Starting phenix.real_space_refine on Wed Mar 20 00:23:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g71_29793/03_2024/8g71_29793.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g71_29793/03_2024/8g71_29793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g71_29793/03_2024/8g71_29793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g71_29793/03_2024/8g71_29793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g71_29793/03_2024/8g71_29793.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g71_29793/03_2024/8g71_29793.pdb" } resolution = 2.1 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= 0.000 sd= 0.032 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 114 5.16 5 C 16386 2.51 5 N 4239 2.21 5 O 5022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25761 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "J" 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: "C" 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: "K" 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: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.97, per 1000 atoms: 0.58 Number of scatterers: 25761 At special positions: 0 Unit cell: (151.84, 161.33, 195.64, 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 114 16.00 O 5022 8.00 N 4239 7.00 C 16386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " 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 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " 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 C 1 " - " NAG C 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 234 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B1074 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 616 " " NAG D1306 " - " ASN D 657 " " NAG D1307 " - " ASN D 709 " " NAG D1308 " - " ASN D1074 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN D 717 " " NAG L 1 " - " ASN D 801 " " NAG M 1 " - " ASN D1098 " " NAG N 1 " - " ASN D1134 " Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 4.6 seconds 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 25.0% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.143A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.035A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.071A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.650A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.144A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.169A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.809A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.115A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.649A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.616A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.625A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.581A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.818A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.727A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.893A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.045A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 370 removed outlier: 4.096A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 390 removed outlier: 3.941A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 removed outlier: 3.936A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA D 411 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.605A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.782A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.961A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.733A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.498A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 4.087A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.379A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.932A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 135 current: chain 'A' and resid 153 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.848A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 7.190A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.741A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.214A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.691A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.830A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.271A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.224A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.865A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.989A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.639A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 135 current: chain 'B' and resid 154 through 157 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.227A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.678A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.481A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.032A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.080A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.920A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.259A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.331A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.278A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.970A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 68 through 70 removed outlier: 3.683A pdb=" N HIS D 69 " --> pdb=" O ARG D 78 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 85 current: chain 'D' and resid 116 through 121 removed outlier: 7.974A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.312A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.925A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.188A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.095A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 1094 through 1097 990 hydrogen bonds defined for protein. 2724 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: 11.35 Time building geometry restraints manager: 10.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8200 1.34 - 1.46: 6462 1.46 - 1.59: 11549 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 26355 Sorted by residual: bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL B 401 " pdb=" CA VAL B 401 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.95e+00 bond pdb=" N VAL D 227 " pdb=" CA VAL D 227 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.22e-02 6.72e+03 8.17e+00 bond pdb=" N PHE B 400 " pdb=" CA PHE B 400 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.20e-02 6.94e+03 7.97e+00 bond pdb=" N SER B 399 " pdb=" CA SER B 399 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.23e-02 6.61e+03 7.68e+00 ... (remaining 26350 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 825 106.95 - 113.73: 14624 113.73 - 120.50: 9654 120.50 - 127.27: 10563 127.27 - 134.04: 219 Bond angle restraints: 35885 Sorted by residual: angle pdb=" C ASN D 61 " pdb=" CA ASN D 61 " pdb=" CB ASN D 61 " ideal model delta sigma weight residual 109.75 116.56 -6.81 1.65e+00 3.67e-01 1.70e+01 angle pdb=" CA LYS A 187 " pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CB LYS A 187 " pdb=" CG LYS A 187 " pdb=" CD LYS A 187 " ideal model delta sigma weight residual 111.30 119.75 -8.45 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CA VAL D 382 " pdb=" C VAL D 382 " pdb=" O VAL D 382 " ideal model delta sigma weight residual 121.64 118.23 3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" CA GLU D 132 " pdb=" C GLU D 132 " pdb=" O GLU D 132 " ideal model delta sigma weight residual 122.36 118.23 4.13 1.21e+00 6.83e-01 1.17e+01 ... (remaining 35880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 14406 18.04 - 36.07: 1413 36.07 - 54.11: 343 54.11 - 72.15: 89 72.15 - 90.18: 40 Dihedral angle restraints: 16291 sinusoidal: 6934 harmonic: 9357 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 164.39 -71.39 1 1.00e+01 1.00e-02 6.54e+01 dihedral pdb=" CB CYS D 336 " pdb=" SG CYS D 336 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -37.24 -48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -39.06 -46.94 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 16288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3925 0.098 - 0.196: 261 0.196 - 0.294: 2 0.294 - 0.391: 0 0.391 - 0.489: 1 Chirality restraints: 4189 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ILE D 128 " pdb=" N ILE D 128 " pdb=" C ILE D 128 " pdb=" CB ILE D 128 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4186 not shown) Planarity restraints: 4637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.033 2.00e-02 2.50e+03 1.94e-02 9.37e+00 pdb=" CG TRP B 353 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 589 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 61 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ASN D 61 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN D 61 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D 62 " -0.012 2.00e-02 2.50e+03 ... (remaining 4634 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 203 2.62 - 3.19: 22188 3.19 - 3.76: 39503 3.76 - 4.33: 56006 4.33 - 4.90: 90094 Nonbonded interactions: 207994 Sorted by model distance: nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.055 2.440 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.073 2.440 nonbonded pdb=" OG SER D 735 " pdb=" OG1 THR D 859 " model vdw 2.144 2.440 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.183 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.186 2.440 ... (remaining 207989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1307)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 22.370 Check model and map are aligned: 0.520 Set scattering table: 0.230 Process input model: 70.330 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.240 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.042 26355 Z= 0.235 Angle : 0.639 9.350 35885 Z= 0.344 Chirality : 0.047 0.489 4189 Planarity : 0.004 0.071 4603 Dihedral : 15.865 90.184 10160 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.27 % Allowed : 18.88 % Favored : 78.85 % 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: -0.70 (0.14), residues: 3187 helix: 1.49 (0.20), residues: 676 sheet: -0.58 (0.17), residues: 785 loop : -1.21 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 353 HIS 0.014 0.001 HIS B1064 PHE 0.023 0.001 PHE D 192 TYR 0.021 0.001 TYR D 453 ARG 0.005 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 150 time to evaluate : 3.277 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 254 SER cc_start: 0.0069 (OUTLIER) cc_final: -0.0931 (p) REVERT: A 438 SER cc_start: 0.5280 (OUTLIER) cc_final: 0.4775 (p) REVERT: A 573 THR cc_start: 0.7171 (OUTLIER) cc_final: 0.6962 (p) REVERT: A 902 MET cc_start: 0.9220 (tpp) cc_final: 0.8944 (tpp) outliers start: 64 outliers final: 45 residues processed: 212 average time/residue: 1.0889 time to fit residues: 278.0005 Evaluate side-chains 186 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 138 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 444 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 702 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 10.0000 chunk 243 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A1002 GLN B 69 HIS B 207 HIS B 542 ASN B 607 GLN B 957 GLN B1002 GLN D 121 ASN D 196 ASN D 218 GLN D 321 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26355 Z= 0.289 Angle : 0.658 12.001 35885 Z= 0.346 Chirality : 0.050 0.485 4189 Planarity : 0.005 0.053 4603 Dihedral : 7.098 65.388 4461 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 3.55 % Allowed : 18.52 % Favored : 77.93 % 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: -0.59 (0.14), residues: 3187 helix: 1.77 (0.20), residues: 674 sheet: -0.56 (0.18), residues: 772 loop : -1.20 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 353 HIS 0.007 0.002 HIS B1048 PHE 0.027 0.002 PHE A 898 TYR 0.023 0.002 TYR A1067 ARG 0.005 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 140 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 ASP cc_start: 0.3802 (OUTLIER) cc_final: 0.3438 (t0) REVERT: A 1092 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: B 580 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5182 (mm-40) REVERT: B 619 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: D 69 HIS cc_start: 0.2574 (OUTLIER) cc_final: 0.1635 (t-170) REVERT: D 957 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8327 (tt0) outliers start: 100 outliers final: 45 residues processed: 232 average time/residue: 1.0482 time to fit residues: 295.0951 Evaluate side-chains 187 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 136 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 198 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 260 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 234 optimal weight: 0.3980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 188 ASN A 603 ASN A1002 GLN B 218 GLN B 354 ASN B 542 ASN B 580 GLN B 607 GLN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 26355 Z= 0.173 Angle : 0.549 9.915 35885 Z= 0.289 Chirality : 0.045 0.429 4189 Planarity : 0.004 0.050 4603 Dihedral : 5.999 58.052 4420 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 3.26 % Allowed : 18.70 % Favored : 78.03 % 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: -0.41 (0.14), residues: 3187 helix: 2.04 (0.20), residues: 683 sheet: -0.48 (0.18), residues: 743 loop : -1.14 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.009 0.001 HIS B1064 PHE 0.029 0.001 PHE B 400 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 146 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0859 (OUTLIER) cc_final: 0.0524 (m) REVERT: A 131 CYS cc_start: 0.1941 (OUTLIER) cc_final: 0.1679 (p) REVERT: A 467 ASP cc_start: 0.3667 (OUTLIER) cc_final: 0.3348 (t0) REVERT: A 539 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7719 (p) REVERT: A 574 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6543 (p0) REVERT: B 153 MET cc_start: 0.0574 (OUTLIER) cc_final: -0.0479 (ttm) REVERT: B 318 PHE cc_start: 0.7978 (t80) cc_final: 0.7683 (p90) REVERT: B 442 ASP cc_start: 0.1215 (OUTLIER) cc_final: 0.0861 (p0) REVERT: D 1081 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8714 (mt) outliers start: 92 outliers final: 37 residues processed: 230 average time/residue: 0.9789 time to fit residues: 274.5910 Evaluate side-chains 180 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.6980 chunk 219 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 139 optimal weight: 7.9990 chunk 196 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 277 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 506 GLN B 542 ASN B 580 GLN B 607 GLN B 957 GLN B1002 GLN D 121 ASN D 196 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26355 Z= 0.205 Angle : 0.570 10.762 35885 Z= 0.299 Chirality : 0.046 0.438 4189 Planarity : 0.004 0.049 4603 Dihedral : 5.761 56.593 4413 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 3.16 % Allowed : 18.74 % Favored : 78.11 % 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: -0.41 (0.14), residues: 3187 helix: 2.12 (0.20), residues: 674 sheet: -0.47 (0.18), residues: 736 loop : -1.16 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.004 0.001 HIS A1048 PHE 0.022 0.001 PHE B 400 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 142 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0892 (OUTLIER) cc_final: 0.0541 (m) REVERT: A 24 LEU cc_start: 0.2059 (OUTLIER) cc_final: 0.1392 (tp) REVERT: A 212 LEU cc_start: 0.3281 (OUTLIER) cc_final: 0.2755 (mm) REVERT: A 393 THR cc_start: 0.5648 (OUTLIER) cc_final: 0.5401 (t) REVERT: A 574 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6490 (p0) REVERT: B 153 MET cc_start: 0.0674 (OUTLIER) cc_final: -0.0398 (ttm) REVERT: B 177 MET cc_start: 0.3192 (OUTLIER) cc_final: 0.2560 (mpm) REVERT: B 190 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.6055 (mmt-90) REVERT: B 318 PHE cc_start: 0.7998 (t80) cc_final: 0.7639 (p90) REVERT: B 422 ASN cc_start: 0.0613 (OUTLIER) cc_final: 0.0167 (t0) REVERT: B 442 ASP cc_start: 0.1142 (OUTLIER) cc_final: 0.0786 (p0) REVERT: B 619 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: B 1092 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6233 (pp20) REVERT: D 957 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: D 1081 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8710 (mt) outliers start: 89 outliers final: 39 residues processed: 223 average time/residue: 1.1033 time to fit residues: 295.3485 Evaluate side-chains 190 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 137 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 214 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 955 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 580 GLN B 607 GLN B 957 GLN B1002 GLN D 196 ASN D1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 26355 Z= 0.478 Angle : 0.799 13.752 35885 Z= 0.422 Chirality : 0.058 0.562 4189 Planarity : 0.006 0.084 4603 Dihedral : 6.801 65.419 4406 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 4.15 % Allowed : 17.92 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.77 (0.14), residues: 3187 helix: 1.58 (0.20), residues: 662 sheet: -0.52 (0.18), residues: 717 loop : -1.35 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 64 HIS 0.013 0.002 HIS A1048 PHE 0.039 0.003 PHE A 898 TYR 0.025 0.003 TYR A1067 ARG 0.007 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 136 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0967 (OUTLIER) cc_final: 0.0606 (m) REVERT: A 52 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6151 (pp30) REVERT: A 131 CYS cc_start: 0.2258 (OUTLIER) cc_final: 0.1906 (p) REVERT: A 153 MET cc_start: -0.0384 (mmm) cc_final: -0.0845 (tpt) REVERT: A 396 TYR cc_start: 0.7388 (m-80) cc_final: 0.7103 (m-10) REVERT: A 444 LYS cc_start: 0.3182 (OUTLIER) cc_final: 0.2906 (mmtm) REVERT: A 574 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6631 (p0) REVERT: B 24 LEU cc_start: 0.1683 (OUTLIER) cc_final: 0.1482 (mm) REVERT: B 153 MET cc_start: 0.0766 (OUTLIER) cc_final: -0.0303 (ttm) REVERT: B 177 MET cc_start: 0.3517 (OUTLIER) cc_final: 0.2882 (mpm) REVERT: B 237 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6838 (mtp180) REVERT: B 353 TRP cc_start: 0.1260 (OUTLIER) cc_final: -0.0185 (m-10) REVERT: B 442 ASP cc_start: 0.1556 (OUTLIER) cc_final: 0.1001 (p0) REVERT: B 619 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: B 820 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: D 571 ASP cc_start: 0.5898 (OUTLIER) cc_final: 0.5230 (p0) REVERT: D 957 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: D 1081 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8698 (mt) outliers start: 117 outliers final: 65 residues processed: 241 average time/residue: 0.9585 time to fit residues: 284.8339 Evaluate side-chains 214 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 133 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 310 optimal weight: 0.3980 chunk 257 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 603 ASN A 913 GLN A1002 GLN B 542 ASN B 607 GLN B 957 GLN B1002 GLN D 196 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 26355 Z= 0.165 Angle : 0.548 9.450 35885 Z= 0.287 Chirality : 0.045 0.419 4189 Planarity : 0.004 0.050 4603 Dihedral : 5.618 56.899 4406 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 3.23 % Allowed : 19.06 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.14), residues: 3187 helix: 2.03 (0.20), residues: 677 sheet: -0.51 (0.18), residues: 710 loop : -1.15 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 64 HIS 0.010 0.001 HIS B1064 PHE 0.017 0.001 PHE B 400 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 138 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0966 (OUTLIER) cc_final: 0.0597 (m) REVERT: A 153 MET cc_start: -0.0520 (mmm) cc_final: -0.0854 (tpt) REVERT: A 212 LEU cc_start: 0.3229 (OUTLIER) cc_final: 0.2675 (mp) REVERT: A 393 THR cc_start: 0.5582 (OUTLIER) cc_final: 0.5284 (t) REVERT: A 396 TYR cc_start: 0.7186 (m-80) cc_final: 0.6898 (m-10) REVERT: A 574 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6429 (p0) REVERT: B 153 MET cc_start: 0.0580 (OUTLIER) cc_final: -0.0398 (ttm) REVERT: B 177 MET cc_start: 0.3528 (OUTLIER) cc_final: 0.2922 (mpm) REVERT: B 190 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.6203 (mmt90) REVERT: B 318 PHE cc_start: 0.7992 (t80) cc_final: 0.7695 (p90) REVERT: B 353 TRP cc_start: 0.0904 (OUTLIER) cc_final: -0.0291 (m-10) REVERT: B 422 ASN cc_start: 0.0603 (OUTLIER) cc_final: 0.0067 (t0) REVERT: B 442 ASP cc_start: 0.1111 (OUTLIER) cc_final: 0.0778 (p0) REVERT: B 619 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: B 1092 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6149 (pp20) REVERT: D 318 PHE cc_start: 0.8092 (p90) cc_final: 0.7780 (p90) REVERT: D 646 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7424 (mtp-110) REVERT: D 1081 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8693 (mt) outliers start: 91 outliers final: 43 residues processed: 217 average time/residue: 1.0445 time to fit residues: 274.3129 Evaluate side-chains 190 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 133 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 176 optimal weight: 0.3980 chunk 226 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 173 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 142 optimal weight: 30.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 603 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 218 GLN B 542 ASN B 580 GLN B 607 GLN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D1101 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26355 Z= 0.207 Angle : 0.575 10.984 35885 Z= 0.301 Chirality : 0.046 0.438 4189 Planarity : 0.004 0.049 4603 Dihedral : 5.537 55.977 4406 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 3.37 % Allowed : 18.67 % Favored : 77.96 % 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: -0.39 (0.14), residues: 3187 helix: 2.08 (0.20), residues: 676 sheet: -0.41 (0.18), residues: 714 loop : -1.14 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.006 0.001 HIS A 207 PHE 0.022 0.001 PHE A 898 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 138 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0950 (OUTLIER) cc_final: 0.0586 (m) REVERT: A 153 MET cc_start: -0.0447 (mmm) cc_final: -0.0815 (tpt) REVERT: A 212 LEU cc_start: 0.3188 (OUTLIER) cc_final: 0.2658 (mp) REVERT: A 396 TYR cc_start: 0.7220 (m-80) cc_final: 0.6971 (m-10) REVERT: A 574 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6449 (p0) REVERT: B 153 MET cc_start: 0.0626 (OUTLIER) cc_final: -0.0379 (ttm) REVERT: B 177 MET cc_start: 0.3566 (OUTLIER) cc_final: 0.2820 (mmp) REVERT: B 318 PHE cc_start: 0.7975 (t80) cc_final: 0.7648 (p90) REVERT: B 353 TRP cc_start: 0.1067 (OUTLIER) cc_final: -0.0186 (m-10) REVERT: B 422 ASN cc_start: 0.0622 (OUTLIER) cc_final: 0.0075 (t0) REVERT: B 442 ASP cc_start: 0.1230 (OUTLIER) cc_final: 0.0906 (p0) REVERT: B 619 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: B 1092 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6269 (pp20) REVERT: D 646 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7433 (mtp-110) REVERT: D 902 MET cc_start: 0.9129 (tpp) cc_final: 0.8859 (tpp) REVERT: D 1081 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8700 (mt) outliers start: 95 outliers final: 56 residues processed: 224 average time/residue: 1.0884 time to fit residues: 294.2786 Evaluate side-chains 202 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 134 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 196 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A 603 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 580 GLN B 607 GLN B 957 GLN B1002 GLN D 121 ASN D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26355 Z= 0.282 Angle : 0.640 12.340 35885 Z= 0.336 Chirality : 0.049 0.446 4189 Planarity : 0.005 0.085 4603 Dihedral : 5.813 57.526 4406 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 3.26 % Allowed : 18.88 % Favored : 77.86 % 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: -0.49 (0.14), residues: 3187 helix: 1.96 (0.20), residues: 669 sheet: -0.46 (0.18), residues: 714 loop : -1.18 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 64 HIS 0.007 0.001 HIS A 207 PHE 0.028 0.002 PHE A 898 TYR 0.024 0.002 TYR A1067 ARG 0.004 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 140 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0957 (OUTLIER) cc_final: 0.0581 (m) REVERT: A 131 CYS cc_start: 0.2221 (OUTLIER) cc_final: 0.1927 (p) REVERT: A 153 MET cc_start: -0.0430 (mmm) cc_final: -0.0838 (tpt) REVERT: A 212 LEU cc_start: 0.3281 (OUTLIER) cc_final: 0.2699 (mp) REVERT: A 396 TYR cc_start: 0.7297 (m-80) cc_final: 0.7004 (m-10) REVERT: A 452 LEU cc_start: 0.4800 (OUTLIER) cc_final: 0.4172 (mt) REVERT: A 574 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6505 (p0) REVERT: B 153 MET cc_start: 0.0635 (OUTLIER) cc_final: -0.0372 (ttm) REVERT: B 177 MET cc_start: 0.3545 (OUTLIER) cc_final: 0.2960 (mmp) REVERT: B 353 TRP cc_start: 0.1162 (OUTLIER) cc_final: -0.0136 (m-10) REVERT: B 422 ASN cc_start: 0.0808 (OUTLIER) cc_final: 0.0225 (t0) REVERT: B 442 ASP cc_start: 0.1361 (OUTLIER) cc_final: 0.0947 (p0) REVERT: B 619 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: B 1092 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6380 (pp20) REVERT: D 646 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7449 (mtp-110) REVERT: D 902 MET cc_start: 0.9206 (tpp) cc_final: 0.8863 (tpp) REVERT: D 957 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: D 1081 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8697 (mt) outliers start: 92 outliers final: 58 residues processed: 221 average time/residue: 1.0845 time to fit residues: 290.7199 Evaluate side-chains 209 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 136 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 288 optimal weight: 0.0050 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 272 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A1002 GLN B 542 ASN B 580 GLN B 607 GLN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26355 Z= 0.188 Angle : 0.559 9.453 35885 Z= 0.293 Chirality : 0.046 0.515 4189 Planarity : 0.004 0.054 4603 Dihedral : 5.409 55.843 4406 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 2.95 % Allowed : 19.41 % Favored : 77.64 % 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: -0.35 (0.14), residues: 3187 helix: 2.08 (0.20), residues: 676 sheet: -0.38 (0.18), residues: 705 loop : -1.10 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 64 HIS 0.007 0.001 HIS B1064 PHE 0.026 0.001 PHE D 192 TYR 0.020 0.001 TYR B1067 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 141 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.0910 (OUTLIER) cc_final: 0.0540 (m) REVERT: A 131 CYS cc_start: 0.2218 (OUTLIER) cc_final: 0.1965 (p) REVERT: A 153 MET cc_start: -0.0439 (mmm) cc_final: -0.0823 (tpt) REVERT: A 212 LEU cc_start: 0.3120 (OUTLIER) cc_final: 0.2512 (tp) REVERT: A 396 TYR cc_start: 0.7213 (m-80) cc_final: 0.6916 (m-10) REVERT: A 452 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4183 (mt) REVERT: A 574 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6435 (p0) REVERT: B 153 MET cc_start: 0.0583 (OUTLIER) cc_final: -0.0396 (ttm) REVERT: B 177 MET cc_start: 0.3545 (mmt) cc_final: 0.2732 (mmp) REVERT: B 318 PHE cc_start: 0.8008 (t80) cc_final: 0.7637 (p90) REVERT: B 353 TRP cc_start: 0.0958 (OUTLIER) cc_final: -0.0281 (m-10) REVERT: B 422 ASN cc_start: 0.0652 (OUTLIER) cc_final: 0.0079 (t0) REVERT: B 442 ASP cc_start: 0.1429 (OUTLIER) cc_final: 0.1068 (p0) REVERT: B 619 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: B 1092 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6233 (pp20) REVERT: D 318 PHE cc_start: 0.8086 (p90) cc_final: 0.7773 (p90) REVERT: D 646 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7437 (mtp-110) REVERT: D 902 MET cc_start: 0.9131 (tpp) cc_final: 0.8886 (tpp) REVERT: D 957 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: D 1081 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8707 (mt) outliers start: 83 outliers final: 53 residues processed: 215 average time/residue: 1.0453 time to fit residues: 272.8813 Evaluate side-chains 201 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 134 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.9980 chunk 304 optimal weight: 0.3980 chunk 186 optimal weight: 0.0770 chunk 144 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 319 optimal weight: 0.1980 chunk 294 optimal weight: 5.9990 chunk 254 optimal weight: 0.0030 chunk 26 optimal weight: 7.9990 chunk 196 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 overall best weight: 0.2748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 580 GLN B 607 GLN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 26355 Z= 0.154 Angle : 0.527 10.021 35885 Z= 0.274 Chirality : 0.045 0.609 4189 Planarity : 0.004 0.054 4603 Dihedral : 5.014 56.576 4406 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 2.31 % Allowed : 19.91 % Favored : 77.79 % 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: -0.17 (0.15), residues: 3187 helix: 2.26 (0.20), residues: 678 sheet: -0.28 (0.18), residues: 735 loop : -1.01 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 64 HIS 0.011 0.001 HIS B1064 PHE 0.016 0.001 PHE D 58 TYR 0.016 0.001 TYR D1067 ARG 0.003 0.000 ARG B 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6374 Ramachandran restraints generated. 3187 Oldfield, 0 Emsley, 3187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 148 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.2421 (OUTLIER) cc_final: 0.2213 (p) REVERT: A 153 MET cc_start: -0.0371 (mmm) cc_final: -0.0803 (tpt) REVERT: A 212 LEU cc_start: 0.3049 (OUTLIER) cc_final: 0.2538 (tp) REVERT: A 393 THR cc_start: 0.5640 (OUTLIER) cc_final: 0.5368 (t) REVERT: A 396 TYR cc_start: 0.7142 (m-80) cc_final: 0.6831 (m-10) REVERT: A 452 LEU cc_start: 0.4775 (OUTLIER) cc_final: 0.4188 (mt) REVERT: A 574 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6445 (p0) REVERT: A 1119 ASN cc_start: 0.8139 (m-40) cc_final: 0.7889 (m110) REVERT: B 153 MET cc_start: 0.0606 (OUTLIER) cc_final: -0.0364 (ttm) REVERT: B 177 MET cc_start: 0.3461 (mmt) cc_final: 0.2790 (mmp) REVERT: B 318 PHE cc_start: 0.7940 (t80) cc_final: 0.7635 (p90) REVERT: B 353 TRP cc_start: 0.1028 (OUTLIER) cc_final: -0.0202 (m-10) REVERT: B 422 ASN cc_start: 0.0395 (OUTLIER) cc_final: -0.0085 (t0) REVERT: B 442 ASP cc_start: 0.1344 (OUTLIER) cc_final: 0.1063 (p0) REVERT: B 542 ASN cc_start: 0.7205 (t0) cc_final: 0.6716 (t0) REVERT: B 1092 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6123 (pp20) REVERT: D 646 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7449 (mtp-110) REVERT: D 902 MET cc_start: 0.9029 (tpp) cc_final: 0.8807 (tpp) outliers start: 65 outliers final: 41 residues processed: 206 average time/residue: 1.0892 time to fit residues: 273.1116 Evaluate side-chains 185 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 133 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 646 ARG Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 708 SER Chi-restraints excluded: chain D residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 607 GLN B 957 GLN B1002 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 540 ASN D1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.237155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173527 restraints weight = 22564.757| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.44 r_work: 0.3363 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 26355 Z= 0.317 Angle : 0.665 12.823 35885 Z= 0.349 Chirality : 0.051 0.565 4189 Planarity : 0.005 0.062 4603 Dihedral : 5.653 53.895 4403 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 2.77 % Allowed : 19.73 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.42 (0.14), residues: 3187 helix: 1.96 (0.20), residues: 669 sheet: -0.35 (0.18), residues: 728 loop : -1.15 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 104 HIS 0.006 0.001 HIS A1048 PHE 0.029 0.002 PHE A 898 TYR 0.023 0.002 TYR A1067 ARG 0.007 0.001 ARG D 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8433.98 seconds wall clock time: 151 minutes 20.08 seconds (9080.08 seconds total)