Starting phenix.real_space_refine on Mon Aug 25 11:33:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yz5_39685/08_2025/8yz5_39685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yz5_39685/08_2025/8yz5_39685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yz5_39685/08_2025/8yz5_39685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yz5_39685/08_2025/8yz5_39685.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yz5_39685/08_2025/8yz5_39685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yz5_39685/08_2025/8yz5_39685.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 122 5.16 5 C 17620 2.51 5 N 4635 2.21 5 O 5300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27677 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8023 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 49, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8138 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 6 Chain: "D" Number of atoms: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8102 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 889 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 884 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.62, per 1000 atoms: 0.24 Number of scatterers: 27677 At special positions: 0 Unit cell: (162.68, 181.77, 150.23, 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 122 16.00 O 5300 8.00 N 4635 7.00 C 17620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.05 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 D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.04 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 86 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 86 " 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 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6616 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 47 sheets defined 20.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.719A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.659A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.072A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.593A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.576A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.594A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.796A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.618A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.981A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.355A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1120 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.239A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.100A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 removed outlier: 4.070A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.765A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.564A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.802A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.173A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.780A pdb=" N ASN A 950 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.157A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 4.122A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.547A pdb=" N GLU D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 385 through 390 removed outlier: 4.025A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.599A pdb=" N VAL D 407 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 408' Processing helix chain 'D' and resid 417 through 422 removed outlier: 4.284A pdb=" N TYR D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 758 through 781 Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 883 Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.816A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 4.309A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 968 removed outlier: 3.657A pdb=" N ALA D 958 " --> pdb=" O GLN D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 982 removed outlier: 4.388A pdb=" N LEU D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 977 through 982' Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.714A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 996 " --> pdb=" O GLN D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1120 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.609A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 81 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.503A pdb=" N ILE J 81 " --> pdb=" O PRO J 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 5.830A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.508A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.869A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.664A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.427A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 312 through 319 removed outlier: 5.443A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 325 through 327 Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.058A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.663A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.679A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 3.822A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.085A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.111A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.973A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.527A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.411A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 664 through 667 removed outlier: 5.883A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 712 through 727 removed outlier: 6.794A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC7, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC8, first strand: chain 'D' and resid 29 through 31 removed outlier: 8.891A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY D 268 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 224 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.111A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 83 through 84 removed outlier: 4.080A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 311 through 318 removed outlier: 3.592A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 324 through 326 removed outlier: 6.872A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE D 326 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 587 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'D' and resid 664 through 667 removed outlier: 5.831A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 711 through 727 removed outlier: 6.516A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA D1070 " --> pdb=" O ASN D 717 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS D1064 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'D' and resid 1081 through 1082 removed outlier: 4.263A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.590A pdb=" N TYR G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.738A pdb=" N ASN K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR K 49 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN K 87 " --> pdb=" O ASN K 34 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 57 through 59 removed outlier: 4.841A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.806A pdb=" N LEU J 11 " --> pdb=" O LYS J 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU J 103 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 19 through 23 Processing sheet with id=AF2, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.969A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) 993 hydrogen bonds defined for protein. 2697 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: 6.29 Time building geometry restraints manager: 3.11 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: 8938 1.34 - 1.46: 6592 1.46 - 1.58: 12610 1.58 - 1.70: 1 1.70 - 1.83: 158 Bond restraints: 28299 Sorted by residual: bond pdb=" N ASN D 331 " pdb=" CA ASN D 331 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.14e-02 7.69e+03 6.56e+00 bond pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.35e+00 bond pdb=" N ASN D 334 " pdb=" CA ASN D 334 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.26e+00 bond pdb=" N THR D 333 " pdb=" CA THR D 333 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.76e+00 bond pdb=" N ILE D 332 " pdb=" CA ILE D 332 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.25e-02 6.40e+03 4.40e+00 ... (remaining 28294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 37991 2.44 - 4.87: 449 4.87 - 7.31: 37 7.31 - 9.75: 11 9.75 - 12.18: 1 Bond angle restraints: 38489 Sorted by residual: angle pdb=" N GLN A 954 " pdb=" CA GLN A 954 " pdb=" CB GLN A 954 " ideal model delta sigma weight residual 110.12 116.65 -6.53 1.47e+00 4.63e-01 1.98e+01 angle pdb=" C ASN C 953 " pdb=" N GLN C 954 " pdb=" CA GLN C 954 " ideal model delta sigma weight residual 121.18 113.02 8.16 1.98e+00 2.55e-01 1.70e+01 angle pdb=" C TYR K 49 " pdb=" N ASP K 50 " pdb=" CA ASP K 50 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 angle pdb=" CA ARG C 765 " pdb=" CB ARG C 765 " pdb=" CG ARG C 765 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA PRO D1057 " pdb=" N PRO D1057 " pdb=" CD PRO D1057 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.32e+01 ... (remaining 38484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 15486 17.86 - 35.71: 1092 35.71 - 53.57: 178 53.57 - 71.42: 46 71.42 - 89.28: 26 Dihedral angle restraints: 16828 sinusoidal: 6526 harmonic: 10302 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -161.26 75.26 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual 93.00 162.68 -69.68 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -19.72 -66.28 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 16825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3090 0.044 - 0.088: 889 0.088 - 0.132: 325 0.132 - 0.177: 42 0.177 - 0.221: 7 Chirality restraints: 4353 Sorted by residual: chirality pdb=" CG LEU D 948 " pdb=" CB LEU D 948 " pdb=" CD1 LEU D 948 " pdb=" CD2 LEU D 948 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CG LEU I 78 " pdb=" CB LEU I 78 " pdb=" CD1 LEU I 78 " pdb=" CD2 LEU I 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLN D 957 " pdb=" N GLN D 957 " pdb=" C GLN D 957 " pdb=" CB GLN D 957 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4350 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1056 " -0.074 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO D1057 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO D1057 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D1057 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.059 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO C 561 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 896 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO D 897 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 897 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 897 " 0.042 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 7 2.16 - 2.85: 9516 2.85 - 3.53: 37429 3.53 - 4.22: 63012 4.22 - 4.90: 106716 Nonbonded interactions: 216680 Sorted by model distance: nonbonded pdb=" OD2 ASP D 142 " pdb=" CZ3 TRP D 258 " model vdw 1.479 3.340 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.053 3.040 nonbonded pdb=" OE2 GLU D 725 " pdb=" NZ LYS D1028 " model vdw 2.094 3.120 nonbonded pdb=" O VAL A 951 " pdb=" ND2 ASN A 955 " model vdw 2.101 3.120 nonbonded pdb=" OD2 ASP A 142 " pdb=" CZ2 TRP A 258 " model vdw 2.120 3.340 ... (remaining 216675 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 20 through 143 or resid 161 or resid 166 through 332 or re \ sid 335 through 356 or (resid 357 and (name N or name CA or name C or name O or \ name CB )) or resid 358 through 377 or (resid 378 and (name N or name CA or name \ C or name O or name CB )) or resid 379 through 390 or (resid 391 and (name N or \ name CA or name C or name O or name CB )) or resid 392 through 518 or resid 530 \ through 579 or (resid 580 and (name N or name CA or name C or name O or name CB \ )) or resid 581 through 1141)) selection = (chain 'C' and (resid 20 through 143 or resid 161 or resid 166 through 1141)) selection = (chain 'D' and (resid 20 through 143 or resid 151 or resid 166 through 332 or re \ sid 335 through 518 or resid 530 through 579 or (resid 580 and (name N or name C \ A or name C or name O or name CB )) or resid 581 through 1141)) } ncs_group { reference = (chain 'G' and resid 1 through 113) selection = chain 'I' } ncs_group { reference = (chain 'J' and resid 1 through 104) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.930 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28340 Z= 0.150 Angle : 0.664 12.182 38571 Z= 0.357 Chirality : 0.047 0.221 4353 Planarity : 0.005 0.109 4992 Dihedral : 12.984 89.276 10089 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 0.07 % Allowed : 0.29 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.14), residues: 3498 helix: -0.58 (0.21), residues: 592 sheet: -0.45 (0.19), residues: 750 loop : -1.66 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 577 TYR 0.029 0.002 TYR A 873 PHE 0.032 0.002 PHE C 275 TRP 0.033 0.002 TRP C 64 HIS 0.011 0.001 HIS D1101 Details of bonding type rmsd covalent geometry : bond 0.00312 (28299) covalent geometry : angle 0.66057 (38489) SS BOND : bond 0.00426 ( 41) SS BOND : angle 1.66222 ( 82) hydrogen bonds : bond 0.15089 ( 993) hydrogen bonds : angle 7.52657 ( 2697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 658 ASN cc_start: 0.5996 (p0) cc_final: 0.5754 (p0) REVERT: A 43 PHE cc_start: 0.7469 (m-10) cc_final: 0.7150 (m-80) REVERT: A 815 ARG cc_start: 0.5600 (ptt-90) cc_final: 0.4166 (mtm110) REVERT: D 237 ARG cc_start: 0.4408 (ppt170) cc_final: 0.4110 (tmm160) REVERT: D 754 LEU cc_start: 0.6408 (mm) cc_final: 0.6096 (mt) REVERT: D 1107 ARG cc_start: 0.4523 (mtm180) cc_final: 0.3888 (tpt90) outliers start: 2 outliers final: 0 residues processed: 376 average time/residue: 0.1892 time to fit residues: 113.9297 Evaluate side-chains 294 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN C 542 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 925 ASN C 926 GLN A 66 HIS A 544 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN D 498 GLN D1054 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 27 GLN J 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.262539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.228952 restraints weight = 49160.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.228443 restraints weight = 53830.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.227171 restraints weight = 43745.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.226472 restraints weight = 35502.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.226896 restraints weight = 33868.032| |-----------------------------------------------------------------------------| r_work (final): 0.4602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 28340 Z= 0.209 Angle : 0.692 13.214 38571 Z= 0.368 Chirality : 0.048 0.269 4353 Planarity : 0.005 0.073 4992 Dihedral : 5.352 26.048 3812 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 1.33 % Allowed : 7.80 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.13), residues: 3498 helix: -0.66 (0.20), residues: 603 sheet: -0.46 (0.19), residues: 748 loop : -1.80 (0.12), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 319 TYR 0.039 0.002 TYR A 873 PHE 0.026 0.002 PHE C 318 TRP 0.021 0.002 TRP C 64 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00443 (28299) covalent geometry : angle 0.68859 (38489) SS BOND : bond 0.00505 ( 41) SS BOND : angle 1.65298 ( 82) hydrogen bonds : bond 0.06252 ( 993) hydrogen bonds : angle 6.88158 ( 2697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 330 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 658 ASN cc_start: 0.6687 (p0) cc_final: 0.6439 (p0) REVERT: C 720 ILE cc_start: 0.8386 (mm) cc_final: 0.8166 (mt) REVERT: A 815 ARG cc_start: 0.5878 (ptt-90) cc_final: 0.4794 (ptt90) REVERT: A 869 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5890 (ttp) REVERT: D 820 ASP cc_start: 0.7035 (m-30) cc_final: 0.6775 (t0) REVERT: D 1089 PHE cc_start: -0.0813 (m-10) cc_final: -0.1235 (m-10) outliers start: 41 outliers final: 29 residues processed: 351 average time/residue: 0.1863 time to fit residues: 105.2914 Evaluate side-chains 318 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 951 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 334 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 690 GLN C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN J 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.258162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.224059 restraints weight = 49170.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.222449 restraints weight = 62173.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.222073 restraints weight = 55280.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.222023 restraints weight = 37810.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.222565 restraints weight = 33966.848| |-----------------------------------------------------------------------------| r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28340 Z= 0.257 Angle : 0.729 12.166 38571 Z= 0.389 Chirality : 0.049 0.281 4353 Planarity : 0.005 0.077 4992 Dihedral : 5.668 26.893 3812 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.70 % Allowed : 10.54 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.13), residues: 3498 helix: -0.95 (0.19), residues: 617 sheet: -0.53 (0.19), residues: 755 loop : -1.97 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 44 TYR 0.047 0.002 TYR D1047 PHE 0.033 0.002 PHE A 898 TRP 0.016 0.002 TRP C 64 HIS 0.014 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00555 (28299) covalent geometry : angle 0.72626 (38489) SS BOND : bond 0.00579 ( 41) SS BOND : angle 1.61651 ( 82) hydrogen bonds : bond 0.06661 ( 993) hydrogen bonds : angle 7.12374 ( 2697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 322 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 720 ILE cc_start: 0.8492 (mm) cc_final: 0.8214 (mt) REVERT: C 869 MET cc_start: 0.7498 (mtm) cc_final: 0.7133 (ttp) REVERT: C 902 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.5560 (ttp) REVERT: C 1045 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7497 (mmmt) REVERT: A 204 TYR cc_start: 0.5697 (OUTLIER) cc_final: 0.5380 (m-80) REVERT: A 789 TYR cc_start: 0.5556 (OUTLIER) cc_final: 0.4814 (m-80) REVERT: A 815 ARG cc_start: 0.6100 (ptt-90) cc_final: 0.4296 (mtm180) REVERT: A 909 ILE cc_start: 0.1531 (OUTLIER) cc_final: 0.0562 (tt) REVERT: D 1089 PHE cc_start: -0.0301 (m-10) cc_final: -0.0923 (m-10) outliers start: 83 outliers final: 53 residues processed: 369 average time/residue: 0.1919 time to fit residues: 111.7452 Evaluate side-chains 344 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 722 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 11 optimal weight: 20.0000 chunk 189 optimal weight: 0.0470 chunk 294 optimal weight: 8.9990 chunk 308 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 165 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 overall best weight: 1.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 925 ASN C 953 ASN C 955 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN D 655 HIS ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.261342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.228060 restraints weight = 49264.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.224501 restraints weight = 64893.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.224113 restraints weight = 53913.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.223638 restraints weight = 42634.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.224505 restraints weight = 38229.898| |-----------------------------------------------------------------------------| r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28340 Z= 0.156 Angle : 0.626 11.606 38571 Z= 0.331 Chirality : 0.046 0.221 4353 Planarity : 0.005 0.070 4992 Dihedral : 5.362 24.078 3812 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.41 % Allowed : 12.85 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.13), residues: 3498 helix: -0.57 (0.20), residues: 592 sheet: -0.50 (0.19), residues: 768 loop : -1.84 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.025 0.002 TYR D1047 PHE 0.025 0.002 PHE C 888 TRP 0.012 0.001 TRP G 47 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00330 (28299) covalent geometry : angle 0.62254 (38489) SS BOND : bond 0.00399 ( 41) SS BOND : angle 1.49556 ( 82) hydrogen bonds : bond 0.05572 ( 993) hydrogen bonds : angle 6.83140 ( 2697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 318 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 SER cc_start: 0.6638 (m) cc_final: 0.6095 (p) REVERT: C 353 TRP cc_start: 0.6055 (p-90) cc_final: 0.5708 (p-90) REVERT: C 720 ILE cc_start: 0.8548 (mm) cc_final: 0.8285 (mt) REVERT: C 869 MET cc_start: 0.7412 (mtm) cc_final: 0.7117 (ttp) REVERT: C 902 MET cc_start: 0.6635 (mmt) cc_final: 0.6223 (ttt) REVERT: C 1045 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7455 (mmmt) REVERT: A 815 ARG cc_start: 0.5975 (ptt-90) cc_final: 0.4151 (mtm180) REVERT: A 1012 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8236 (mt) REVERT: D 770 ILE cc_start: 0.7827 (mt) cc_final: 0.7204 (mt) REVERT: D 774 GLN cc_start: 0.7352 (mt0) cc_final: 0.7034 (mp10) REVERT: D 977 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5978 (pt) REVERT: D 1089 PHE cc_start: -0.0578 (m-10) cc_final: -0.1091 (m-10) REVERT: D 1109 PHE cc_start: 0.3406 (t80) cc_final: 0.2819 (t80) REVERT: I 98 GLU cc_start: 0.1349 (OUTLIER) cc_final: 0.0252 (tm-30) REVERT: J 24 GLN cc_start: 0.5096 (pp30) cc_final: 0.4780 (pp30) outliers start: 74 outliers final: 54 residues processed: 367 average time/residue: 0.1804 time to fit residues: 107.8450 Evaluate side-chains 343 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 182 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 254 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 350 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.261818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.230253 restraints weight = 48791.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.228043 restraints weight = 61271.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.225324 restraints weight = 46964.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.224952 restraints weight = 38745.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.225424 restraints weight = 36874.456| |-----------------------------------------------------------------------------| r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28340 Z= 0.146 Angle : 0.613 11.480 38571 Z= 0.324 Chirality : 0.045 0.246 4353 Planarity : 0.004 0.069 4992 Dihedral : 5.208 28.239 3812 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.57 % Allowed : 13.53 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.14), residues: 3498 helix: -0.52 (0.20), residues: 603 sheet: -0.46 (0.19), residues: 772 loop : -1.79 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1014 TYR 0.023 0.001 TYR A 873 PHE 0.027 0.001 PHE C 888 TRP 0.010 0.001 TRP A 104 HIS 0.016 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00310 (28299) covalent geometry : angle 0.61025 (38489) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.35110 ( 82) hydrogen bonds : bond 0.05307 ( 993) hydrogen bonds : angle 6.67375 ( 2697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 311 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 SER cc_start: 0.6622 (m) cc_final: 0.6102 (p) REVERT: C 869 MET cc_start: 0.7215 (mtm) cc_final: 0.6964 (ttp) REVERT: C 902 MET cc_start: 0.6828 (mmt) cc_final: 0.5951 (ttt) REVERT: C 1045 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7353 (mmmt) REVERT: A 815 ARG cc_start: 0.5952 (ptt-90) cc_final: 0.4231 (mtm180) REVERT: A 962 LEU cc_start: 0.7905 (mt) cc_final: 0.7681 (mp) REVERT: A 1004 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6320 (tp) REVERT: D 332 ILE cc_start: 0.4558 (OUTLIER) cc_final: 0.3879 (mm) REVERT: D 740 MET cc_start: 0.5448 (tpp) cc_final: 0.4591 (tpp) REVERT: D 770 ILE cc_start: 0.7592 (mt) cc_final: 0.6960 (mt) REVERT: D 774 GLN cc_start: 0.7300 (mt0) cc_final: 0.6893 (mp10) REVERT: D 904 TYR cc_start: 0.4210 (OUTLIER) cc_final: 0.2095 (t80) REVERT: D 1089 PHE cc_start: -0.0435 (m-10) cc_final: -0.0940 (m-10) REVERT: K 4 MET cc_start: -0.0895 (ptp) cc_final: -0.1904 (ppp) REVERT: I 33 TYR cc_start: 0.3763 (m-80) cc_final: 0.2770 (m-80) REVERT: I 98 GLU cc_start: 0.1060 (OUTLIER) cc_final: 0.0023 (tm-30) outliers start: 79 outliers final: 54 residues processed: 364 average time/residue: 0.1559 time to fit residues: 92.4000 Evaluate side-chains 344 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 950 ASN Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 116 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 chunk 140 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.259502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.227013 restraints weight = 48654.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.223241 restraints weight = 61988.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.220986 restraints weight = 52015.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.220672 restraints weight = 40510.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.221051 restraints weight = 42172.868| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28340 Z= 0.189 Angle : 0.640 11.677 38571 Z= 0.340 Chirality : 0.046 0.299 4353 Planarity : 0.005 0.070 4992 Dihedral : 5.281 25.469 3812 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.86 % Allowed : 14.60 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.14), residues: 3498 helix: -0.56 (0.20), residues: 595 sheet: -0.54 (0.19), residues: 779 loop : -1.79 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1000 TYR 0.030 0.002 TYR D1047 PHE 0.024 0.002 PHE C 888 TRP 0.013 0.001 TRP C 353 HIS 0.016 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00410 (28299) covalent geometry : angle 0.63631 (38489) SS BOND : bond 0.00459 ( 41) SS BOND : angle 1.57606 ( 82) hydrogen bonds : bond 0.05586 ( 993) hydrogen bonds : angle 6.77050 ( 2697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 298 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 SER cc_start: 0.6845 (m) cc_final: 0.6368 (p) REVERT: C 869 MET cc_start: 0.7249 (mtm) cc_final: 0.6979 (ttp) REVERT: C 902 MET cc_start: 0.7047 (mmt) cc_final: 0.6067 (ttt) REVERT: C 925 ASN cc_start: 0.7655 (m-40) cc_final: 0.7312 (m110) REVERT: C 949 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6311 (mm110) REVERT: C 1045 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7416 (mmmt) REVERT: A 279 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6312 (m-80) REVERT: A 559 PHE cc_start: 0.4784 (m-10) cc_final: 0.4577 (m-10) REVERT: A 815 ARG cc_start: 0.6085 (ptt-90) cc_final: 0.4919 (mtm110) REVERT: A 909 ILE cc_start: 0.1134 (OUTLIER) cc_final: 0.0504 (mp) REVERT: D 332 ILE cc_start: 0.4443 (OUTLIER) cc_final: 0.3297 (mm) REVERT: D 770 ILE cc_start: 0.7776 (mt) cc_final: 0.7548 (mt) REVERT: D 774 GLN cc_start: 0.7506 (mt0) cc_final: 0.7097 (mp10) REVERT: D 904 TYR cc_start: 0.4112 (OUTLIER) cc_final: 0.2100 (t80) REVERT: D 1089 PHE cc_start: -0.0103 (m-10) cc_final: -0.0595 (m-10) REVERT: D 1109 PHE cc_start: 0.3138 (OUTLIER) cc_final: 0.2531 (t80) REVERT: K 4 MET cc_start: -0.0765 (ptp) cc_final: -0.1759 (ppp) REVERT: I 33 TYR cc_start: 0.3693 (m-80) cc_final: 0.2733 (m-80) outliers start: 88 outliers final: 60 residues processed: 359 average time/residue: 0.1669 time to fit residues: 96.6669 Evaluate side-chains 350 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 284 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 48 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 324 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS D1058 HIS ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.258888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.226730 restraints weight = 48741.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.225286 restraints weight = 58797.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.226472 restraints weight = 49595.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.225000 restraints weight = 37066.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.225425 restraints weight = 38911.383| |-----------------------------------------------------------------------------| r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28340 Z= 0.194 Angle : 0.651 11.961 38571 Z= 0.346 Chirality : 0.047 0.326 4353 Planarity : 0.005 0.071 4992 Dihedral : 5.336 25.989 3812 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.02 % Allowed : 14.86 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.13), residues: 3498 helix: -0.70 (0.20), residues: 602 sheet: -0.57 (0.19), residues: 766 loop : -1.82 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1000 TYR 0.031 0.002 TYR D1047 PHE 0.022 0.002 PHE C 888 TRP 0.013 0.001 TRP C1102 HIS 0.012 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00420 (28299) covalent geometry : angle 0.64827 (38489) SS BOND : bond 0.00478 ( 41) SS BOND : angle 1.42286 ( 82) hydrogen bonds : bond 0.05694 ( 993) hydrogen bonds : angle 6.86255 ( 2697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 301 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 SER cc_start: 0.6754 (m) cc_final: 0.6371 (p) REVERT: C 869 MET cc_start: 0.7340 (mtm) cc_final: 0.7073 (ttp) REVERT: C 901 GLN cc_start: 0.5063 (OUTLIER) cc_final: 0.2987 (mt0) REVERT: C 902 MET cc_start: 0.6969 (mmt) cc_final: 0.5946 (ttt) REVERT: C 1014 ARG cc_start: 0.6956 (ttm110) cc_final: 0.6435 (ttp80) REVERT: C 1045 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7466 (mmmt) REVERT: A 43 PHE cc_start: 0.7610 (m-80) cc_final: 0.7023 (m-80) REVERT: A 789 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.4895 (m-80) REVERT: A 815 ARG cc_start: 0.6139 (ptt-90) cc_final: 0.5425 (mtm110) REVERT: D 332 ILE cc_start: 0.4340 (OUTLIER) cc_final: 0.3199 (mm) REVERT: D 770 ILE cc_start: 0.7790 (mt) cc_final: 0.7579 (mt) REVERT: D 774 GLN cc_start: 0.7440 (mt0) cc_final: 0.7055 (mp10) REVERT: D 873 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: D 904 TYR cc_start: 0.4082 (OUTLIER) cc_final: 0.2073 (t80) REVERT: D 1089 PHE cc_start: -0.0014 (m-10) cc_final: -0.0536 (m-10) REVERT: D 1109 PHE cc_start: 0.3182 (OUTLIER) cc_final: 0.2529 (t80) REVERT: I 33 TYR cc_start: 0.3429 (m-80) cc_final: 0.2616 (m-80) outliers start: 93 outliers final: 74 residues processed: 366 average time/residue: 0.1667 time to fit residues: 98.8195 Evaluate side-chains 374 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 294 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 898 PHE Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 215 optimal weight: 30.0000 chunk 173 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 246 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 655 HIS D 755 GLN G 73 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.256495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.221132 restraints weight = 49007.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.219844 restraints weight = 61749.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.221213 restraints weight = 51050.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.221461 restraints weight = 32404.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.221860 restraints weight = 31846.223| |-----------------------------------------------------------------------------| r_work (final): 0.4546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 28340 Z= 0.256 Angle : 0.727 13.804 38571 Z= 0.387 Chirality : 0.050 0.562 4353 Planarity : 0.005 0.073 4992 Dihedral : 5.678 29.817 3812 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.77 % Allowed : 14.93 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.13), residues: 3498 helix: -1.08 (0.19), residues: 613 sheet: -0.66 (0.19), residues: 756 loop : -2.00 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1000 TYR 0.042 0.002 TYR D1047 PHE 0.025 0.002 PHE D 898 TRP 0.018 0.002 TRP C1102 HIS 0.016 0.002 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00560 (28299) covalent geometry : angle 0.72487 (38489) SS BOND : bond 0.00560 ( 41) SS BOND : angle 1.50390 ( 82) hydrogen bonds : bond 0.06384 ( 993) hydrogen bonds : angle 7.19186 ( 2697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 304 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 SER cc_start: 0.6939 (m) cc_final: 0.6575 (p) REVERT: C 869 MET cc_start: 0.7505 (mtm) cc_final: 0.7210 (ttp) REVERT: C 901 GLN cc_start: 0.5073 (OUTLIER) cc_final: 0.4063 (tt0) REVERT: C 902 MET cc_start: 0.6886 (mmt) cc_final: 0.6245 (ttp) REVERT: C 949 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6549 (mm110) REVERT: C 1045 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7498 (mmmt) REVERT: A 63 THR cc_start: 0.5787 (OUTLIER) cc_final: 0.5410 (p) REVERT: A 279 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.6173 (m-80) REVERT: A 297 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7682 (t) REVERT: A 789 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: A 815 ARG cc_start: 0.6165 (ptt-90) cc_final: 0.5402 (mtm110) REVERT: A 909 ILE cc_start: 0.2139 (OUTLIER) cc_final: 0.1237 (mp) REVERT: A 969 ASN cc_start: 0.6269 (OUTLIER) cc_final: 0.6044 (t0) REVERT: D 332 ILE cc_start: 0.4086 (OUTLIER) cc_final: 0.3733 (mt) REVERT: D 620 VAL cc_start: 0.4196 (OUTLIER) cc_final: 0.3970 (m) REVERT: D 770 ILE cc_start: 0.7943 (mt) cc_final: 0.7690 (mt) REVERT: D 774 GLN cc_start: 0.7511 (mt0) cc_final: 0.7105 (mp10) REVERT: D 904 TYR cc_start: 0.4266 (OUTLIER) cc_final: 0.2369 (t80) REVERT: D 1089 PHE cc_start: 0.0316 (m-10) cc_final: -0.0252 (m-10) REVERT: D 1109 PHE cc_start: 0.3588 (OUTLIER) cc_final: 0.2939 (t80) REVERT: K 4 MET cc_start: -0.0728 (ptp) cc_final: -0.1653 (ppp) REVERT: I 33 TYR cc_start: 0.3201 (m-80) cc_final: 0.2565 (m-80) outliers start: 116 outliers final: 77 residues processed: 389 average time/residue: 0.1729 time to fit residues: 108.0303 Evaluate side-chains 386 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 297 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 898 PHE Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 975 SER Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 174 optimal weight: 0.0040 chunk 326 optimal weight: 50.0000 chunk 187 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 112 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 305 optimal weight: 0.0270 chunk 339 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.0030 overall best weight: 0.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 655 HIS ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN D 49 HIS D 207 HIS D 422 ASN D 655 HIS ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1058 HIS ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 34 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.263460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.225836 restraints weight = 49068.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.225708 restraints weight = 47131.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.224229 restraints weight = 31989.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.223851 restraints weight = 25651.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.224473 restraints weight = 25889.062| |-----------------------------------------------------------------------------| r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28340 Z= 0.130 Angle : 0.646 14.389 38571 Z= 0.336 Chirality : 0.047 0.342 4353 Planarity : 0.004 0.066 4992 Dihedral : 5.147 23.843 3812 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.76 % Allowed : 16.85 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.14), residues: 3498 helix: -0.93 (0.19), residues: 636 sheet: -0.45 (0.19), residues: 744 loop : -1.77 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 44 TYR 0.028 0.001 TYR A 741 PHE 0.027 0.001 PHE C 888 TRP 0.016 0.001 TRP C 436 HIS 0.029 0.002 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00276 (28299) covalent geometry : angle 0.64473 (38489) SS BOND : bond 0.00385 ( 41) SS BOND : angle 1.21310 ( 82) hydrogen bonds : bond 0.04770 ( 993) hydrogen bonds : angle 6.69713 ( 2697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 338 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 SER cc_start: 0.7091 (m) cc_final: 0.6647 (p) REVERT: C 900 MET cc_start: 0.4066 (mmt) cc_final: 0.3809 (mmt) REVERT: C 902 MET cc_start: 0.6637 (mmt) cc_final: 0.6212 (ttt) REVERT: C 925 ASN cc_start: 0.7548 (m-40) cc_final: 0.7210 (m110) REVERT: C 929 SER cc_start: 0.7939 (p) cc_final: 0.7331 (t) REVERT: C 949 GLN cc_start: 0.6964 (mm-40) cc_final: 0.5934 (tt0) REVERT: C 966 LEU cc_start: 0.4603 (tt) cc_final: 0.4173 (tt) REVERT: C 1007 TYR cc_start: 0.6378 (t80) cc_final: 0.5158 (t80) REVERT: C 1045 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7653 (mmmt) REVERT: A 189 LEU cc_start: 0.6266 (tt) cc_final: 0.5535 (tp) REVERT: A 815 ARG cc_start: 0.5911 (ptt-90) cc_final: 0.4777 (mtm110) REVERT: A 965 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6883 (mp10) REVERT: A 969 ASN cc_start: 0.5790 (t0) cc_final: 0.5558 (t0) REVERT: D 620 VAL cc_start: 0.3885 (OUTLIER) cc_final: 0.3637 (m) REVERT: D 904 TYR cc_start: 0.4022 (OUTLIER) cc_final: 0.1953 (t80) REVERT: D 1089 PHE cc_start: -0.0386 (m-10) cc_final: -0.0753 (m-10) REVERT: D 1109 PHE cc_start: 0.3329 (OUTLIER) cc_final: 0.2755 (t80) REVERT: K 4 MET cc_start: -0.0787 (ptp) cc_final: -0.1711 (ppp) REVERT: J 24 GLN cc_start: 0.5710 (pp30) cc_final: 0.5463 (pp30) outliers start: 54 outliers final: 41 residues processed: 379 average time/residue: 0.1661 time to fit residues: 101.6121 Evaluate side-chains 347 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 898 PHE Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 43 optimal weight: 0.1980 chunk 323 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 253 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 306 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN D 655 HIS ** D1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.260505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.223929 restraints weight = 48764.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.221387 restraints weight = 58411.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.224114 restraints weight = 44705.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.224438 restraints weight = 29463.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.224954 restraints weight = 28639.360| |-----------------------------------------------------------------------------| r_work (final): 0.4581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28340 Z= 0.166 Angle : 0.669 20.825 38571 Z= 0.350 Chirality : 0.048 0.390 4353 Planarity : 0.005 0.084 4992 Dihedral : 5.175 26.114 3812 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.29 % Favored : 92.68 % Rotamer: Outliers : 1.69 % Allowed : 17.30 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.14), residues: 3498 helix: -0.93 (0.20), residues: 616 sheet: -0.42 (0.19), residues: 735 loop : -1.80 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 44 TYR 0.022 0.002 TYR D1047 PHE 0.035 0.002 PHE A 43 TRP 0.011 0.001 TRP A 104 HIS 0.013 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00366 (28299) covalent geometry : angle 0.66751 (38489) SS BOND : bond 0.00372 ( 41) SS BOND : angle 1.28845 ( 82) hydrogen bonds : bond 0.05220 ( 993) hydrogen bonds : angle 6.76100 ( 2697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6996 Ramachandran restraints generated. 3498 Oldfield, 0 Emsley, 3498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 SER cc_start: 0.7149 (m) cc_final: 0.6796 (p) REVERT: C 901 GLN cc_start: 0.4924 (OUTLIER) cc_final: 0.3743 (tt0) REVERT: C 902 MET cc_start: 0.6672 (mmt) cc_final: 0.6046 (ttt) REVERT: C 949 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.5872 (tt0) REVERT: C 1014 ARG cc_start: 0.7003 (ttm110) cc_final: 0.6572 (ttp80) REVERT: C 1045 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7571 (mmmt) REVERT: A 63 THR cc_start: 0.5737 (OUTLIER) cc_final: 0.5367 (p) REVERT: A 815 ARG cc_start: 0.5974 (ptt-90) cc_final: 0.4631 (mtm110) REVERT: A 969 ASN cc_start: 0.6011 (t0) cc_final: 0.5782 (t0) REVERT: D 620 VAL cc_start: 0.3991 (OUTLIER) cc_final: 0.3728 (m) REVERT: D 904 TYR cc_start: 0.4048 (OUTLIER) cc_final: 0.1993 (t80) REVERT: D 1089 PHE cc_start: -0.0067 (m-10) cc_final: -0.0594 (m-10) REVERT: D 1109 PHE cc_start: 0.3481 (OUTLIER) cc_final: 0.2879 (t80) REVERT: K 4 MET cc_start: -0.0730 (ptp) cc_final: -0.1739 (ppp) REVERT: I 100 MET cc_start: 0.1229 (tpt) cc_final: 0.0991 (tpt) REVERT: J 24 GLN cc_start: 0.5617 (pp30) cc_final: 0.5315 (pp30) outliers start: 52 outliers final: 43 residues processed: 347 average time/residue: 0.1657 time to fit residues: 93.0442 Evaluate side-chains 346 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 655 HIS Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 655 HIS Chi-restraints excluded: chain D residue 733 LYS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 904 TYR Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1109 PHE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 87 optimal weight: 0.7980 chunk 138 optimal weight: 0.0470 chunk 106 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 ASN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** 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 = 0.4908 r_free = 0.4908 target = 0.260531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.224744 restraints weight = 48674.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.223223 restraints weight = 60114.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.223594 restraints weight = 46502.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.223108 restraints weight = 32862.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.223684 restraints weight = 33187.550| |-----------------------------------------------------------------------------| r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 28340 Z= 0.202 Angle : 0.779 59.193 38571 Z= 0.430 Chirality : 0.047 0.387 4353 Planarity : 0.005 0.066 4992 Dihedral : 5.171 26.106 3812 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.35 % Favored : 92.62 % Rotamer: Outliers : 1.89 % Allowed : 17.27 % Favored : 80.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.14), residues: 3498 helix: -0.89 (0.20), residues: 610 sheet: -0.42 (0.19), residues: 735 loop : -1.80 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.001 ARG A 44 TYR 0.021 0.002 TYR D1047 PHE 0.043 0.002 PHE A 718 TRP 0.011 0.001 TRP A 104 HIS 0.086 0.003 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00430 (28299) covalent geometry : angle 0.77807 (38489) SS BOND : bond 0.00521 ( 41) SS BOND : angle 1.26847 ( 82) hydrogen bonds : bond 0.05216 ( 993) hydrogen bonds : angle 6.77265 ( 2697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.08 seconds wall clock time: 79 minutes 19.84 seconds (4759.84 seconds total)