Starting phenix.real_space_refine on Tue Mar 19 07:45:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r17_14233/03_2024/7r17_14233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r17_14233/03_2024/7r17_14233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r17_14233/03_2024/7r17_14233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r17_14233/03_2024/7r17_14233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r17_14233/03_2024/7r17_14233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r17_14233/03_2024/7r17_14233.pdb" } resolution = 3.7 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= 0.005 sd= 0.070 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 107 5.16 5 C 15092 2.51 5 N 3886 2.21 5 O 4541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23626 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 51, 'TRANS': 942} Chain breaks: 9 Chain: "B" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7821 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 50, 'TRANS': 949} Chain breaks: 9 Chain: "C" Number of atoms: 7707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7707 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 50, 'TRANS': 936} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 12.32, per 1000 atoms: 0.52 Number of scatterers: 23626 At special positions: 0 Unit cell: (146.745, 136.962, 196.747, 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 107 16.00 O 4541 8.00 N 3886 7.00 C 15092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 717 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " Time building additional restraints: 9.39 Conformation dependent library (CDL) restraints added in 4.3 seconds 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5572 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 49 sheets defined 23.9% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.553A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.692A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.912A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.769A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.037A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) 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 removed outlier: 3.619A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.990A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.017A 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 337 through 341 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.801A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.274A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.541A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.063A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.595A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.655A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 947 through 966 removed outlier: 3.940A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.568A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.729A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.987A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.438A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.716A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.787A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.638A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.504A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.547A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.039A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.903A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.595A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.676A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.470A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 145 removed outlier: 7.242A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 4.084A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.716A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.627A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.384A pdb=" N ASN A 450 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 10.622A pdb=" N GLN A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.886A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.647A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.070A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.070A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.783A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.886A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 4.037A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.314A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.539A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.513A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.662A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.662A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.501A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.731A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.779A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.845A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.528A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.584A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.727A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.792A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF1, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.586A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 899 hydrogen bonds defined for protein. 2457 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: 9.56 Time building geometry restraints manager: 10.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7525 1.34 - 1.46: 5521 1.46 - 1.58: 10982 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 24162 Sorted by residual: bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.55e+01 bond pdb=" N ILE B 418 " pdb=" CA ILE B 418 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.07e-02 8.73e+03 1.45e+01 bond pdb=" N ILE B1132 " pdb=" CA ILE B1132 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.71e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.24e-02 6.50e+03 8.14e+00 ... (remaining 24157 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.18: 623 106.18 - 113.14: 13011 113.14 - 120.10: 8147 120.10 - 127.06: 10875 127.06 - 134.01: 206 Bond angle restraints: 32862 Sorted by residual: angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 113.10 109.54 3.56 9.70e-01 1.06e+00 1.35e+01 angle pdb=" CA ASN A 331 " pdb=" C ASN A 331 " pdb=" O ASN A 331 " ideal model delta sigma weight residual 122.64 118.08 4.56 1.25e+00 6.40e-01 1.33e+01 angle pdb=" CA GLN B 613 " pdb=" C GLN B 613 " pdb=" O GLN B 613 " ideal model delta sigma weight residual 120.42 116.55 3.87 1.06e+00 8.90e-01 1.33e+01 angle pdb=" CA GLN B 271 " pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 118.16 121.99 -3.83 1.08e+00 8.57e-01 1.26e+01 angle pdb=" CA ASN B 422 " pdb=" C ASN B 422 " pdb=" N TYR B 423 " ideal model delta sigma weight residual 119.98 116.97 3.01 8.50e-01 1.38e+00 1.25e+01 ... (remaining 32857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13462 17.98 - 35.95: 939 35.95 - 53.93: 197 53.93 - 71.90: 41 71.90 - 89.88: 20 Dihedral angle restraints: 14659 sinusoidal: 6001 harmonic: 8658 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -152.08 66.08 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -148.36 62.36 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -35.51 -50.49 1 1.00e+01 1.00e-02 3.49e+01 ... (remaining 14656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3316 0.071 - 0.141: 445 0.141 - 0.212: 20 0.212 - 0.283: 1 0.283 - 0.353: 1 Chirality restraints: 3783 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.49e+00 chirality pdb=" CA VAL A 327 " pdb=" N VAL A 327 " pdb=" C VAL A 327 " pdb=" CB VAL A 327 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3780 not shown) Planarity restraints: 4247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.301 2.00e-02 2.50e+03 2.53e-01 8.02e+02 pdb=" C7 NAG A1301 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.435 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.90e+00 pdb=" N PRO B 986 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 295 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.028 5.00e-02 4.00e+02 ... (remaining 4244 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3190 2.76 - 3.29: 22467 3.29 - 3.83: 37410 3.83 - 4.36: 41524 4.36 - 4.90: 73076 Nonbonded interactions: 177667 Sorted by model distance: nonbonded pdb=" OG SER B 968 " pdb=" O GLN C 755 " model vdw 2.221 2.440 nonbonded pdb=" OD1 ASN A 969 " pdb=" OG SER A 975 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A 94 " pdb=" O ALA A 264 " model vdw 2.260 2.440 nonbonded pdb=" O ASN A 448 " pdb=" OG SER A 494 " model vdw 2.263 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.274 2.440 ... (remaining 177662 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' and (resid 26 through 65 or resid 81 through 94 or resid 103 through \ 143 or resid 153 through 175 or resid 188 through 209 or resid 215 through 263 o \ r resid 265 through 827 or resid 855 through 1146 or resid 1301 through 1305)) selection = (chain 'B' and (resid 26 through 94 or resid 103 through 119 or resid 132 throug \ h 143 or resid 153 through 175 or resid 188 through 209 or resid 215 through 114 \ 6 or resid 1301 through 1305)) selection = (chain 'C' and (resid 26 through 65 or resid 81 through 119 or resid 132 through \ 263 or resid 265 through 827 or resid 855 through 1146 or resid 1301 through 13 \ 05)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.250 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 63.830 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.004 0.041 24162 Z= 0.237 Angle : 0.527 5.786 32862 Z= 0.302 Chirality : 0.045 0.353 3783 Planarity : 0.005 0.253 4226 Dihedral : 12.980 89.879 8973 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.50 % Allowed : 0.15 % Favored : 99.35 % 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: 0.37 (0.16), residues: 2917 helix: 2.68 (0.21), residues: 606 sheet: 0.49 (0.20), residues: 632 loop : -0.81 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.003 0.001 HIS A1064 PHE 0.025 0.001 PHE B 906 TYR 0.027 0.001 TYR C 873 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8800 (t80) cc_final: 0.8272 (t80) REVERT: A 153 MET cc_start: 0.7721 (mmp) cc_final: 0.7514 (mmm) REVERT: A 198 ASP cc_start: 0.7772 (m-30) cc_final: 0.7432 (m-30) REVERT: A 396 TYR cc_start: 0.8390 (m-10) cc_final: 0.8117 (m-10) REVERT: A 774 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8362 (mm-40) REVERT: B 265 TYR cc_start: 0.8334 (p90) cc_final: 0.8031 (p90) REVERT: B 342 PHE cc_start: 0.7644 (m-80) cc_final: 0.6810 (m-80) REVERT: B 418 ILE cc_start: 0.2775 (OUTLIER) cc_final: 0.2526 (mp) REVERT: B 740 MET cc_start: 0.8671 (tpp) cc_final: 0.8435 (tpt) REVERT: B 759 PHE cc_start: 0.7819 (p90) cc_final: 0.7600 (p90) REVERT: C 237 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7074 (ttm110) REVERT: C 421 TYR cc_start: 0.8486 (m-10) cc_final: 0.8143 (m-10) REVERT: C 979 ASP cc_start: 0.8914 (m-30) cc_final: 0.8575 (m-30) outliers start: 13 outliers final: 2 residues processed: 239 average time/residue: 0.3137 time to fit residues: 122.0670 Evaluate side-chains 155 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.3980 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 0.2980 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 218 GLN A 644 GLN A 655 HIS C 563 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24162 Z= 0.173 Angle : 0.502 9.354 32862 Z= 0.265 Chirality : 0.043 0.299 3783 Planarity : 0.004 0.059 4226 Dihedral : 6.088 56.725 3649 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.69 % Allowed : 6.90 % Favored : 92.41 % 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 (0.16), residues: 2917 helix: 2.81 (0.21), residues: 624 sheet: 0.52 (0.20), residues: 611 loop : -0.81 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 436 HIS 0.003 0.001 HIS B1048 PHE 0.037 0.001 PHE A 275 TYR 0.025 0.001 TYR A 365 ARG 0.004 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8791 (t80) cc_final: 0.8375 (t80) REVERT: A 153 MET cc_start: 0.7597 (mmp) cc_final: 0.7384 (mmm) REVERT: A 224 GLU cc_start: 0.8353 (mp0) cc_final: 0.8024 (mp0) REVERT: A 396 TYR cc_start: 0.8349 (m-10) cc_final: 0.8104 (m-10) REVERT: A 774 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8356 (mm-40) REVERT: B 265 TYR cc_start: 0.8126 (p90) cc_final: 0.7839 (p90) REVERT: B 342 PHE cc_start: 0.7623 (m-80) cc_final: 0.6763 (m-80) REVERT: B 418 ILE cc_start: 0.2464 (OUTLIER) cc_final: 0.2193 (mp) REVERT: B 436 TRP cc_start: 0.8241 (p-90) cc_final: 0.7953 (p-90) REVERT: B 1141 LEU cc_start: 0.9149 (tp) cc_final: 0.8947 (tt) REVERT: C 421 TYR cc_start: 0.8502 (m-10) cc_final: 0.8123 (m-10) REVERT: C 979 ASP cc_start: 0.8791 (m-30) cc_final: 0.8567 (m-30) outliers start: 18 outliers final: 9 residues processed: 186 average time/residue: 0.3043 time to fit residues: 95.4185 Evaluate side-chains 166 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 224 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 240 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 655 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24162 Z= 0.183 Angle : 0.471 7.157 32862 Z= 0.248 Chirality : 0.042 0.276 3783 Planarity : 0.004 0.061 4226 Dihedral : 5.572 55.709 3647 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.00 % Allowed : 9.13 % Favored : 89.88 % 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: 0.43 (0.16), residues: 2917 helix: 2.78 (0.21), residues: 625 sheet: 0.51 (0.20), residues: 609 loop : -0.80 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 PHE 0.036 0.001 PHE A 275 TYR 0.023 0.001 TYR C 904 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8780 (t80) cc_final: 0.8356 (t80) REVERT: A 224 GLU cc_start: 0.8360 (mp0) cc_final: 0.8034 (mp0) REVERT: A 374 PHE cc_start: 0.8432 (m-80) cc_final: 0.7841 (m-80) REVERT: A 396 TYR cc_start: 0.8286 (m-10) cc_final: 0.8044 (m-10) REVERT: A 774 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8415 (mm-40) REVERT: B 265 TYR cc_start: 0.8116 (p90) cc_final: 0.7735 (p90) REVERT: B 342 PHE cc_start: 0.7848 (m-80) cc_final: 0.7034 (m-80) REVERT: B 396 TYR cc_start: 0.8179 (m-80) cc_final: 0.7594 (m-80) REVERT: B 418 ILE cc_start: 0.2563 (OUTLIER) cc_final: 0.2343 (mp) REVERT: B 436 TRP cc_start: 0.8240 (p-90) cc_final: 0.7961 (p-90) REVERT: B 1141 LEU cc_start: 0.9152 (tp) cc_final: 0.8942 (tt) REVERT: C 421 TYR cc_start: 0.8476 (m-10) cc_final: 0.8126 (m-10) REVERT: C 979 ASP cc_start: 0.8784 (m-30) cc_final: 0.8523 (m-30) outliers start: 26 outliers final: 19 residues processed: 185 average time/residue: 0.2858 time to fit residues: 89.6987 Evaluate side-chains 170 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.5980 chunk 203 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 181 optimal weight: 0.0470 chunk 271 optimal weight: 0.6980 chunk 287 optimal weight: 2.9990 chunk 141 optimal weight: 30.0000 chunk 256 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN B 81 ASN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24162 Z= 0.142 Angle : 0.454 9.023 32862 Z= 0.234 Chirality : 0.041 0.256 3783 Planarity : 0.004 0.060 4226 Dihedral : 5.037 52.746 3647 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.23 % Allowed : 10.43 % Favored : 88.34 % 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: 0.53 (0.16), residues: 2917 helix: 2.97 (0.21), residues: 614 sheet: 0.58 (0.20), residues: 603 loop : -0.76 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.003 0.001 HIS A 655 PHE 0.016 0.001 PHE B 201 TYR 0.017 0.001 TYR C1067 ARG 0.002 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8796 (t80) cc_final: 0.8305 (t80) REVERT: A 153 MET cc_start: 0.7701 (mmm) cc_final: 0.7348 (mmm) REVERT: A 224 GLU cc_start: 0.8221 (mp0) cc_final: 0.7912 (mp0) REVERT: A 774 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8381 (mm-40) REVERT: B 265 TYR cc_start: 0.8065 (p90) cc_final: 0.7637 (p90) REVERT: B 342 PHE cc_start: 0.7859 (m-80) cc_final: 0.7065 (m-80) REVERT: B 396 TYR cc_start: 0.8242 (m-80) cc_final: 0.7578 (m-80) REVERT: B 418 ILE cc_start: 0.2549 (OUTLIER) cc_final: 0.2257 (mp) REVERT: B 436 TRP cc_start: 0.8259 (p-90) cc_final: 0.7973 (p-90) REVERT: B 1141 LEU cc_start: 0.9164 (tp) cc_final: 0.8953 (tt) REVERT: C 238 PHE cc_start: 0.8455 (p90) cc_final: 0.8217 (p90) REVERT: C 421 TYR cc_start: 0.8458 (m-10) cc_final: 0.8024 (m-10) REVERT: C 896 ILE cc_start: 0.9585 (tp) cc_final: 0.9344 (tt) REVERT: C 954 GLN cc_start: 0.8036 (tt0) cc_final: 0.7540 (tt0) REVERT: C 979 ASP cc_start: 0.8776 (m-30) cc_final: 0.8506 (m-30) outliers start: 32 outliers final: 17 residues processed: 208 average time/residue: 0.2944 time to fit residues: 103.7988 Evaluate side-chains 180 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 257 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C1054 GLN C1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24162 Z= 0.293 Angle : 0.519 7.626 32862 Z= 0.272 Chirality : 0.043 0.266 3783 Planarity : 0.004 0.060 4226 Dihedral : 4.991 52.624 3647 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.50 % Allowed : 12.31 % Favored : 86.20 % 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: 0.29 (0.16), residues: 2917 helix: 2.55 (0.21), residues: 628 sheet: 0.37 (0.20), residues: 605 loop : -0.83 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.007 0.001 HIS A1064 PHE 0.022 0.002 PHE B 823 TYR 0.024 0.001 TYR C1067 ARG 0.003 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8786 (t80) cc_final: 0.8306 (t80) REVERT: A 153 MET cc_start: 0.7973 (mmm) cc_final: 0.7632 (mmm) REVERT: A 224 GLU cc_start: 0.8412 (mp0) cc_final: 0.8084 (mp0) REVERT: A 661 GLU cc_start: 0.6922 (pp20) cc_final: 0.6561 (pp20) REVERT: B 200 TYR cc_start: 0.8043 (m-80) cc_final: 0.7787 (m-80) REVERT: B 265 TYR cc_start: 0.8143 (p90) cc_final: 0.7664 (p90) REVERT: B 342 PHE cc_start: 0.7972 (m-80) cc_final: 0.7087 (m-80) REVERT: B 396 TYR cc_start: 0.8226 (m-80) cc_final: 0.7538 (m-80) REVERT: B 418 ILE cc_start: 0.2683 (OUTLIER) cc_final: 0.2390 (mp) REVERT: B 436 TRP cc_start: 0.8326 (p-90) cc_final: 0.8023 (p-90) REVERT: B 723 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 748 GLU cc_start: 0.8425 (pm20) cc_final: 0.8033 (pm20) REVERT: C 238 PHE cc_start: 0.8505 (p90) cc_final: 0.8267 (p90) REVERT: C 417 ASN cc_start: 0.8955 (m-40) cc_final: 0.8722 (p0) REVERT: C 421 TYR cc_start: 0.8347 (m-10) cc_final: 0.8044 (m-10) REVERT: C 778 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8668 (t) REVERT: C 979 ASP cc_start: 0.8812 (m-30) cc_final: 0.8537 (m-30) outliers start: 39 outliers final: 25 residues processed: 193 average time/residue: 0.2978 time to fit residues: 97.7409 Evaluate side-chains 177 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 1.9990 chunk 258 optimal weight: 0.0370 chunk 56 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 70 optimal weight: 0.0170 chunk 287 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 133 optimal weight: 0.0060 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24162 Z= 0.120 Angle : 0.458 9.251 32862 Z= 0.235 Chirality : 0.041 0.242 3783 Planarity : 0.004 0.057 4226 Dihedral : 4.432 52.642 3647 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.96 % Allowed : 13.61 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.54 (0.16), residues: 2917 helix: 2.88 (0.21), residues: 620 sheet: 0.53 (0.20), residues: 617 loop : -0.70 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.005 0.001 HIS A 519 PHE 0.023 0.001 PHE B 823 TYR 0.016 0.001 TYR B1067 ARG 0.002 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8792 (t80) cc_final: 0.8320 (t80) REVERT: A 153 MET cc_start: 0.7950 (mmm) cc_final: 0.7583 (mmm) REVERT: A 224 GLU cc_start: 0.8239 (mp0) cc_final: 0.7933 (mp0) REVERT: A 661 GLU cc_start: 0.6845 (pp20) cc_final: 0.6519 (pp20) REVERT: B 200 TYR cc_start: 0.7904 (m-80) cc_final: 0.7665 (m-80) REVERT: B 265 TYR cc_start: 0.8042 (p90) cc_final: 0.7620 (p90) REVERT: B 342 PHE cc_start: 0.7982 (m-80) cc_final: 0.7086 (m-80) REVERT: B 396 TYR cc_start: 0.8222 (m-80) cc_final: 0.7543 (m-80) REVERT: B 418 ILE cc_start: 0.2610 (OUTLIER) cc_final: 0.2332 (mp) REVERT: B 436 TRP cc_start: 0.8322 (p-90) cc_final: 0.7999 (p-90) REVERT: B 748 GLU cc_start: 0.8331 (pm20) cc_final: 0.8038 (pm20) REVERT: C 238 PHE cc_start: 0.8454 (p90) cc_final: 0.8208 (p90) REVERT: C 417 ASN cc_start: 0.8919 (m-40) cc_final: 0.8707 (p0) REVERT: C 421 TYR cc_start: 0.8290 (m-10) cc_final: 0.8011 (m-10) REVERT: C 896 ILE cc_start: 0.9578 (tp) cc_final: 0.9358 (tt) REVERT: C 979 ASP cc_start: 0.8758 (m-30) cc_final: 0.8507 (m-30) outliers start: 25 outliers final: 21 residues processed: 193 average time/residue: 0.2846 time to fit residues: 94.1348 Evaluate side-chains 188 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 162 optimal weight: 0.0770 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24162 Z= 0.167 Angle : 0.458 9.228 32862 Z= 0.236 Chirality : 0.042 0.245 3783 Planarity : 0.004 0.057 4226 Dihedral : 4.296 52.597 3647 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.27 % Allowed : 13.92 % Favored : 84.82 % 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: 0.52 (0.16), residues: 2917 helix: 2.85 (0.21), residues: 620 sheet: 0.57 (0.20), residues: 602 loop : -0.72 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.023 0.001 PHE B 823 TYR 0.021 0.001 TYR A 396 ARG 0.002 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8794 (t80) cc_final: 0.8311 (t80) REVERT: A 153 MET cc_start: 0.7976 (mmm) cc_final: 0.7597 (mmm) REVERT: A 224 GLU cc_start: 0.8250 (mp0) cc_final: 0.7950 (mp0) REVERT: A 661 GLU cc_start: 0.6902 (pp20) cc_final: 0.6506 (pp20) REVERT: B 200 TYR cc_start: 0.7949 (m-80) cc_final: 0.7722 (m-80) REVERT: B 265 TYR cc_start: 0.8070 (p90) cc_final: 0.7614 (p90) REVERT: B 342 PHE cc_start: 0.7988 (m-80) cc_final: 0.7173 (m-80) REVERT: B 396 TYR cc_start: 0.8249 (m-80) cc_final: 0.7554 (m-80) REVERT: B 418 ILE cc_start: 0.2667 (OUTLIER) cc_final: 0.2385 (mp) REVERT: B 436 TRP cc_start: 0.8340 (p-90) cc_final: 0.8002 (p-90) REVERT: B 748 GLU cc_start: 0.8342 (pm20) cc_final: 0.8128 (pm20) REVERT: C 84 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8161 (mm) REVERT: C 417 ASN cc_start: 0.8956 (m-40) cc_final: 0.8731 (p0) REVERT: C 421 TYR cc_start: 0.8315 (m-10) cc_final: 0.8054 (m-10) REVERT: C 767 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8334 (mm) REVERT: C 896 ILE cc_start: 0.9594 (tp) cc_final: 0.9372 (tt) REVERT: C 979 ASP cc_start: 0.8777 (m-30) cc_final: 0.8511 (m-30) outliers start: 33 outliers final: 26 residues processed: 189 average time/residue: 0.2983 time to fit residues: 96.6540 Evaluate side-chains 184 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 195 optimal weight: 0.0570 chunk 141 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24162 Z= 0.174 Angle : 0.462 9.263 32862 Z= 0.240 Chirality : 0.042 0.242 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.233 52.613 3647 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.42 % Allowed : 14.00 % Favored : 84.59 % 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: 0.52 (0.16), residues: 2917 helix: 2.84 (0.21), residues: 620 sheet: 0.55 (0.20), residues: 605 loop : -0.72 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.019 0.001 PHE A 55 TYR 0.019 0.001 TYR A 396 ARG 0.003 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8795 (t80) cc_final: 0.8322 (t80) REVERT: A 153 MET cc_start: 0.8006 (mmm) cc_final: 0.7508 (mmm) REVERT: A 198 ASP cc_start: 0.7647 (p0) cc_final: 0.7427 (p0) REVERT: A 224 GLU cc_start: 0.8305 (mp0) cc_final: 0.7994 (mp0) REVERT: A 661 GLU cc_start: 0.6880 (pp20) cc_final: 0.6448 (pp20) REVERT: B 200 TYR cc_start: 0.7949 (m-80) cc_final: 0.7731 (m-10) REVERT: B 265 TYR cc_start: 0.8069 (p90) cc_final: 0.7588 (p90) REVERT: B 342 PHE cc_start: 0.7967 (m-80) cc_final: 0.7181 (m-80) REVERT: B 396 TYR cc_start: 0.8264 (m-80) cc_final: 0.7552 (m-80) REVERT: B 418 ILE cc_start: 0.2844 (OUTLIER) cc_final: 0.2561 (mp) REVERT: B 436 TRP cc_start: 0.8355 (p-90) cc_final: 0.8040 (p-90) REVERT: B 748 GLU cc_start: 0.8323 (pm20) cc_final: 0.8085 (pm20) REVERT: C 84 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8172 (mm) REVERT: C 417 ASN cc_start: 0.8939 (m-40) cc_final: 0.8737 (p0) REVERT: C 421 TYR cc_start: 0.8228 (m-10) cc_final: 0.7950 (m-10) REVERT: C 767 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8364 (mm) REVERT: C 896 ILE cc_start: 0.9604 (tp) cc_final: 0.9387 (tt) REVERT: C 979 ASP cc_start: 0.8788 (m-30) cc_final: 0.8527 (m-30) outliers start: 37 outliers final: 30 residues processed: 190 average time/residue: 0.2972 time to fit residues: 97.0105 Evaluate side-chains 190 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 250 optimal weight: 0.2980 chunk 266 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 116 optimal weight: 0.0050 chunk 209 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24162 Z= 0.127 Angle : 0.453 10.158 32862 Z= 0.231 Chirality : 0.041 0.232 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.019 52.543 3647 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.04 % Allowed : 14.65 % Favored : 84.32 % 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: 0.62 (0.16), residues: 2917 helix: 2.94 (0.21), residues: 620 sheet: 0.66 (0.21), residues: 603 loop : -0.68 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS B1048 PHE 0.019 0.001 PHE C 92 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8815 (t80) cc_final: 0.8341 (t80) REVERT: A 153 MET cc_start: 0.7946 (mmm) cc_final: 0.7679 (mmm) REVERT: A 198 ASP cc_start: 0.7606 (p0) cc_final: 0.7396 (p0) REVERT: A 224 GLU cc_start: 0.8286 (mp0) cc_final: 0.7819 (mp0) REVERT: A 661 GLU cc_start: 0.6876 (pp20) cc_final: 0.6466 (pp20) REVERT: B 200 TYR cc_start: 0.7888 (m-80) cc_final: 0.7657 (m-80) REVERT: B 265 TYR cc_start: 0.8019 (p90) cc_final: 0.7496 (p90) REVERT: B 342 PHE cc_start: 0.8024 (m-80) cc_final: 0.7262 (m-80) REVERT: B 396 TYR cc_start: 0.8360 (m-80) cc_final: 0.7689 (m-80) REVERT: B 418 ILE cc_start: 0.2830 (OUTLIER) cc_final: 0.2548 (mp) REVERT: B 436 TRP cc_start: 0.8365 (p-90) cc_final: 0.8079 (p-90) REVERT: C 417 ASN cc_start: 0.8937 (m-40) cc_final: 0.8709 (p0) REVERT: C 421 TYR cc_start: 0.8168 (m-10) cc_final: 0.7901 (m-10) REVERT: C 767 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8240 (mm) REVERT: C 896 ILE cc_start: 0.9575 (tp) cc_final: 0.9351 (tt) REVERT: C 979 ASP cc_start: 0.8770 (m-30) cc_final: 0.8508 (m-30) outliers start: 27 outliers final: 23 residues processed: 193 average time/residue: 0.2852 time to fit residues: 94.6236 Evaluate side-chains 187 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 196 optimal weight: 0.6980 chunk 295 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24162 Z= 0.176 Angle : 0.466 9.900 32862 Z= 0.239 Chirality : 0.042 0.238 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.079 52.557 3647 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.27 % Allowed : 14.42 % Favored : 84.32 % 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: 0.58 (0.16), residues: 2917 helix: 2.91 (0.21), residues: 620 sheet: 0.58 (0.20), residues: 607 loop : -0.68 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.003 0.001 HIS A1064 PHE 0.021 0.001 PHE A 55 TYR 0.018 0.001 TYR C1067 ARG 0.003 0.000 ARG A 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8823 (t80) cc_final: 0.8354 (t80) REVERT: A 153 MET cc_start: 0.7895 (mmm) cc_final: 0.7627 (mmm) REVERT: A 224 GLU cc_start: 0.8308 (mp0) cc_final: 0.7847 (mp0) REVERT: A 661 GLU cc_start: 0.6885 (pp20) cc_final: 0.6453 (pp20) REVERT: B 200 TYR cc_start: 0.7916 (m-80) cc_final: 0.7701 (m-80) REVERT: B 265 TYR cc_start: 0.8054 (p90) cc_final: 0.7541 (p90) REVERT: B 342 PHE cc_start: 0.7986 (m-80) cc_final: 0.7227 (m-80) REVERT: B 396 TYR cc_start: 0.8391 (m-80) cc_final: 0.7714 (m-80) REVERT: B 418 ILE cc_start: 0.2905 (OUTLIER) cc_final: 0.2616 (mp) REVERT: B 436 TRP cc_start: 0.8368 (p-90) cc_final: 0.8115 (p-90) REVERT: C 84 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8029 (mm) REVERT: C 417 ASN cc_start: 0.8927 (m-40) cc_final: 0.8717 (p0) REVERT: C 421 TYR cc_start: 0.8190 (m-10) cc_final: 0.7915 (m-10) REVERT: C 767 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8313 (mm) REVERT: C 896 ILE cc_start: 0.9594 (tp) cc_final: 0.9373 (tt) REVERT: C 979 ASP cc_start: 0.8789 (m-30) cc_final: 0.8526 (m-30) outliers start: 33 outliers final: 28 residues processed: 184 average time/residue: 0.2874 time to fit residues: 90.5692 Evaluate side-chains 183 residues out of total 2608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 242 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.117644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082294 restraints weight = 62763.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081761 restraints weight = 36298.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082602 restraints weight = 25148.200| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24162 Z= 0.135 Angle : 0.457 10.313 32862 Z= 0.233 Chirality : 0.042 0.232 3783 Planarity : 0.004 0.056 4226 Dihedral : 3.998 52.638 3647 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.11 % Allowed : 14.88 % Favored : 84.01 % 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: 0.63 (0.16), residues: 2917 helix: 2.98 (0.21), residues: 614 sheet: 0.63 (0.20), residues: 610 loop : -0.66 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.002 0.000 HIS A1064 PHE 0.016 0.001 PHE A 55 TYR 0.017 0.001 TYR A 495 ARG 0.003 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.51 seconds wall clock time: 71 minutes 50.19 seconds (4310.19 seconds total)