Starting phenix.real_space_refine on Fri Jun 20 15:50:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r17_14233/06_2025/7r17_14233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r17_14233/06_2025/7r17_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/cci-nas-00/data/ceres_data/7r17_14233/06_2025/7r17_14233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r17_14233/06_2025/7r17_14233.map" model { file = "/net/cci-nas-00/data/ceres_data/7r17_14233/06_2025/7r17_14233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r17_14233/06_2025/7r17_14233.cif" } 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. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.09, per 1000 atoms: 0.68 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 6.12 Conformation dependent library (CDL) restraints added in 3.2 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: 3.28 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: 11.41 Time building geometry restraints manager: 7.31 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: 0.00 - 1.16: 31526 1.16 - 2.31: 988 2.31 - 3.47: 300 3.47 - 4.63: 38 4.63 - 5.79: 10 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 3.040 nonbonded pdb=" OD1 ASN A 969 " pdb=" OG SER A 975 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 94 " pdb=" O ALA A 264 " model vdw 2.260 3.040 nonbonded pdb=" O ASN A 448 " pdb=" OG SER A 494 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.274 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 7.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 60.710 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.270 ------------------------------------------------------------------------------- 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 24222 Z= 0.202 Angle : 0.537 8.187 33004 Z= 0.304 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 21) link_NAG-ASN : angle 2.31363 ( 63) link_BETA1-4 : bond 0.00020 ( 1) link_BETA1-4 : angle 1.23213 ( 3) hydrogen bonds : bond 0.23125 ( 874) hydrogen bonds : angle 8.09062 ( 2457) SS BOND : bond 0.00176 ( 38) SS BOND : angle 0.89211 ( 76) covalent geometry : bond 0.00362 (24162) covalent geometry : angle 0.52673 (32862) *********************** 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 to be fit. rotamer outliers: 13 poor density : 231 time to evaluate : 3.098 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: 0.3408 time to fit residues: 133.9364 Evaluate side-chains 155 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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: 0.2980 chunk 225 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 0.0570 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS C 563 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.117665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079057 restraints weight = 62377.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.082328 restraints weight = 31227.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083119 restraints weight = 16475.654| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24222 Z= 0.106 Angle : 0.514 9.818 33004 Z= 0.268 Chirality : 0.043 0.300 3783 Planarity : 0.004 0.058 4226 Dihedral : 5.878 58.091 3649 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.65 % Allowed : 6.52 % Favored : 92.83 % 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: 2.87 (0.21), residues: 618 sheet: 0.62 (0.20), residues: 634 loop : -0.77 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 436 HIS 0.002 0.000 HIS A 655 PHE 0.040 0.001 PHE A 275 TYR 0.030 0.001 TYR A 365 ARG 0.009 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 21) link_NAG-ASN : angle 1.83837 ( 63) link_BETA1-4 : bond 0.00156 ( 1) link_BETA1-4 : angle 1.07143 ( 3) hydrogen bonds : bond 0.04694 ( 874) hydrogen bonds : angle 5.78302 ( 2457) SS BOND : bond 0.00211 ( 38) SS BOND : angle 0.74738 ( 76) covalent geometry : bond 0.00222 (24162) covalent geometry : angle 0.50716 (32862) *********************** 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 205 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7785 (t70) cc_final: 0.7554 (t70) REVERT: A 144 TYR cc_start: 0.8932 (t80) cc_final: 0.8460 (t80) REVERT: A 153 MET cc_start: 0.7726 (mmp) cc_final: 0.7511 (mmm) REVERT: A 224 GLU cc_start: 0.8443 (mp0) cc_final: 0.8016 (mp0) REVERT: A 774 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8483 (mm-40) REVERT: B 265 TYR cc_start: 0.8043 (p90) cc_final: 0.7669 (p90) REVERT: B 342 PHE cc_start: 0.7645 (m-80) cc_final: 0.6828 (m-80) REVERT: B 368 LEU cc_start: 0.7733 (tt) cc_final: 0.7501 (mm) REVERT: B 418 ILE cc_start: 0.2376 (OUTLIER) cc_final: 0.2117 (mp) REVERT: B 436 TRP cc_start: 0.8249 (p-90) cc_final: 0.7929 (p-90) REVERT: B 1141 LEU cc_start: 0.9168 (tp) cc_final: 0.8963 (tt) REVERT: C 118 LEU cc_start: 0.9174 (tp) cc_final: 0.8824 (mm) REVERT: C 237 ARG cc_start: 0.7241 (ttm110) cc_final: 0.7021 (ttm110) REVERT: C 421 TYR cc_start: 0.8499 (m-10) cc_final: 0.8111 (m-10) REVERT: C 461 LEU cc_start: 0.7709 (mt) cc_final: 0.7417 (mt) REVERT: C 586 ASP cc_start: 0.7965 (t70) cc_final: 0.7645 (t0) REVERT: C 979 ASP cc_start: 0.8809 (m-30) cc_final: 0.8563 (m-30) outliers start: 17 outliers final: 8 residues processed: 198 average time/residue: 0.3063 time to fit residues: 100.5236 Evaluate side-chains 172 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 LEU Chi-restraints excluded: chain C residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 295 optimal weight: 0.9980 chunk 270 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 198 optimal weight: 0.3980 chunk 239 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.116298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.077382 restraints weight = 62935.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080794 restraints weight = 31750.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081439 restraints weight = 16786.355| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24222 Z= 0.134 Angle : 0.489 7.988 33004 Z= 0.256 Chirality : 0.042 0.271 3783 Planarity : 0.004 0.060 4226 Dihedral : 5.379 55.863 3647 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.04 % Allowed : 9.16 % Favored : 89.80 % 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: 0.45 (0.16), residues: 2917 helix: 2.71 (0.21), residues: 625 sheet: 0.53 (0.20), residues: 609 loop : -0.75 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.004 0.001 HIS B1048 PHE 0.035 0.001 PHE A 275 TYR 0.023 0.001 TYR C 904 ARG 0.003 0.000 ARG B1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 21) link_NAG-ASN : angle 1.70800 ( 63) link_BETA1-4 : bond 0.00158 ( 1) link_BETA1-4 : angle 0.99630 ( 3) hydrogen bonds : bond 0.04673 ( 874) hydrogen bonds : angle 5.32817 ( 2457) SS BOND : bond 0.00196 ( 38) SS BOND : angle 0.80681 ( 76) covalent geometry : bond 0.00308 (24162) covalent geometry : angle 0.48297 (32862) *********************** 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 197 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7713 (t70) cc_final: 0.7451 (t70) REVERT: A 144 TYR cc_start: 0.8940 (t80) cc_final: 0.8527 (t80) REVERT: A 224 GLU cc_start: 0.8399 (mp0) cc_final: 0.8047 (mp0) REVERT: A 374 PHE cc_start: 0.8451 (m-80) cc_final: 0.7812 (m-80) REVERT: A 380 TYR cc_start: 0.8823 (m-10) cc_final: 0.8616 (m-10) REVERT: A 774 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8533 (mm-40) REVERT: B 265 TYR cc_start: 0.8074 (p90) cc_final: 0.7646 (p90) REVERT: B 342 PHE cc_start: 0.7855 (m-80) cc_final: 0.7130 (m-80) REVERT: B 418 ILE cc_start: 0.2515 (OUTLIER) cc_final: 0.2310 (mp) REVERT: B 436 TRP cc_start: 0.8314 (p-90) cc_final: 0.7994 (p-90) REVERT: B 1141 LEU cc_start: 0.9149 (tp) cc_final: 0.8944 (tt) REVERT: C 118 LEU cc_start: 0.9208 (tp) cc_final: 0.8873 (mm) REVERT: C 237 ARG cc_start: 0.7231 (ttm110) cc_final: 0.7002 (ttm110) REVERT: C 421 TYR cc_start: 0.8517 (m-10) cc_final: 0.8156 (m-10) REVERT: C 979 ASP cc_start: 0.8833 (m-30) cc_final: 0.8557 (m-30) outliers start: 27 outliers final: 17 residues processed: 188 average time/residue: 0.3157 time to fit residues: 100.0314 Evaluate side-chains 177 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR 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 B residue 1006 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 430 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 256 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 100 optimal weight: 0.0570 chunk 255 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN C 207 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.116670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.077498 restraints weight = 63695.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080867 restraints weight = 33070.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081396 restraints weight = 18183.892| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24222 Z= 0.113 Angle : 0.475 10.234 33004 Z= 0.245 Chirality : 0.042 0.256 3783 Planarity : 0.004 0.059 4226 Dihedral : 4.938 52.995 3646 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.04 % Allowed : 10.77 % Favored : 88.19 % 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: 0.50 (0.16), residues: 2917 helix: 2.78 (0.21), residues: 621 sheet: 0.55 (0.20), residues: 609 loop : -0.72 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.004 0.001 HIS C 519 PHE 0.018 0.001 PHE C 238 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 21) link_NAG-ASN : angle 1.61845 ( 63) link_BETA1-4 : bond 0.00475 ( 1) link_BETA1-4 : angle 1.06959 ( 3) hydrogen bonds : bond 0.04256 ( 874) hydrogen bonds : angle 5.07578 ( 2457) SS BOND : bond 0.00231 ( 38) SS BOND : angle 0.76980 ( 76) covalent geometry : bond 0.00254 (24162) covalent geometry : angle 0.46898 (32862) *********************** 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 196 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8995 (t80) cc_final: 0.8570 (t80) REVERT: A 153 MET cc_start: 0.7856 (mmm) cc_final: 0.7473 (mmm) REVERT: A 374 PHE cc_start: 0.8520 (m-80) cc_final: 0.8079 (m-80) REVERT: A 380 TYR cc_start: 0.8870 (m-10) cc_final: 0.8595 (m-10) REVERT: A 774 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8531 (mm-40) REVERT: B 265 TYR cc_start: 0.7995 (p90) cc_final: 0.7573 (p90) REVERT: B 342 PHE cc_start: 0.7918 (m-80) cc_final: 0.7189 (m-80) REVERT: B 418 ILE cc_start: 0.2416 (OUTLIER) cc_final: 0.2173 (mp) REVERT: B 436 TRP cc_start: 0.8332 (p-90) cc_final: 0.8011 (p-90) REVERT: B 983 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8095 (ttp-110) REVERT: B 1141 LEU cc_start: 0.9186 (tp) cc_final: 0.8980 (tt) REVERT: C 421 TYR cc_start: 0.8509 (m-10) cc_final: 0.8128 (m-10) REVERT: C 979 ASP cc_start: 0.8860 (m-30) cc_final: 0.8586 (m-30) REVERT: C 1029 MET cc_start: 0.8244 (ttm) cc_final: 0.8009 (ttt) outliers start: 27 outliers final: 16 residues processed: 189 average time/residue: 0.3148 time to fit residues: 99.5236 Evaluate side-chains 173 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR 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 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 120 VAL 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 524 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 10 optimal weight: 5.9990 chunk 222 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3818 r_free = 0.3818 target = 0.116971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.078256 restraints weight = 63384.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081401 restraints weight = 33509.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081968 restraints weight = 19048.085| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24222 Z= 0.120 Angle : 0.479 8.812 33004 Z= 0.248 Chirality : 0.042 0.249 3783 Planarity : 0.004 0.059 4226 Dihedral : 4.662 53.031 3646 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.46 % Allowed : 11.66 % Favored : 86.89 % 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: 0.50 (0.16), residues: 2917 helix: 2.74 (0.21), residues: 621 sheet: 0.62 (0.20), residues: 597 loop : -0.72 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.023 0.001 PHE B 823 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 21) link_NAG-ASN : angle 1.60129 ( 63) link_BETA1-4 : bond 0.00321 ( 1) link_BETA1-4 : angle 1.11171 ( 3) hydrogen bonds : bond 0.04246 ( 874) hydrogen bonds : angle 4.96797 ( 2457) SS BOND : bond 0.00211 ( 38) SS BOND : angle 1.26648 ( 76) covalent geometry : bond 0.00274 (24162) covalent geometry : angle 0.47089 (32862) *********************** 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 205 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8902 (t80) cc_final: 0.8411 (t80) REVERT: A 153 MET cc_start: 0.7998 (mmm) cc_final: 0.7631 (mmm) REVERT: A 374 PHE cc_start: 0.8343 (m-80) cc_final: 0.8056 (m-80) REVERT: A 380 TYR cc_start: 0.8847 (m-10) cc_final: 0.8620 (m-10) REVERT: A 661 GLU cc_start: 0.6860 (pp20) cc_final: 0.6560 (pp20) REVERT: B 200 TYR cc_start: 0.7961 (m-80) cc_final: 0.7686 (m-80) REVERT: B 265 TYR cc_start: 0.8053 (p90) cc_final: 0.7585 (p90) REVERT: B 342 PHE cc_start: 0.7968 (m-80) cc_final: 0.7145 (m-80) REVERT: B 418 ILE cc_start: 0.2525 (OUTLIER) cc_final: 0.2265 (mp) REVERT: B 436 TRP cc_start: 0.8339 (p-90) cc_final: 0.7986 (p-90) REVERT: B 983 ARG cc_start: 0.8720 (ttp-110) cc_final: 0.8094 (ttp-110) REVERT: C 105 ILE cc_start: 0.7959 (mp) cc_final: 0.7716 (mp) REVERT: C 118 LEU cc_start: 0.9158 (tp) cc_final: 0.8848 (mm) REVERT: C 238 PHE cc_start: 0.8280 (p90) cc_final: 0.8019 (p90) REVERT: C 421 TYR cc_start: 0.8541 (m-10) cc_final: 0.8187 (m-10) REVERT: C 979 ASP cc_start: 0.8802 (m-30) cc_final: 0.8531 (m-30) REVERT: C 1029 MET cc_start: 0.8179 (ttm) cc_final: 0.7918 (ttt) outliers start: 38 outliers final: 21 residues processed: 194 average time/residue: 0.2952 time to fit residues: 97.2528 Evaluate side-chains 180 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 433 VAL 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 240 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL 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 524 VAL Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 139 optimal weight: 20.0000 chunk 262 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 4 optimal weight: 0.0370 chunk 184 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 237 optimal weight: 0.0870 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN C 321 GLN C1071 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.116916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.081156 restraints weight = 62535.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080512 restraints weight = 37268.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.081516 restraints weight = 25280.606| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24222 Z= 0.120 Angle : 0.477 9.022 33004 Z= 0.246 Chirality : 0.042 0.246 3783 Planarity : 0.004 0.057 4226 Dihedral : 4.476 53.151 3646 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.23 % Allowed : 12.85 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2917 helix: 2.74 (0.21), residues: 621 sheet: 0.58 (0.20), residues: 610 loop : -0.68 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.023 0.001 PHE B 823 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 21) link_NAG-ASN : angle 1.59895 ( 63) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 1.11587 ( 3) hydrogen bonds : bond 0.04194 ( 874) hydrogen bonds : angle 4.90048 ( 2457) SS BOND : bond 0.00195 ( 38) SS BOND : angle 1.18212 ( 76) covalent geometry : bond 0.00278 (24162) covalent geometry : angle 0.46935 (32862) *********************** 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 197 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8873 (t80) cc_final: 0.8405 (t80) REVERT: A 153 MET cc_start: 0.7943 (mmm) cc_final: 0.7558 (mmm) REVERT: A 374 PHE cc_start: 0.8236 (m-80) cc_final: 0.8035 (m-80) REVERT: A 380 TYR cc_start: 0.8890 (m-10) cc_final: 0.8674 (m-10) REVERT: A 508 TYR cc_start: 0.7623 (m-10) cc_final: 0.7351 (m-10) REVERT: A 661 GLU cc_start: 0.6973 (pp20) cc_final: 0.6586 (pp20) REVERT: B 200 TYR cc_start: 0.7975 (m-80) cc_final: 0.7715 (m-80) REVERT: B 265 TYR cc_start: 0.8043 (p90) cc_final: 0.7555 (p90) REVERT: B 342 PHE cc_start: 0.7990 (m-80) cc_final: 0.7130 (m-80) REVERT: B 418 ILE cc_start: 0.2539 (OUTLIER) cc_final: 0.2267 (mp) REVERT: B 436 TRP cc_start: 0.8310 (p-90) cc_final: 0.7973 (p-90) REVERT: B 983 ARG cc_start: 0.8732 (ttp-110) cc_final: 0.8496 (ttp-110) REVERT: C 118 LEU cc_start: 0.9219 (tp) cc_final: 0.8972 (mm) REVERT: C 421 TYR cc_start: 0.8556 (m-10) cc_final: 0.8218 (m-10) REVERT: C 979 ASP cc_start: 0.8817 (m-30) cc_final: 0.8537 (m-30) REVERT: C 1029 MET cc_start: 0.8183 (ttm) cc_final: 0.7908 (ttt) outliers start: 32 outliers final: 23 residues processed: 186 average time/residue: 0.2897 time to fit residues: 91.9503 Evaluate side-chains 175 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 62 VAL 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 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 171 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 195 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 125 optimal weight: 0.0970 chunk 279 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.117057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078313 restraints weight = 63005.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081678 restraints weight = 34315.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081831 restraints weight = 20296.138| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24222 Z= 0.113 Angle : 0.477 9.690 33004 Z= 0.245 Chirality : 0.042 0.241 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.335 53.107 3646 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.30 % Allowed : 13.27 % 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: 2.75 (0.21), residues: 620 sheet: 0.59 (0.20), residues: 620 loop : -0.68 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.036 0.001 PHE C 238 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 21) link_NAG-ASN : angle 1.56575 ( 63) link_BETA1-4 : bond 0.00285 ( 1) link_BETA1-4 : angle 1.18618 ( 3) hydrogen bonds : bond 0.04095 ( 874) hydrogen bonds : angle 4.83446 ( 2457) SS BOND : bond 0.00169 ( 38) SS BOND : angle 1.06724 ( 76) covalent geometry : bond 0.00259 (24162) covalent geometry : angle 0.47060 (32862) *********************** 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 198 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 2.777 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8932 (t80) cc_final: 0.8466 (t80) REVERT: A 153 MET cc_start: 0.8008 (mmm) cc_final: 0.7502 (mmm) REVERT: A 374 PHE cc_start: 0.8050 (m-80) cc_final: 0.7776 (m-80) REVERT: A 380 TYR cc_start: 0.8960 (m-10) cc_final: 0.8752 (m-10) REVERT: A 661 GLU cc_start: 0.7008 (pp20) cc_final: 0.6577 (pp20) REVERT: B 200 TYR cc_start: 0.7916 (m-80) cc_final: 0.7666 (m-80) REVERT: B 265 TYR cc_start: 0.8038 (p90) cc_final: 0.7625 (p90) REVERT: B 342 PHE cc_start: 0.8024 (m-80) cc_final: 0.7240 (m-80) REVERT: B 418 ILE cc_start: 0.2630 (OUTLIER) cc_final: 0.2179 (mp) REVERT: B 436 TRP cc_start: 0.8390 (p-90) cc_final: 0.8039 (p-90) REVERT: C 118 LEU cc_start: 0.9226 (tp) cc_final: 0.8919 (mp) REVERT: C 979 ASP cc_start: 0.8813 (m-30) cc_final: 0.8533 (m-30) REVERT: C 1029 MET cc_start: 0.8170 (ttm) cc_final: 0.7907 (ttt) outliers start: 34 outliers final: 26 residues processed: 191 average time/residue: 0.3003 time to fit residues: 96.7441 Evaluate side-chains 181 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 62 VAL 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 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 896 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 148 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 217 optimal weight: 0.3980 chunk 238 optimal weight: 0.0050 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.116859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078331 restraints weight = 63658.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081736 restraints weight = 34479.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082006 restraints weight = 19939.211| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24222 Z= 0.119 Angle : 0.482 9.531 33004 Z= 0.249 Chirality : 0.042 0.239 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.278 53.076 3646 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.42 % Allowed : 13.50 % Favored : 85.08 % 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: 2.71 (0.21), residues: 621 sheet: 0.64 (0.20), residues: 612 loop : -0.67 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 PHE 0.031 0.001 PHE C 238 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 21) link_NAG-ASN : angle 1.56028 ( 63) link_BETA1-4 : bond 0.00193 ( 1) link_BETA1-4 : angle 1.14562 ( 3) hydrogen bonds : bond 0.04128 ( 874) hydrogen bonds : angle 4.81745 ( 2457) SS BOND : bond 0.00181 ( 38) SS BOND : angle 1.01936 ( 76) covalent geometry : bond 0.00275 (24162) covalent geometry : angle 0.47549 (32862) *********************** 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 195 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 2.576 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8936 (t80) cc_final: 0.8508 (t80) REVERT: A 153 MET cc_start: 0.8084 (mmm) cc_final: 0.7777 (mmm) REVERT: A 508 TYR cc_start: 0.7705 (m-10) cc_final: 0.7404 (m-10) REVERT: A 661 GLU cc_start: 0.7023 (pp20) cc_final: 0.6560 (pp20) REVERT: B 200 TYR cc_start: 0.7908 (m-80) cc_final: 0.7665 (m-80) REVERT: B 265 TYR cc_start: 0.8036 (p90) cc_final: 0.7619 (p90) REVERT: B 342 PHE cc_start: 0.8036 (m-80) cc_final: 0.7330 (m-80) REVERT: B 418 ILE cc_start: 0.2440 (OUTLIER) cc_final: 0.2179 (mp) REVERT: B 436 TRP cc_start: 0.8403 (p-90) cc_final: 0.8071 (p-90) REVERT: B 745 ASP cc_start: 0.8223 (p0) cc_final: 0.7730 (p0) REVERT: B 983 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.8033 (ttp-110) REVERT: C 118 LEU cc_start: 0.9263 (tp) cc_final: 0.8968 (mp) REVERT: C 417 ASN cc_start: 0.9320 (m-40) cc_final: 0.8849 (p0) REVERT: C 421 TYR cc_start: 0.8444 (m-80) cc_final: 0.7778 (m-10) REVERT: C 979 ASP cc_start: 0.8820 (m-30) cc_final: 0.8534 (m-30) REVERT: C 1029 MET cc_start: 0.8186 (ttm) cc_final: 0.7910 (ttt) outliers start: 37 outliers final: 30 residues processed: 185 average time/residue: 0.3174 time to fit residues: 99.4208 Evaluate side-chains 178 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 62 VAL 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 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 223 optimal weight: 0.0000 chunk 207 optimal weight: 0.0060 chunk 286 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082997 restraints weight = 63419.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082625 restraints weight = 36425.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083472 restraints weight = 24928.522| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24222 Z= 0.088 Angle : 0.470 10.340 33004 Z= 0.240 Chirality : 0.042 0.251 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.072 53.129 3646 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.04 % Allowed : 14.07 % Favored : 84.89 % 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: 0.66 (0.16), residues: 2917 helix: 2.84 (0.21), residues: 620 sheet: 0.74 (0.20), residues: 647 loop : -0.66 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.001 0.000 HIS B1048 PHE 0.031 0.001 PHE C 238 TYR 0.029 0.001 TYR A 396 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 21) link_NAG-ASN : angle 1.49825 ( 63) link_BETA1-4 : bond 0.00279 ( 1) link_BETA1-4 : angle 1.13058 ( 3) hydrogen bonds : bond 0.03653 ( 874) hydrogen bonds : angle 4.65112 ( 2457) SS BOND : bond 0.00149 ( 38) SS BOND : angle 0.87248 ( 76) covalent geometry : bond 0.00191 (24162) covalent geometry : angle 0.46487 (32862) *********************** 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 195 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 2.825 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8883 (t80) cc_final: 0.8460 (t80) REVERT: A 153 MET cc_start: 0.8029 (mmm) cc_final: 0.7740 (mmm) REVERT: A 508 TYR cc_start: 0.7610 (m-10) cc_final: 0.7283 (m-10) REVERT: A 661 GLU cc_start: 0.6968 (pp20) cc_final: 0.6603 (pp20) REVERT: B 200 TYR cc_start: 0.7874 (m-80) cc_final: 0.7624 (m-80) REVERT: B 265 TYR cc_start: 0.7975 (p90) cc_final: 0.7513 (p90) REVERT: B 342 PHE cc_start: 0.8012 (m-80) cc_final: 0.7202 (m-80) REVERT: B 418 ILE cc_start: 0.2498 (OUTLIER) cc_final: 0.2236 (mp) REVERT: B 436 TRP cc_start: 0.8333 (p-90) cc_final: 0.8038 (p-90) REVERT: B 983 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8003 (ttp-110) REVERT: C 84 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8234 (mm) REVERT: C 118 LEU cc_start: 0.9262 (tp) cc_final: 0.8984 (mt) REVERT: C 421 TYR cc_start: 0.8373 (m-80) cc_final: 0.7756 (m-10) REVERT: C 979 ASP cc_start: 0.8806 (m-30) cc_final: 0.8536 (m-30) REVERT: C 1029 MET cc_start: 0.8090 (ttm) cc_final: 0.7847 (ttt) outliers start: 27 outliers final: 22 residues processed: 190 average time/residue: 0.3348 time to fit residues: 107.9714 Evaluate side-chains 184 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE 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 538 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 727 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 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 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 171 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 197 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 chunk 282 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 144 optimal weight: 0.0570 chunk 97 optimal weight: 5.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.078324 restraints weight = 64030.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081523 restraints weight = 34955.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081951 restraints weight = 19493.763| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24222 Z= 0.128 Angle : 0.491 9.964 33004 Z= 0.252 Chirality : 0.042 0.238 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.132 52.639 3646 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.96 % Allowed : 14.15 % Favored : 84.89 % 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: 0.57 (0.16), residues: 2917 helix: 2.77 (0.21), residues: 620 sheet: 0.64 (0.21), residues: 597 loop : -0.65 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.029 0.001 PHE C 238 TYR 0.023 0.001 TYR A 396 ARG 0.006 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 21) link_NAG-ASN : angle 1.54540 ( 63) link_BETA1-4 : bond 0.00333 ( 1) link_BETA1-4 : angle 1.14368 ( 3) hydrogen bonds : bond 0.04085 ( 874) hydrogen bonds : angle 4.71343 ( 2457) SS BOND : bond 0.00219 ( 38) SS BOND : angle 1.02272 ( 76) covalent geometry : bond 0.00296 (24162) covalent geometry : angle 0.48442 (32862) ********************** 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 179 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 3.040 Fit side-chains revert: symmetry clash REVERT: A 144 TYR cc_start: 0.8959 (t80) cc_final: 0.8543 (t80) REVERT: A 153 MET cc_start: 0.8061 (mmm) cc_final: 0.7765 (mmm) REVERT: A 508 TYR cc_start: 0.7726 (m-10) cc_final: 0.7437 (m-10) REVERT: A 661 GLU cc_start: 0.7055 (pp20) cc_final: 0.6621 (pp20) REVERT: A 697 MET cc_start: 0.8699 (ttp) cc_final: 0.8486 (ttp) REVERT: B 265 TYR cc_start: 0.8028 (p90) cc_final: 0.7460 (p90) REVERT: B 342 PHE cc_start: 0.8064 (m-80) cc_final: 0.7257 (m-80) REVERT: B 418 ILE cc_start: 0.2582 (OUTLIER) cc_final: 0.2319 (mp) REVERT: B 436 TRP cc_start: 0.8403 (p-90) cc_final: 0.8090 (p-90) REVERT: B 983 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.8055 (ttp-110) REVERT: C 84 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8176 (mm) REVERT: C 118 LEU cc_start: 0.9278 (tp) cc_final: 0.8969 (mp) REVERT: C 417 ASN cc_start: 0.9296 (m-40) cc_final: 0.8856 (p0) REVERT: C 421 TYR cc_start: 0.8393 (m-80) cc_final: 0.7736 (m-10) REVERT: C 979 ASP cc_start: 0.8844 (m-30) cc_final: 0.8559 (m-30) REVERT: C 1029 MET cc_start: 0.8164 (ttm) cc_final: 0.7901 (ttt) outliers start: 25 outliers final: 23 residues processed: 175 average time/residue: 0.3215 time to fit residues: 96.0562 Evaluate side-chains 176 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 785 VAL 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 538 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 727 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 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 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 204 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 181 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3801 r_free = 0.3801 target = 0.115846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.077149 restraints weight = 63709.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080514 restraints weight = 35551.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.080619 restraints weight = 20676.264| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24222 Z= 0.147 Angle : 0.503 10.044 33004 Z= 0.260 Chirality : 0.043 0.243 3783 Planarity : 0.004 0.056 4226 Dihedral : 4.268 52.677 3646 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.15 % Allowed : 14.15 % Favored : 84.70 % 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: 0.48 (0.16), residues: 2917 helix: 2.64 (0.21), residues: 623 sheet: 0.53 (0.20), residues: 617 loop : -0.68 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS B1048 PHE 0.038 0.001 PHE C 238 TYR 0.021 0.001 TYR A 396 ARG 0.005 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 21) link_NAG-ASN : angle 1.58362 ( 63) link_BETA1-4 : bond 0.00247 ( 1) link_BETA1-4 : angle 1.13082 ( 3) hydrogen bonds : bond 0.04412 ( 874) hydrogen bonds : angle 4.77859 ( 2457) SS BOND : bond 0.00200 ( 38) SS BOND : angle 1.04543 ( 76) covalent geometry : bond 0.00344 (24162) covalent geometry : angle 0.49713 (32862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8129.20 seconds wall clock time: 144 minutes 51.04 seconds (8691.04 seconds total)