: A 190 ARG cc_start: 0.7055 (mpt-90) cc_final: 0.6710 (mpt-90) REVERT: A 220 PHE cc_start: 0.7760 (t80) cc_final: 0.7493 (t80) REVERT: A 285 ILE cc_start: 0.7328 (mt) cc_final: 0.7037 (mt) REVERT: A 287 ASP cc_start: 0.7124 (t0) cc_final: 0.6637 (m-30) REVERT: A 297 SER cc_start: 0.7213 (m) cc_final: 0.6545 (t) REVERT: A 320 VAL cc_start: 0.7741 (m) cc_final: 0.7418 (p) REVERT: A 384 PRO cc_start: 0.6171 (Cg_endo) cc_final: 0.5965 (Cg_exo) REVERT: A 409 GLN cc_start: 0.7121 (tp40) cc_final: 0.6668 (tp-100) REVERT: A 452 TRP cc_start: 0.7414 (m-10) cc_final: 0.7170 (m100) REVERT: A 537 CYS cc_start: 0.6728 (m) cc_final: 0.6301 (m) REVERT: A 563 GLN cc_start: 0.7226 (mp-120) cc_final: 0.6982 (mp10) REVERT: A 591 PHE cc_start: 0.7909 (p90) cc_final: 0.7414 (p90) REVERT: A 645 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7547 (mtm180) REVERT: A 658 SER cc_start: 0.8309 (m) cc_final: 0.7836 (p) REVERT: A 662 ASP cc_start: 0.7368 (t70) cc_final: 0.6974 (t70) REVERT: A 724 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6872 (tm-30) REVERT: A 736 ASP cc_start: 0.7265 (t0) cc_final: 0.6869 (t0) REVERT: A 739 MET cc_start: 0.7365 (ttm) cc_final: 0.7051 (tpp) REVERT: A 747 GLU cc_start: 0.7160 (mp0) cc_final: 0.6704 (mp0) REVERT: A 763 LYS cc_start: 0.7626 (ttpp) cc_final: 0.7302 (mtpp) REVERT: A 778 GLN cc_start: 0.7666 (tp40) cc_final: 0.7424 (tp40) REVERT: A 789 LYS cc_start: 0.8271 (mttp) cc_final: 0.7801 (mmtp) REVERT: A 810 LYS cc_start: 0.7208 (ptpt) cc_final: 0.6779 (ptpt) REVERT: A 813 LYS cc_start: 0.7880 (mmtm) cc_final: 0.7516 (mmtm) REVERT: A 858 THR cc_start: 0.7898 (t) cc_final: 0.7607 (p) REVERT: A 948 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7147 (mm-40) REVERT: A 966 SER cc_start: 0.7998 (t) cc_final: 0.7764 (p) REVERT: A 968 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7784 (mttm) REVERT: A 978 ASP cc_start: 0.7179 (t0) cc_final: 0.6893 (t0) REVERT: A 993 ASP cc_start: 0.7675 (t0) cc_final: 0.7445 (t0) REVERT: A 1033 LEU cc_start: 0.8054 (mp) cc_final: 0.7765 (mp) REVERT: A 1049 MET cc_start: 0.7775 (ptm) cc_final: 0.7435 (ptp) REVERT: A 1072 LYS cc_start: 0.7758 (tptp) cc_final: 0.7311 (tppt) REVERT: A 1083 ASP cc_start: 0.7237 (t70) cc_final: 0.6962 (m-30) REVERT: A 1090 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7635 (mtt90) REVERT: A 1106 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7311 (mtt180) REVERT: A 1110 GLU cc_start: 0.7787 (tt0) cc_final: 0.7514 (tt0) REVERT: B 30 ASN cc_start: 0.7707 (p0) cc_final: 0.7457 (p0) REVERT: B 87 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.6309 (p0) REVERT: B 269 TYR cc_start: 0.6853 (m-80) cc_final: 0.6481 (m-80) REVERT: B 278 LYS cc_start: 0.7950 (tttt) cc_final: 0.7722 (tttt) REVERT: B 281 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7044 (mm-30) REVERT: B 309 GLU cc_start: 0.7608 (mp0) cc_final: 0.7045 (mp0) REVERT: B 313 TYR cc_start: 0.7668 (m-80) cc_final: 0.6898 (m-80) REVERT: B 317 ASN cc_start: 0.7590 (m-40) cc_final: 0.7193 (m-40) REVERT: B 319 ARG cc_start: 0.7454 (ptp-110) cc_final: 0.6560 (ptm160) REVERT: B 321 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7127 (mm110) REVERT: B 324 GLU cc_start: 0.6684 (mp0) cc_final: 0.6008 (mp0) REVERT: B 531 ASN cc_start: 0.7852 (t0) cc_final: 0.7468 (m-40) REVERT: B 548 THR cc_start: 0.8168 (p) cc_final: 0.7845 (m) REVERT: B 556 LYS cc_start: 0.7836 (mptt) cc_final: 0.7503 (mtpp) REVERT: B 563 GLN cc_start: 0.7655 (mm110) cc_final: 0.7322 (mm-40) REVERT: B 577 ASP cc_start: 0.7696 (m-30) cc_final: 0.7278 (m-30) REVERT: B 582 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.5514 (tm-30) REVERT: B 583 ILE cc_start: 0.5876 (tp) cc_final: 0.5156 (mt) REVERT: B 591 PHE cc_start: 0.7952 (p90) cc_final: 0.7550 (p90) REVERT: B 618 GLU cc_start: 0.7360 (tp30) cc_final: 0.7019 (tp30) REVERT: B 627 GLN cc_start: 0.7258 (mt0) cc_final: 0.6708 (mt0) REVERT: B 653 GLU cc_start: 0.7942 (pm20) cc_final: 0.7459 (pm20) REVERT: B 657 ASN cc_start: 0.8090 (m-40) cc_final: 0.7825 (m-40) REVERT: B 696 MET cc_start: 0.7533 (ttp) cc_final: 0.7246 (ptp) REVERT: B 724 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6867 (tm-30) REVERT: B 772 GLU cc_start: 0.6935 (tt0) cc_final: 0.6489 (tt0) REVERT: B 778 GLN cc_start: 0.7450 (tp40) cc_final: 0.6910 (tm-30) REVERT: B 785 LYS cc_start: 0.7884 (mmtm) cc_final: 0.7376 (mmtm) REVERT: B 789 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7770 (mtpp) REVERT: B 866 ASP cc_start: 0.6776 (p0) cc_final: 0.6007 (p0) REVERT: B 867 GLU cc_start: 0.6801 (mp0) cc_final: 0.6169 (mp0) REVERT: B 877 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7015 (mp) REVERT: B 918 ASN cc_start: 0.7430 (m110) cc_final: 0.7199 (m110) REVERT: B 948 GLN cc_start: 0.7585 (tp40) cc_final: 0.7351 (tp-100) REVERT: B 952 ASN cc_start: 0.7757 (m-40) cc_final: 0.7534 (m-40) REVERT: B 959 ASN cc_start: 0.7411 (m-40) cc_final: 0.7171 (t0) REVERT: B 964 GLN cc_start: 0.7744 (mt0) cc_final: 0.7327 (mt0) REVERT: B 968 LYS cc_start: 0.8327 (mtmm) cc_final: 0.7988 (mtpp) REVERT: B 978 ASP cc_start: 0.7236 (t0) cc_final: 0.6958 (t0) REVERT: B 989 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6778 (mt-10) REVERT: B 1027 LYS cc_start: 0.7525 (mttm) cc_final: 0.6954 (mttm) REVERT: B 1040 ASP cc_start: 0.7781 (m-30) cc_final: 0.7410 (m-30) REVERT: B 1044 LYS cc_start: 0.7842 (tptp) cc_final: 0.7571 (tptp) REVERT: B 1070 GLN cc_start: 0.7632 (mt0) cc_final: 0.7402 (mt0) REVERT: B 1112 GLN cc_start: 0.7538 (mt0) cc_final: 0.7063 (mm-40) REVERT: B 1134 ASN cc_start: 0.7381 (t0) cc_final: 0.7015 (m-40) REVERT: B 1135 THR cc_start: 0.7983 (m) cc_final: 0.7262 (m) REVERT: C 45 SER cc_start: 0.8085 (p) cc_final: 0.7739 (t) REVERT: C 55 PHE cc_start: 0.7710 (m-80) cc_final: 0.7296 (m-80) REVERT: C 269 TYR cc_start: 0.7986 (m-80) cc_final: 0.7305 (m-10) REVERT: C 278 LYS cc_start: 0.7311 (ttpm) cc_final: 0.6949 (ttpm) REVERT: C 314 GLN cc_start: 0.8317 (tp40) cc_final: 0.8037 (tp40) REVERT: C 317 ASN cc_start: 0.8183 (m-40) cc_final: 0.7835 (m-40) REVERT: C 356 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7567 (p) REVERT: C 357 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7183 (ttm110) REVERT: C 398 ASP cc_start: 0.6650 (m-30) cc_final: 0.6418 (m-30) REVERT: C 409 GLN cc_start: 0.7524 (mt0) cc_final: 0.6830 (mp10) REVERT: C 418 ILE cc_start: 0.6248 (mm) cc_final: 0.5668 (mm) REVERT: C 436 TRP cc_start: 0.5220 (p90) cc_final: 0.4597 (p90) REVERT: C 453 TYR cc_start: 0.6427 (p90) cc_final: 0.5848 (p90) REVERT: C 510 VAL cc_start: 0.6651 (t) cc_final: 0.6262 (m) REVERT: C 527 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7477 (ttmm) REVERT: C 528 LYS cc_start: 0.7604 (tptp) cc_final: 0.7096 (tptp) REVERT: C 529 SER cc_start: 0.7818 (t) cc_final: 0.7180 (m) REVERT: C 534 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8391 (mttp) REVERT: C 605 ASN cc_start: 0.8716 (m-40) cc_final: 0.8488 (m-40) REVERT: C 645 ARG cc_start: 0.7706 (mtm180) cc_final: 0.7445 (mtm180) REVERT: C 674 GLN cc_start: 0.7103 (pp30) cc_final: 0.6840 (pp30) REVERT: C 702 ASN cc_start: 0.7624 (t0) cc_final: 0.7360 (t0) REVERT: C 720 SER cc_start: 0.8510 (t) cc_final: 0.8009 (p) REVERT: C 739 MET cc_start: 0.7657 (ttm) cc_final: 0.7240 (ttm) REVERT: C 746 THR cc_start: 0.6942 (p) cc_final: 0.6485 (m) REVERT: C 749 SER cc_start: 0.7193 (t) cc_final: 0.6845 (m) REVERT: C 755 TYR cc_start: 0.8561 (m-80) cc_final: 0.8282 (m-80) REVERT: C 772 GLU cc_start: 0.7270 (tt0) cc_final: 0.6896 (tt0) REVERT: C 779 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7457 (mt-10) REVERT: C 803 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7919 (mm-40) REVERT: C 910 VAL cc_start: 0.7802 (t) cc_final: 0.7469 (p) REVERT: C 934 GLN cc_start: 0.7741 (mt0) cc_final: 0.7495 (tt0) REVERT: C 978 ASP cc_start: 0.7063 (m-30) cc_final: 0.6773 (m-30) REVERT: C 982 ARG cc_start: 0.6962 (ttp80) cc_final: 0.6690 (mtp-110) REVERT: C 1044 LYS cc_start: 0.8158 (tptp) cc_final: 0.7730 (tptp) REVERT: C 1072 LYS cc_start: 0.7764 (tptp) cc_final: 0.7168 (tptp) REVERT: C 1083 ASP cc_start: 0.7273 (t0) cc_final: 0.6724 (t0) REVERT: C 1091 GLU cc_start: 0.7480 (pm20) cc_final: 0.7107 (pm20) REVERT: C 1124 ASN cc_start: 0.7054 (p0) cc_final: 0.6840 (p0) REVERT: C 1134 ASN cc_start: 0.6798 (t0) cc_final: 0.5889 (m110) REVERT: C 1135 THR cc_start: 0.7207 (m) cc_final: 0.6540 (p) outliers start: 68 outliers final: 41 residues processed: 619 average time/residue: 0.3673 time to fit residues: 349.7664 Evaluate side-chains 622 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 576 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 963 LYS Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 0.2980 chunk 165 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 217 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 262 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 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 87 ASN A 137 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN C 543 ASN C 709 ASN C1087 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24795 Z= 0.222 Angle : 0.559 7.468 33745 Z= 0.292 Chirality : 0.045 0.346 3912 Planarity : 0.004 0.060 4309 Dihedral : 6.301 59.937 3998 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.75 % Rotamer: Outliers : 2.97 % Allowed : 14.97 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.43 (0.15), residues: 2981 helix: 1.10 (0.19), residues: 706 sheet: -0.85 (0.20), residues: 644 loop : -2.00 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.000 HIS C1082 PHE 0.028 0.001 PHE B 168 TYR 0.023 0.001 TYR A 396 ARG 0.007 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 598 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6797 (m-80) cc_final: 0.6109 (m-80) REVERT: A 48 LEU cc_start: 0.8126 (mp) cc_final: 0.7821 (mt) REVERT: A 62 VAL cc_start: 0.7251 (t) cc_final: 0.7003 (m) REVERT: A 90 VAL cc_start: 0.8309 (m) cc_final: 0.8084 (t) REVERT: A 116 SER cc_start: 0.6262 (m) cc_final: 0.5660 (p) REVERT: A 127 PHE cc_start: 0.5664 (m-80) cc_final: 0.5225 (m-10) REVERT: A 128 ILE cc_start: 0.6862 (mt) cc_final: 0.6478 (mp) REVERT: A 190 ARG cc_start: 0.7043 (mpt-90) cc_final: 0.6660 (mpt-90) REVERT: A 220 PHE cc_start: 0.7719 (t80) cc_final: 0.7482 (t80) REVERT: A 273 ARG cc_start: 0.7206 (ttm170) cc_final: 0.6724 (ttm110) REVERT: A 285 ILE cc_start: 0.7334 (mt) cc_final: 0.7046 (mt) REVERT: A 287 ASP cc_start: 0.7123 (t0) cc_final: 0.6815 (m-30) REVERT: A 297 SER cc_start: 0.7192 (m) cc_final: 0.6503 (t) REVERT: A 321 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7116 (mm110) REVERT: A 384 PRO cc_start: 0.6131 (Cg_endo) cc_final: 0.5914 (Cg_exo) REVERT: A 409 GLN cc_start: 0.7113 (tp40) cc_final: 0.6649 (tp-100) REVERT: A 452 TRP cc_start: 0.7424 (m-10) cc_final: 0.7184 (m100) REVERT: A 563 GLN cc_start: 0.7199 (mp-120) cc_final: 0.6945 (mp10) REVERT: A 591 PHE cc_start: 0.7902 (p90) cc_final: 0.7376 (p90) REVERT: A 595 SER cc_start: 0.8639 (m) cc_final: 0.8274 (p) REVERT: A 645 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7548 (mtm180) REVERT: A 658 SER cc_start: 0.8354 (m) cc_final: 0.7867 (p) REVERT: A 662 ASP cc_start: 0.7417 (t70) cc_final: 0.7008 (t70) REVERT: A 724 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6689 (tm-30) REVERT: A 736 ASP cc_start: 0.7314 (t0) cc_final: 0.6882 (t0) REVERT: A 739 MET cc_start: 0.7335 (ttm) cc_final: 0.7056 (tpp) REVERT: A 747 GLU cc_start: 0.7148 (mp0) cc_final: 0.6680 (mp0) REVERT: A 763 LYS cc_start: 0.7621 (ttpp) cc_final: 0.7300 (mtpp) REVERT: A 778 GLN cc_start: 0.7666 (tp40) cc_final: 0.7441 (tp40) REVERT: A 789 LYS cc_start: 0.8276 (mttp) cc_final: 0.7810 (mmtp) REVERT: A 858 THR cc_start: 0.7882 (t) cc_final: 0.7592 (p) REVERT: A 966 SER cc_start: 0.7992 (t) cc_final: 0.7764 (p) REVERT: A 968 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7791 (mttm) REVERT: A 978 ASP cc_start: 0.7188 (t0) cc_final: 0.6885 (t0) REVERT: A 993 ASP cc_start: 0.7664 (t0) cc_final: 0.7404 (t0) REVERT: A 1033 LEU cc_start: 0.8053 (mp) cc_final: 0.7783 (mp) REVERT: A 1049 MET cc_start: 0.7797 (ptm) cc_final: 0.7423 (ptp) REVERT: A 1072 LYS cc_start: 0.7731 (tptp) cc_final: 0.7343 (tppt) REVERT: A 1083 ASP cc_start: 0.7242 (t70) cc_final: 0.7021 (m-30) REVERT: A 1090 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7615 (mtt90) REVERT: A 1110 GLU cc_start: 0.7788 (tt0) cc_final: 0.7523 (tt0) REVERT: A 1134 ASN cc_start: 0.7485 (t0) cc_final: 0.7192 (m-40) REVERT: B 30 ASN cc_start: 0.7723 (p0) cc_final: 0.7457 (p0) REVERT: B 87 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6087 (p0) REVERT: B 269 TYR cc_start: 0.6878 (m-80) cc_final: 0.6423 (m-80) REVERT: B 278 LYS cc_start: 0.7935 (tttt) cc_final: 0.7703 (tttt) REVERT: B 309 GLU cc_start: 0.7613 (mp0) cc_final: 0.7053 (mp0) REVERT: B 313 TYR cc_start: 0.7659 (m-80) cc_final: 0.6884 (m-80) REVERT: B 317 ASN cc_start: 0.7579 (m-40) cc_final: 0.7173 (m-40) REVERT: B 319 ARG cc_start: 0.7459 (ptp-110) cc_final: 0.6514 (ptm160) REVERT: B 321 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7179 (mm-40) REVERT: B 324 GLU cc_start: 0.6739 (mp0) cc_final: 0.6040 (mp0) REVERT: B 531 ASN cc_start: 0.7849 (t0) cc_final: 0.7497 (m-40) REVERT: B 548 THR cc_start: 0.8181 (p) cc_final: 0.7817 (m) REVERT: B 553 LYS cc_start: 0.6630 (tppt) cc_final: 0.6331 (tppt) REVERT: B 556 LYS cc_start: 0.7829 (mptt) cc_final: 0.7520 (mtpp) REVERT: B 563 GLN cc_start: 0.7672 (mm110) cc_final: 0.7358 (mm-40) REVERT: B 577 ASP cc_start: 0.7672 (m-30) cc_final: 0.7314 (m-30) REVERT: B 582 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5609 (tm-30) REVERT: B 591 PHE cc_start: 0.7957 (p90) cc_final: 0.7527 (p90) REVERT: B 618 GLU cc_start: 0.7337 (tp30) cc_final: 0.6989 (tp30) REVERT: B 627 GLN cc_start: 0.7263 (mt0) cc_final: 0.6703 (mt0) REVERT: B 653 GLU cc_start: 0.7933 (pm20) cc_final: 0.7471 (pm20) REVERT: B 657 ASN cc_start: 0.8082 (m-40) cc_final: 0.7822 (m-40) REVERT: B 662 ASP cc_start: 0.7591 (m-30) cc_final: 0.7319 (m-30) REVERT: B 674 GLN cc_start: 0.6030 (tm-30) cc_final: 0.5806 (tm-30) REVERT: B 696 MET cc_start: 0.7546 (ttp) cc_final: 0.7269 (ptp) REVERT: B 724 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6835 (tm-30) REVERT: B 761 GLN cc_start: 0.7388 (mt0) cc_final: 0.7006 (mt0) REVERT: B 772 GLU cc_start: 0.6951 (tt0) cc_final: 0.6463 (tt0) REVERT: B 778 GLN cc_start: 0.7438 (tp40) cc_final: 0.6941 (tm-30) REVERT: B 785 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7544 (mmtm) REVERT: B 789 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7764 (mtpp) REVERT: B 866 ASP cc_start: 0.6752 (p0) cc_final: 0.5965 (p0) REVERT: B 867 GLU cc_start: 0.6806 (mp0) cc_final: 0.6172 (mp0) REVERT: B 918 ASN cc_start: 0.7435 (m110) cc_final: 0.7190 (m110) REVERT: B 948 GLN cc_start: 0.7606 (tp40) cc_final: 0.7378 (tp-100) REVERT: B 952 ASN cc_start: 0.7754 (m-40) cc_final: 0.7528 (m-40) REVERT: B 959 ASN cc_start: 0.7418 (m-40) cc_final: 0.7174 (t0) REVERT: B 964 GLN cc_start: 0.7731 (mt0) cc_final: 0.7303 (mt0) REVERT: B 968 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8030 (mtpp) REVERT: B 978 ASP cc_start: 0.7265 (t0) cc_final: 0.6924 (t0) REVERT: B 1027 LYS cc_start: 0.7529 (mttm) cc_final: 0.6958 (mttm) REVERT: B 1044 LYS cc_start: 0.7830 (tptp) cc_final: 0.7594 (tptp) REVERT: B 1070 GLN cc_start: 0.7640 (mt0) cc_final: 0.7438 (mt0) REVERT: B 1112 GLN cc_start: 0.7538 (mt0) cc_final: 0.7057 (mm-40) REVERT: B 1134 ASN cc_start: 0.7395 (t0) cc_final: 0.7053 (m-40) REVERT: B 1135 THR cc_start: 0.7991 (m) cc_final: 0.7270 (m) REVERT: C 45 SER cc_start: 0.8072 (p) cc_final: 0.7733 (t) REVERT: C 55 PHE cc_start: 0.7701 (m-80) cc_final: 0.7248 (m-80) REVERT: C 269 TYR cc_start: 0.7981 (m-10) cc_final: 0.7305 (m-10) REVERT: C 278 LYS cc_start: 0.7307 (ttpm) cc_final: 0.6977 (ttpm) REVERT: C 314 GLN cc_start: 0.8326 (tp40) cc_final: 0.8068 (tp40) REVERT: C 317 ASN cc_start: 0.8185 (m-40) cc_final: 0.7789 (m-40) REVERT: C 356 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7553 (p) REVERT: C 357 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7237 (ttm110) REVERT: C 398 ASP cc_start: 0.6655 (m-30) cc_final: 0.6421 (m-30) REVERT: C 409 GLN cc_start: 0.7542 (mt0) cc_final: 0.6890 (mp10) REVERT: C 418 ILE cc_start: 0.6368 (mm) cc_final: 0.5830 (mm) REVERT: C 436 TRP cc_start: 0.5156 (p90) cc_final: 0.4655 (p90) REVERT: C 510 VAL cc_start: 0.6649 (t) cc_final: 0.6246 (m) REVERT: C 527 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7495 (ttmm) REVERT: C 573 ASP cc_start: 0.7147 (t0) cc_final: 0.6776 (t0) REVERT: C 576 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7019 (ptt180) REVERT: C 605 ASN cc_start: 0.8718 (m-40) cc_final: 0.8484 (m-40) REVERT: C 645 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7443 (mtm180) REVERT: C 674 GLN cc_start: 0.7116 (pp30) cc_final: 0.6871 (pp30) REVERT: C 702 ASN cc_start: 0.7612 (t0) cc_final: 0.7280 (t0) REVERT: C 720 SER cc_start: 0.8519 (t) cc_final: 0.8009 (p) REVERT: C 739 MET cc_start: 0.7687 (ttm) cc_final: 0.7180 (ttm) REVERT: C 746 THR cc_start: 0.6873 (p) cc_final: 0.6539 (m) REVERT: C 749 SER cc_start: 0.7196 (t) cc_final: 0.6850 (m) REVERT: C 772 GLU cc_start: 0.7252 (tt0) cc_final: 0.6787 (tt0) REVERT: C 779 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 803 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7933 (mm-40) REVERT: C 910 VAL cc_start: 0.7770 (t) cc_final: 0.7492 (p) REVERT: C 918 ASN cc_start: 0.7786 (m-40) cc_final: 0.7582 (m-40) REVERT: C 934 GLN cc_start: 0.7722 (mt0) cc_final: 0.7503 (tt0) REVERT: C 978 ASP cc_start: 0.7080 (m-30) cc_final: 0.6797 (m-30) REVERT: C 982 ARG cc_start: 0.6958 (ttp80) cc_final: 0.6723 (mtp-110) REVERT: C 1044 LYS cc_start: 0.8138 (tptp) cc_final: 0.7733 (tptp) REVERT: C 1071 GLU cc_start: 0.7987 (mp0) cc_final: 0.7715 (mp0) REVERT: C 1072 LYS cc_start: 0.7770 (tptp) cc_final: 0.7182 (tptp) REVERT: C 1083 ASP cc_start: 0.7254 (t0) cc_final: 0.6839 (t0) REVERT: C 1091 GLU cc_start: 0.7459 (pm20) cc_final: 0.7087 (pm20) REVERT: C 1134 ASN cc_start: 0.6789 (t0) cc_final: 0.5905 (m110) REVERT: C 1135 THR cc_start: 0.7226 (m) cc_final: 0.6581 (p) outliers start: 79 outliers final: 53 residues processed: 625 average time/residue: 0.3807 time to fit residues: 363.8455 Evaluate side-chains 637 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 580 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 824 LYS Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 963 LYS Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 0.5980 chunk 262 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN C 709 ASN C 776 ASN C1087 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24795 Z= 0.210 Angle : 0.557 8.182 33745 Z= 0.289 Chirality : 0.045 0.345 3912 Planarity : 0.004 0.062 4309 Dihedral : 6.170 59.369 3998 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.91 % Favored : 92.96 % Rotamer: Outliers : 3.01 % Allowed : 16.03 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.15), residues: 2981 helix: 1.15 (0.19), residues: 714 sheet: -0.71 (0.20), residues: 638 loop : -1.94 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.000 HIS C1082 PHE 0.027 0.001 PHE B 168 TYR 0.031 0.001 TYR A 396 ARG 0.008 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 590 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6806 (m-80) cc_final: 0.6116 (m-80) REVERT: A 48 LEU cc_start: 0.8119 (mp) cc_final: 0.7812 (mt) REVERT: A 62 VAL cc_start: 0.7255 (t) cc_final: 0.7025 (m) REVERT: A 116 SER cc_start: 0.6284 (m) cc_final: 0.5672 (p) REVERT: A 127 PHE cc_start: 0.5669 (m-10) cc_final: 0.5232 (m-10) REVERT: A 128 ILE cc_start: 0.6859 (mt) cc_final: 0.6469 (mp) REVERT: A 190 ARG cc_start: 0.7030 (mpt-90) cc_final: 0.6629 (mpt-90) REVERT: A 220 PHE cc_start: 0.7710 (t80) cc_final: 0.7449 (t80) REVERT: A 273 ARG cc_start: 0.7229 (ttm170) cc_final: 0.6726 (ttm110) REVERT: A 281 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 285 ILE cc_start: 0.7331 (mt) cc_final: 0.6505 (mm) REVERT: A 287 ASP cc_start: 0.7122 (t0) cc_final: 0.6800 (m-30) REVERT: A 293 LEU cc_start: 0.7295 (mp) cc_final: 0.7063 (mp) REVERT: A 384 PRO cc_start: 0.6097 (Cg_endo) cc_final: 0.5884 (Cg_exo) REVERT: A 409 GLN cc_start: 0.7108 (tp40) cc_final: 0.6639 (tp-100) REVERT: A 452 TRP cc_start: 0.7426 (m-10) cc_final: 0.7186 (m100) REVERT: A 563 GLN cc_start: 0.7130 (mp-120) cc_final: 0.6864 (mp10) REVERT: A 591 PHE cc_start: 0.7835 (p90) cc_final: 0.7317 (p90) REVERT: A 645 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7538 (mtm180) REVERT: A 658 SER cc_start: 0.8362 (m) cc_final: 0.7868 (p) REVERT: A 662 ASP cc_start: 0.7410 (t70) cc_final: 0.7040 (t70) REVERT: A 724 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6673 (tm-30) REVERT: A 736 ASP cc_start: 0.7319 (t0) cc_final: 0.6937 (t0) REVERT: A 739 MET cc_start: 0.7320 (ttm) cc_final: 0.7084 (tpp) REVERT: A 747 GLU cc_start: 0.7158 (mp0) cc_final: 0.6717 (mp0) REVERT: A 763 LYS cc_start: 0.7619 (ttpp) cc_final: 0.7299 (mtpp) REVERT: A 778 GLN cc_start: 0.7721 (tp40) cc_final: 0.7446 (tp40) REVERT: A 789 LYS cc_start: 0.8294 (mttp) cc_final: 0.7816 (mmtp) REVERT: A 858 THR cc_start: 0.7902 (t) cc_final: 0.7602 (p) REVERT: A 966 SER cc_start: 0.7984 (t) cc_final: 0.7756 (p) REVERT: A 968 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7789 (mttm) REVERT: A 978 ASP cc_start: 0.7194 (t0) cc_final: 0.6885 (t0) REVERT: A 993 ASP cc_start: 0.7643 (t0) cc_final: 0.7374 (t0) REVERT: A 1033 LEU cc_start: 0.8036 (mp) cc_final: 0.7767 (mp) REVERT: A 1072 LYS cc_start: 0.7717 (tptp) cc_final: 0.7329 (tppt) REVERT: A 1083 ASP cc_start: 0.7240 (t70) cc_final: 0.6882 (m-30) REVERT: A 1090 ARG cc_start: 0.7859 (mtt-85) cc_final: 0.7621 (mtt90) REVERT: A 1110 GLU cc_start: 0.7788 (tt0) cc_final: 0.7529 (tt0) REVERT: A 1134 ASN cc_start: 0.7484 (t0) cc_final: 0.7124 (m-40) REVERT: B 30 ASN cc_start: 0.7720 (p0) cc_final: 0.7448 (p0) REVERT: B 87 ASN cc_start: 0.6692 (OUTLIER) cc_final: 0.6111 (p0) REVERT: B 192 PHE cc_start: 0.6254 (m-80) cc_final: 0.5930 (m-80) REVERT: B 269 TYR cc_start: 0.6849 (m-80) cc_final: 0.6394 (m-80) REVERT: B 278 LYS cc_start: 0.7930 (tttt) cc_final: 0.7699 (tttt) REVERT: B 309 GLU cc_start: 0.7597 (mp0) cc_final: 0.7033 (mp0) REVERT: B 313 TYR cc_start: 0.7644 (m-80) cc_final: 0.6874 (m-80) REVERT: B 317 ASN cc_start: 0.7549 (m-40) cc_final: 0.7165 (m-40) REVERT: B 319 ARG cc_start: 0.7462 (ptp-110) cc_final: 0.6470 (ptm160) REVERT: B 321 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7197 (mm-40) REVERT: B 324 GLU cc_start: 0.6738 (mp0) cc_final: 0.6041 (mp0) REVERT: B 531 ASN cc_start: 0.7841 (t0) cc_final: 0.7488 (m-40) REVERT: B 548 THR cc_start: 0.8168 (p) cc_final: 0.7896 (m) REVERT: B 556 LYS cc_start: 0.7813 (mptt) cc_final: 0.7454 (mtpp) REVERT: B 557 LYS cc_start: 0.7994 (mppt) cc_final: 0.7326 (mppt) REVERT: B 563 GLN cc_start: 0.7675 (mm110) cc_final: 0.7366 (mm-40) REVERT: B 577 ASP cc_start: 0.7655 (m-30) cc_final: 0.7450 (m-30) REVERT: B 591 PHE cc_start: 0.7938 (p90) cc_final: 0.7514 (p90) REVERT: B 594 VAL cc_start: 0.8106 (p) cc_final: 0.7905 (m) REVERT: B 618 GLU cc_start: 0.7346 (tp30) cc_final: 0.7006 (tp30) REVERT: B 627 GLN cc_start: 0.7281 (mt0) cc_final: 0.6675 (mt0) REVERT: B 653 GLU cc_start: 0.7931 (pm20) cc_final: 0.7471 (pm20) REVERT: B 657 ASN cc_start: 0.8082 (m-40) cc_final: 0.7821 (m-40) REVERT: B 662 ASP cc_start: 0.7604 (m-30) cc_final: 0.7316 (m-30) REVERT: B 696 MET cc_start: 0.7556 (ttp) cc_final: 0.7270 (ptp) REVERT: B 724 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6841 (tm-30) REVERT: B 736 ASP cc_start: 0.6801 (t0) cc_final: 0.6548 (t0) REVERT: B 755 TYR cc_start: 0.8050 (m-80) cc_final: 0.7828 (m-80) REVERT: B 772 GLU cc_start: 0.6967 (tt0) cc_final: 0.6452 (tt0) REVERT: B 778 GLN cc_start: 0.7447 (tp40) cc_final: 0.6978 (tm-30) REVERT: B 785 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7551 (mmtm) REVERT: B 789 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7774 (mtpp) REVERT: B 866 ASP cc_start: 0.6761 (p0) cc_final: 0.5993 (p0) REVERT: B 867 GLU cc_start: 0.6808 (mp0) cc_final: 0.6200 (mp0) REVERT: B 918 ASN cc_start: 0.7414 (m110) cc_final: 0.7189 (m110) REVERT: B 948 GLN cc_start: 0.7551 (tp40) cc_final: 0.7336 (tp-100) REVERT: B 952 ASN cc_start: 0.7747 (m-40) cc_final: 0.7519 (m-40) REVERT: B 959 ASN cc_start: 0.7373 (m-40) cc_final: 0.7163 (t0) REVERT: B 964 GLN cc_start: 0.7691 (mt0) cc_final: 0.7260 (mt0) REVERT: B 968 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8060 (mtpp) REVERT: B 978 ASP cc_start: 0.7291 (t0) cc_final: 0.6927 (t0) REVERT: B 1027 LYS cc_start: 0.7531 (mttm) cc_final: 0.6999 (mttm) REVERT: B 1044 LYS cc_start: 0.7833 (tptp) cc_final: 0.7597 (tptp) REVERT: B 1070 GLN cc_start: 0.7636 (mt0) cc_final: 0.7430 (mt0) REVERT: B 1112 GLN cc_start: 0.7546 (mt0) cc_final: 0.7054 (mm-40) REVERT: B 1134 ASN cc_start: 0.7408 (t0) cc_final: 0.7089 (m-40) REVERT: B 1135 THR cc_start: 0.8008 (m) cc_final: 0.7304 (m) REVERT: C 45 SER cc_start: 0.8057 (p) cc_final: 0.7723 (t) REVERT: C 55 PHE cc_start: 0.7723 (m-80) cc_final: 0.7267 (m-80) REVERT: C 269 TYR cc_start: 0.8009 (m-10) cc_final: 0.7331 (m-10) REVERT: C 278 LYS cc_start: 0.7337 (ttpm) cc_final: 0.6997 (ttpm) REVERT: C 317 ASN cc_start: 0.8184 (m-40) cc_final: 0.7783 (m-40) REVERT: C 356 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7549 (p) REVERT: C 357 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7116 (ttm110) REVERT: C 398 ASP cc_start: 0.6664 (m-30) cc_final: 0.6407 (m-30) REVERT: C 409 GLN cc_start: 0.7538 (mt0) cc_final: 0.6854 (mp10) REVERT: C 418 ILE cc_start: 0.6458 (mm) cc_final: 0.5925 (mm) REVERT: C 436 TRP cc_start: 0.5134 (p90) cc_final: 0.4742 (p90) REVERT: C 510 VAL cc_start: 0.6641 (t) cc_final: 0.6240 (m) REVERT: C 527 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7471 (ttmm) REVERT: C 573 ASP cc_start: 0.7117 (t0) cc_final: 0.6746 (t0) REVERT: C 576 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6972 (ptt180) REVERT: C 605 ASN cc_start: 0.8707 (m-40) cc_final: 0.8484 (m-40) REVERT: C 645 ARG cc_start: 0.7694 (mtm180) cc_final: 0.7442 (mtm180) REVERT: C 674 GLN cc_start: 0.7119 (pp30) cc_final: 0.6877 (pp30) REVERT: C 702 ASN cc_start: 0.7593 (t0) cc_final: 0.7280 (t0) REVERT: C 720 SER cc_start: 0.8500 (t) cc_final: 0.7999 (p) REVERT: C 739 MET cc_start: 0.7713 (ttm) cc_final: 0.7104 (ttm) REVERT: C 746 THR cc_start: 0.6881 (p) cc_final: 0.6564 (m) REVERT: C 749 SER cc_start: 0.7227 (t) cc_final: 0.6873 (m) REVERT: C 772 GLU cc_start: 0.7275 (tt0) cc_final: 0.6878 (tt0) REVERT: C 779 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7408 (mt-10) REVERT: C 803 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7945 (mm-40) REVERT: C 810 LYS cc_start: 0.7546 (ptpt) cc_final: 0.7311 (ptpt) REVERT: C 910 VAL cc_start: 0.7752 (t) cc_final: 0.7416 (p) REVERT: C 918 ASN cc_start: 0.7737 (m-40) cc_final: 0.7528 (m-40) REVERT: C 934 GLN cc_start: 0.7743 (mt0) cc_final: 0.7535 (tt0) REVERT: C 978 ASP cc_start: 0.7094 (m-30) cc_final: 0.6810 (m-30) REVERT: C 982 ARG cc_start: 0.6942 (ttp80) cc_final: 0.6721 (mtp-110) REVERT: C 1044 LYS cc_start: 0.8120 (tptp) cc_final: 0.7693 (tptp) REVERT: C 1071 GLU cc_start: 0.7989 (mp0) cc_final: 0.7708 (mp0) REVERT: C 1072 LYS cc_start: 0.7741 (tptp) cc_final: 0.7064 (tptp) REVERT: C 1083 ASP cc_start: 0.7228 (t0) cc_final: 0.6818 (t0) REVERT: C 1134 ASN cc_start: 0.6781 (t0) cc_final: 0.5941 (m110) REVERT: C 1135 THR cc_start: 0.7223 (m) cc_final: 0.6574 (p) outliers start: 80 outliers final: 61 residues processed: 617 average time/residue: 0.3705 time to fit residues: 349.4877 Evaluate side-chains 641 residues out of total 2658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 577 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 824 LYS Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7692 > 50: distance: 43 - 65: 11.987 distance: 47 - 73: 22.982 distance: 54 - 60: 10.049 distance: 55 - 85: 11.933 distance: 60 - 61: 9.742 distance: 61 - 62: 16.191 distance: 61 - 64: 19.471 distance: 62 - 63: 3.172 distance: 62 - 65: 11.616 distance: 66 - 67: 15.123 distance: 66 - 69: 11.465 distance: 67 - 68: 19.384 distance: 67 - 73: 19.086 distance: 69 - 70: 13.923 distance: 70 - 71: 23.576 distance: 70 - 72: 22.978 distance: 73 - 74: 25.582 distance: 74 - 75: 14.091 distance: 74 - 77: 17.038 distance: 75 - 76: 12.339 distance: 75 - 85: 25.581 distance: 77 - 78: 8.746 distance: 78 - 79: 23.089 distance: 78 - 80: 12.901 distance: 79 - 81: 21.030 distance: 80 - 82: 16.232 distance: 81 - 83: 16.448 distance: 82 - 83: 28.831 distance: 83 - 84: 10.787 distance: 85 - 86: 13.926 distance: 86 - 87: 5.244 distance: 86 - 89: 14.236 distance: 87 - 88: 9.312 distance: 87 - 93: 6.141 distance: 89 - 90: 12.956 distance: 90 - 91: 22.663 distance: 90 - 92: 17.557 distance: 93 - 94: 20.244 distance: 94 - 95: 6.066 distance: 94 - 97: 25.229 distance: 95 - 96: 9.580 distance: 95 - 105: 18.242 distance: 97 - 98: 10.678 distance: 98 - 99: 12.167 distance: 98 - 100: 8.394 distance: 99 - 101: 15.949 distance: 100 - 102: 10.776 distance: 101 - 103: 17.997 distance: 102 - 103: 4.416 distance: 103 - 104: 15.014 distance: 105 - 106: 12.331 distance: 106 - 107: 23.653 distance: 106 - 109: 6.686 distance: 107 - 108: 19.549 distance: 107 - 114: 30.683 distance: 109 - 110: 7.926 distance: 110 - 111: 16.203 distance: 112 - 113: 43.257 distance: 114 - 115: 17.238 distance: 115 - 116: 4.380 distance: 115 - 118: 25.546 distance: 116 - 117: 3.919 distance: 116 - 122: 10.717 distance: 118 - 119: 16.655 distance: 119 - 120: 7.373 distance: 119 - 121: 39.769 distance: 122 - 123: 18.391 distance: 122 - 128: 16.560 distance: 123 - 124: 8.863 distance: 123 - 126: 21.206 distance: 124 - 125: 9.302 distance: 124 - 129: 8.196 distance: 126 - 127: 38.035 distance: 127 - 128: 11.930 distance: 129 - 130: 8.491 distance: 130 - 131: 22.072 distance: 130 - 133: 7.223 distance: 131 - 132: 20.832 distance: 131 - 137: 13.717 distance: 133 - 134: 12.927 distance: 134 - 135: 12.220 distance: 134 - 136: 4.300 distance: 137 - 138: 14.987 distance: 138 - 139: 5.684 distance: 138 - 141: 18.232 distance: 139 - 140: 19.255 distance: 139 - 145: 24.623 distance: 141 - 142: 22.586 distance: 142 - 143: 14.723 distance: 142 - 144: 5.163