Starting phenix.real_space_refine on Tue Mar 19 09:54:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyl_23594/03_2024/7lyl_23594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyl_23594/03_2024/7lyl_23594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyl_23594/03_2024/7lyl_23594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyl_23594/03_2024/7lyl_23594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyl_23594/03_2024/7lyl_23594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyl_23594/03_2024/7lyl_23594.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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 103 5.16 5 C 15206 2.51 5 N 3928 2.21 5 O 4589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23826 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7812 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 8 Chain: "B" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7812 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 8 Chain: "C" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.26, per 1000 atoms: 0.51 Number of scatterers: 23826 At special positions: 0 Unit cell: (129.349, 134.694, 175.316, 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 103 16.00 O 4589 8.00 N 3928 7.00 C 15206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.04 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=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 801 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 8.28 Conformation dependent library (CDL) restraints added in 4.0 seconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 49 sheets defined 27.5% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.659A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.908A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.249A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.906A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.002A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.540A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 965 removed outlier: 3.566A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.771A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.364A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.788A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.796A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.658A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.849A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.017A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.709A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.553A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.053A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.854A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.258A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.656A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 342' Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.675A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.947A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.930A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.003A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.314A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.605A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.508A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) 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 965 removed outlier: 4.158A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.893A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.831A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.585A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.897A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.746A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.133A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.320A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.854A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.783A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.652A pdb=" N VAL A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LYS B 790 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.729A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.180A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.200A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.755A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.542A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.815A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.574A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.752A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.188A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.257A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.257A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.966A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.763A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.988A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.859A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.384A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.295A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.783A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.370A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.351A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.865A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.990A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.653A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.582A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.999A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.643A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.34 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6874 1.34 - 1.46: 4250 1.46 - 1.58: 13097 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24348 Sorted by residual: bond pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 1.514 1.539 -0.024 5.50e-03 3.31e+04 1.98e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 24343 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.85: 386 104.85 - 112.48: 11332 112.48 - 120.11: 11246 120.11 - 127.74: 10044 127.74 - 135.37: 108 Bond angle restraints: 33116 Sorted by residual: angle pdb=" CA GLY A 416 " pdb=" C GLY A 416 " pdb=" N ASN A 417 " ideal model delta sigma weight residual 114.23 119.87 -5.64 8.80e-01 1.29e+00 4.11e+01 angle pdb=" C LYS C 790 " pdb=" N THR C 791 " pdb=" CA THR C 791 " ideal model delta sigma weight residual 120.39 128.08 -7.69 1.39e+00 5.18e-01 3.06e+01 angle pdb=" N THR C 315 " pdb=" CA THR C 315 " pdb=" C THR C 315 " ideal model delta sigma weight residual 111.28 117.11 -5.83 1.09e+00 8.42e-01 2.86e+01 angle pdb=" CA PHE A 106 " pdb=" CB PHE A 106 " pdb=" CG PHE A 106 " ideal model delta sigma weight residual 113.80 118.92 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" OE1 GLN B1106 " pdb=" CD GLN B1106 " pdb=" NE2 GLN B1106 " ideal model delta sigma weight residual 122.60 117.63 4.97 1.00e+00 1.00e+00 2.47e+01 ... (remaining 33111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13755 17.66 - 35.33: 875 35.33 - 52.99: 138 52.99 - 70.66: 53 70.66 - 88.32: 30 Dihedral angle restraints: 14851 sinusoidal: 6127 harmonic: 8724 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.16 64.16 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.15 57.15 1 1.00e+01 1.00e-02 4.39e+01 ... (remaining 14848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2330 0.083 - 0.166: 1306 0.166 - 0.250: 193 0.250 - 0.333: 30 0.333 - 0.416: 4 Chirality restraints: 3863 Sorted by residual: chirality pdb=" CA ASN C 487 " pdb=" N ASN C 487 " pdb=" C ASN C 487 " pdb=" CB ASN C 487 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CG LEU B 229 " pdb=" CB LEU B 229 " pdb=" CD1 LEU B 229 " pdb=" CD2 LEU B 229 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 3860 not shown) Planarity restraints: 4271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " 0.239 2.00e-02 2.50e+03 1.30e-01 3.40e+02 pdb=" CG TYR A 904 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " -0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " -0.060 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " 0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.142 2.00e-02 2.50e+03 1.51e-01 2.86e+02 pdb=" CG ASN B 331 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.231 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " 0.143 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" CG ASN B 709 " -0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.182 2.00e-02 2.50e+03 ... (remaining 4268 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 12916 3.01 - 3.48: 23493 3.48 - 3.96: 38983 3.96 - 4.43: 43190 4.43 - 4.90: 72424 Nonbonded interactions: 191006 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.538 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.540 2.440 nonbonded pdb=" OG SER B 813 " pdb=" OE1 GLU B 868 " model vdw 2.544 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.550 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.551 2.440 ... (remaining 191001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 1147 or resid 1 \ 301 through 1308)) selection = (chain 'B' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 1147 or resid 1 \ 301 through 1308)) selection = (chain 'C' and (resid 27 through 1147 or resid 1301 through 1308)) } 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.190 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 64.970 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.013 0.078 24348 Z= 0.835 Angle : 1.704 8.391 33116 Z= 1.138 Chirality : 0.093 0.416 3863 Planarity : 0.013 0.147 4243 Dihedral : 13.015 88.323 9121 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 0.69 % Allowed : 2.37 % Favored : 96.94 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 2949 helix: -0.72 (0.17), residues: 688 sheet: 0.13 (0.20), residues: 560 loop : -0.88 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.024 TRP A 64 HIS 0.016 0.003 HIS A1048 PHE 0.074 0.011 PHE B 927 TYR 0.239 0.019 TYR A 904 ARG 0.009 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7901 (p90) cc_final: 0.7375 (p90) REVERT: A 902 MET cc_start: 0.9358 (mmm) cc_final: 0.9000 (tpt) REVERT: A 1050 MET cc_start: 0.8765 (ttp) cc_final: 0.8538 (ttp) REVERT: B 111 ASP cc_start: 0.8003 (p0) cc_final: 0.7784 (p0) REVERT: B 290 ASP cc_start: 0.7669 (t0) cc_final: 0.6824 (t0) REVERT: B 347 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7434 (t80) REVERT: B 752 LEU cc_start: 0.9363 (mt) cc_final: 0.8740 (mm) REVERT: C 297 SER cc_start: 0.9155 (m) cc_final: 0.8513 (t) REVERT: C 400 PHE cc_start: 0.7614 (p90) cc_final: 0.6864 (p90) REVERT: C 408 ARG cc_start: 0.9022 (ptt90) cc_final: 0.8326 (mmp80) REVERT: C 596 SER cc_start: 0.9172 (t) cc_final: 0.8852 (m) REVERT: C 1029 MET cc_start: 0.9465 (tpp) cc_final: 0.9119 (tpp) REVERT: C 1047 TYR cc_start: 0.8937 (m-80) cc_final: 0.8693 (m-80) outliers start: 18 outliers final: 5 residues processed: 249 average time/residue: 0.3759 time to fit residues: 143.9719 Evaluate side-chains 116 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 207 HIS C 317 ASN C 675 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24348 Z= 0.186 Angle : 0.637 8.941 33116 Z= 0.339 Chirality : 0.046 0.245 3863 Planarity : 0.004 0.042 4243 Dihedral : 7.248 58.375 3804 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.42 % Rotamer: Outliers : 1.38 % Allowed : 5.12 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2949 helix: 1.20 (0.20), residues: 686 sheet: 0.01 (0.19), residues: 675 loop : -0.52 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 353 HIS 0.006 0.001 HIS A 207 PHE 0.016 0.002 PHE C 377 TYR 0.025 0.002 TYR C 369 ARG 0.006 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7523 (p90) cc_final: 0.7093 (p90) REVERT: A 269 TYR cc_start: 0.7973 (m-80) cc_final: 0.7030 (m-80) REVERT: A 353 TRP cc_start: 0.8830 (p-90) cc_final: 0.8044 (p90) REVERT: B 347 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7735 (t80) REVERT: C 314 GLN cc_start: 0.8436 (tp40) cc_final: 0.8061 (tp40) REVERT: C 346 ARG cc_start: 0.7534 (ptm-80) cc_final: 0.7326 (ptm-80) REVERT: C 384 PRO cc_start: 0.8806 (Cg_endo) cc_final: 0.8572 (Cg_exo) REVERT: C 400 PHE cc_start: 0.7565 (p90) cc_final: 0.6956 (p90) REVERT: C 596 SER cc_start: 0.9002 (t) cc_final: 0.8798 (m) outliers start: 36 outliers final: 12 residues processed: 163 average time/residue: 0.3240 time to fit residues: 87.1910 Evaluate side-chains 116 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 294 optimal weight: 0.5980 chunk 243 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 93 optimal weight: 0.1980 chunk 218 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 675 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 655 HIS C 448 ASN C 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24348 Z= 0.165 Angle : 0.560 12.280 33116 Z= 0.294 Chirality : 0.045 0.229 3863 Planarity : 0.004 0.051 4243 Dihedral : 6.439 56.693 3802 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.26 % Allowed : 6.80 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 2949 helix: 1.61 (0.21), residues: 679 sheet: -0.06 (0.19), residues: 678 loop : -0.33 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 436 HIS 0.003 0.001 HIS A1064 PHE 0.018 0.001 PHE C 592 TYR 0.029 0.001 TYR B 904 ARG 0.008 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7489 (p90) cc_final: 0.7062 (p90) REVERT: A 269 TYR cc_start: 0.8045 (m-80) cc_final: 0.7175 (m-80) REVERT: A 318 PHE cc_start: 0.7425 (t80) cc_final: 0.7152 (t80) REVERT: B 347 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7649 (t80) REVERT: B 780 GLU cc_start: 0.8723 (tp30) cc_final: 0.8499 (tp30) REVERT: C 314 GLN cc_start: 0.8368 (tp40) cc_final: 0.8136 (tp40) REVERT: C 346 ARG cc_start: 0.7520 (ptm-80) cc_final: 0.7203 (ptm-80) REVERT: C 400 PHE cc_start: 0.7648 (p90) cc_final: 0.6784 (p90) outliers start: 33 outliers final: 20 residues processed: 144 average time/residue: 0.2996 time to fit residues: 73.9756 Evaluate side-chains 119 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 289 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 914 ASN A1142 GLN B 207 HIS B 540 ASN B 607 GLN C 613 GLN C 762 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 24348 Z= 0.478 Angle : 0.681 14.229 33116 Z= 0.353 Chirality : 0.047 0.209 3863 Planarity : 0.004 0.045 4243 Dihedral : 6.712 55.034 3802 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.10 % Allowed : 7.99 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2949 helix: 1.32 (0.20), residues: 684 sheet: -0.22 (0.19), residues: 696 loop : -0.47 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.010 0.002 HIS A1064 PHE 0.023 0.002 PHE A 927 TYR 0.026 0.002 TYR B 904 ARG 0.004 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 101 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7574 (p90) cc_final: 0.7174 (p90) REVERT: A 269 TYR cc_start: 0.8153 (m-80) cc_final: 0.7316 (m-80) REVERT: A 347 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: A 731 MET cc_start: 0.9003 (ptt) cc_final: 0.8684 (ptt) REVERT: A 979 ASP cc_start: 0.8393 (m-30) cc_final: 0.7959 (t70) REVERT: A 1041 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 347 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7798 (t80) REVERT: B 780 GLU cc_start: 0.8748 (tp30) cc_final: 0.8540 (tp30) REVERT: B 979 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: C 387 LEU cc_start: 0.9023 (mt) cc_final: 0.8799 (mp) REVERT: C 400 PHE cc_start: 0.7762 (p90) cc_final: 0.7113 (p90) outliers start: 55 outliers final: 38 residues processed: 145 average time/residue: 0.3115 time to fit residues: 77.3601 Evaluate side-chains 133 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 91 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 4 optimal weight: 0.0050 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 580 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24348 Z= 0.236 Angle : 0.550 13.479 33116 Z= 0.287 Chirality : 0.044 0.197 3863 Planarity : 0.003 0.042 4243 Dihedral : 6.382 56.148 3802 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.83 % Allowed : 8.79 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2949 helix: 1.63 (0.21), residues: 680 sheet: -0.15 (0.19), residues: 678 loop : -0.41 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.001 PHE A 92 TYR 0.019 0.001 TYR C 369 ARG 0.003 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 105 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7502 (p90) cc_final: 0.7109 (p90) REVERT: A 269 TYR cc_start: 0.8183 (m-80) cc_final: 0.7443 (m-80) REVERT: A 979 ASP cc_start: 0.8357 (m-30) cc_final: 0.7941 (t70) REVERT: B 347 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7822 (t80) REVERT: B 780 GLU cc_start: 0.8742 (tp30) cc_final: 0.8521 (tp30) REVERT: B 912 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8217 (p) REVERT: C 400 PHE cc_start: 0.7667 (p90) cc_final: 0.7024 (p90) REVERT: C 1029 MET cc_start: 0.9126 (tpp) cc_final: 0.8721 (ttm) outliers start: 48 outliers final: 36 residues processed: 143 average time/residue: 0.3587 time to fit residues: 86.6852 Evaluate side-chains 130 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 290 optimal weight: 4.9990 chunk 240 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 955 ASN C 314 GLN C 613 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24348 Z= 0.228 Angle : 0.540 12.146 33116 Z= 0.279 Chirality : 0.044 0.188 3863 Planarity : 0.003 0.042 4243 Dihedral : 6.202 57.134 3802 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.06 % Allowed : 9.55 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 2949 helix: 1.75 (0.21), residues: 682 sheet: -0.09 (0.20), residues: 643 loop : -0.44 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.004 0.001 HIS A 519 PHE 0.019 0.001 PHE C 592 TYR 0.029 0.001 TYR B 369 ARG 0.012 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 111 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7453 (p90) cc_final: 0.7102 (p90) REVERT: A 269 TYR cc_start: 0.8188 (m-80) cc_final: 0.7494 (m-80) REVERT: A 979 ASP cc_start: 0.8377 (m-30) cc_final: 0.7959 (t70) REVERT: A 1107 ARG cc_start: 0.8057 (mpt-90) cc_final: 0.7563 (mpt-90) REVERT: B 313 TYR cc_start: 0.8279 (m-80) cc_final: 0.7945 (m-80) REVERT: B 347 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7875 (t80) REVERT: B 776 LYS cc_start: 0.9089 (tppt) cc_final: 0.8774 (tptp) REVERT: B 780 GLU cc_start: 0.8752 (tp30) cc_final: 0.8507 (tp30) REVERT: B 904 TYR cc_start: 0.8038 (m-10) cc_final: 0.7796 (m-80) REVERT: B 912 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8188 (p) REVERT: C 380 TYR cc_start: 0.7560 (m-80) cc_final: 0.7157 (m-80) REVERT: C 400 PHE cc_start: 0.7566 (p90) cc_final: 0.6732 (p90) REVERT: C 436 TRP cc_start: 0.6000 (p90) cc_final: 0.5659 (p90) REVERT: C 1029 MET cc_start: 0.9088 (tpp) cc_final: 0.8728 (ttm) outliers start: 54 outliers final: 38 residues processed: 155 average time/residue: 0.3578 time to fit residues: 90.9632 Evaluate side-chains 138 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 162 optimal weight: 6.9990 chunk 289 optimal weight: 0.7980 chunk 180 optimal weight: 0.2980 chunk 176 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS B 115 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24348 Z= 0.182 Angle : 0.522 11.849 33116 Z= 0.270 Chirality : 0.044 0.189 3863 Planarity : 0.003 0.041 4243 Dihedral : 6.067 57.747 3802 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.99 % Allowed : 10.01 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2949 helix: 1.96 (0.21), residues: 676 sheet: -0.01 (0.20), residues: 623 loop : -0.41 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.005 0.001 HIS A 519 PHE 0.021 0.001 PHE A 92 TYR 0.017 0.001 TYR C 369 ARG 0.002 0.000 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 101 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7388 (p90) cc_final: 0.7037 (p90) REVERT: A 269 TYR cc_start: 0.8176 (m-80) cc_final: 0.7530 (m-80) REVERT: A 979 ASP cc_start: 0.8386 (m-30) cc_final: 0.7978 (t70) REVERT: A 1041 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7782 (t0) REVERT: B 313 TYR cc_start: 0.8260 (m-80) cc_final: 0.7961 (m-80) REVERT: B 347 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7893 (t80) REVERT: B 776 LYS cc_start: 0.9088 (tppt) cc_final: 0.8789 (tptp) REVERT: B 780 GLU cc_start: 0.8735 (tp30) cc_final: 0.8519 (tp30) REVERT: B 912 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8182 (p) REVERT: C 380 TYR cc_start: 0.7554 (m-80) cc_final: 0.7207 (m-80) REVERT: C 400 PHE cc_start: 0.7749 (p90) cc_final: 0.7152 (p90) REVERT: C 1029 MET cc_start: 0.9047 (tpp) cc_final: 0.8717 (ttm) outliers start: 52 outliers final: 42 residues processed: 144 average time/residue: 0.3256 time to fit residues: 79.3136 Evaluate side-chains 141 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 96 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24348 Z= 0.354 Angle : 0.595 13.056 33116 Z= 0.307 Chirality : 0.045 0.182 3863 Planarity : 0.004 0.041 4243 Dihedral : 6.254 58.329 3802 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.25 % Allowed : 9.78 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2949 helix: 1.66 (0.20), residues: 690 sheet: -0.04 (0.20), residues: 622 loop : -0.51 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.020 0.002 HIS A 519 PHE 0.022 0.002 PHE C 592 TYR 0.030 0.001 TYR B 369 ARG 0.003 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 95 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7489 (p90) cc_final: 0.7104 (p90) REVERT: A 269 TYR cc_start: 0.8198 (m-80) cc_final: 0.7554 (m-80) REVERT: A 979 ASP cc_start: 0.8444 (m-30) cc_final: 0.8033 (t70) REVERT: A 1041 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7966 (t0) REVERT: B 313 TYR cc_start: 0.8321 (m-80) cc_final: 0.8049 (m-80) REVERT: B 403 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8125 (ptm-80) REVERT: B 776 LYS cc_start: 0.9089 (tppt) cc_final: 0.8774 (tptp) REVERT: B 780 GLU cc_start: 0.8768 (tp30) cc_final: 0.8542 (tp30) REVERT: B 912 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8246 (p) REVERT: C 380 TYR cc_start: 0.7595 (m-80) cc_final: 0.7276 (m-80) REVERT: C 387 LEU cc_start: 0.9028 (mt) cc_final: 0.8787 (mp) REVERT: C 400 PHE cc_start: 0.7604 (p90) cc_final: 0.6965 (p90) REVERT: C 1029 MET cc_start: 0.9123 (tpp) cc_final: 0.8778 (ttm) outliers start: 59 outliers final: 48 residues processed: 146 average time/residue: 0.3434 time to fit residues: 84.7955 Evaluate side-chains 141 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 90 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.9990 chunk 252 optimal weight: 0.9990 chunk 269 optimal weight: 0.8980 chunk 276 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 0.0370 chunk 254 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24348 Z= 0.132 Angle : 0.517 10.989 33116 Z= 0.266 Chirality : 0.043 0.194 3863 Planarity : 0.003 0.041 4243 Dihedral : 5.864 58.012 3800 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.57 % Allowed : 10.51 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2949 helix: 1.87 (0.21), residues: 689 sheet: 0.08 (0.20), residues: 621 loop : -0.36 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 104 HIS 0.003 0.001 HIS A 519 PHE 0.026 0.001 PHE A 92 TYR 0.021 0.001 TYR C 313 ARG 0.004 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 109 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7453 (p90) cc_final: 0.7128 (p90) REVERT: A 886 TRP cc_start: 0.8505 (OUTLIER) cc_final: 0.7318 (p-90) REVERT: A 979 ASP cc_start: 0.8370 (m-30) cc_final: 0.7980 (t70) REVERT: A 1041 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7784 (t0) REVERT: B 313 TYR cc_start: 0.8133 (m-80) cc_final: 0.7912 (m-80) REVERT: B 776 LYS cc_start: 0.9068 (tppt) cc_final: 0.8799 (tptp) REVERT: C 241 LEU cc_start: 0.9455 (mp) cc_final: 0.9042 (pp) REVERT: C 380 TYR cc_start: 0.7562 (m-80) cc_final: 0.7274 (m-80) REVERT: C 400 PHE cc_start: 0.7632 (p90) cc_final: 0.7009 (p90) REVERT: C 1029 MET cc_start: 0.8986 (tpp) cc_final: 0.8695 (ttm) outliers start: 41 outliers final: 33 residues processed: 141 average time/residue: 0.3333 time to fit residues: 78.8345 Evaluate side-chains 129 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.7980 chunk 284 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 237 optimal weight: 0.0050 chunk 24 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24348 Z= 0.173 Angle : 0.517 11.249 33116 Z= 0.264 Chirality : 0.043 0.254 3863 Planarity : 0.003 0.041 4243 Dihedral : 5.686 57.338 3798 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.45 % Allowed : 10.93 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2949 helix: 1.91 (0.21), residues: 688 sheet: 0.11 (0.20), residues: 624 loop : -0.30 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 436 HIS 0.004 0.001 HIS A 519 PHE 0.022 0.001 PHE C 592 TYR 0.027 0.001 TYR B 369 ARG 0.003 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7476 (p90) cc_final: 0.7144 (p90) REVERT: A 886 TRP cc_start: 0.8493 (OUTLIER) cc_final: 0.7422 (p-90) REVERT: A 979 ASP cc_start: 0.8371 (m-30) cc_final: 0.8017 (t70) REVERT: A 1041 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7818 (t0) REVERT: B 313 TYR cc_start: 0.8179 (m-80) cc_final: 0.7953 (m-80) REVERT: B 347 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7920 (t80) REVERT: B 776 LYS cc_start: 0.9063 (tppt) cc_final: 0.8795 (tptp) REVERT: C 374 PHE cc_start: 0.6464 (m-10) cc_final: 0.6095 (m-10) REVERT: C 400 PHE cc_start: 0.7718 (p90) cc_final: 0.7107 (p90) REVERT: C 1029 MET cc_start: 0.9008 (tpp) cc_final: 0.8704 (ttm) outliers start: 38 outliers final: 30 residues processed: 126 average time/residue: 0.3096 time to fit residues: 66.8762 Evaluate side-chains 122 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.5980 chunk 253 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 238 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.092043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064488 restraints weight = 72491.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.067240 restraints weight = 37401.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067787 restraints weight = 20512.860| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 24348 Z= 0.148 Angle : 0.522 11.409 33116 Z= 0.268 Chirality : 0.044 0.392 3863 Planarity : 0.003 0.056 4243 Dihedral : 5.618 57.925 3796 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.45 % Allowed : 11.08 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2949 helix: 1.99 (0.21), residues: 675 sheet: 0.13 (0.20), residues: 621 loop : -0.28 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP C 436 HIS 0.005 0.001 HIS A 519 PHE 0.025 0.001 PHE A 92 TYR 0.016 0.001 TYR C 369 ARG 0.003 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3585.18 seconds wall clock time: 67 minutes 11.80 seconds (4031.80 seconds total)