Starting phenix.real_space_refine on Sat Jun 21 05:11:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmt_38488/06_2025/8xmt_38488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmt_38488/06_2025/8xmt_38488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmt_38488/06_2025/8xmt_38488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmt_38488/06_2025/8xmt_38488.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmt_38488/06_2025/8xmt_38488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmt_38488/06_2025/8xmt_38488.cif" } resolution = 3.31 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= 0.021 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 108 5.16 5 C 15471 2.51 5 N 4003 2.21 5 O 4635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24217 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7978 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 55, 'TRANS': 963} Chain breaks: 7 Chain: "B" Number of atoms: 7903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7903 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 55, 'TRANS': 953} Chain breaks: 8 Chain: "C" Number of atoms: 7958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7958 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 55, 'TRANS': 961} Chain breaks: 7 Chain: "A" 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: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 25.59, per 1000 atoms: 1.06 Number of scatterers: 24217 At special positions: 0 Unit cell: (138.168, 129.28, 164.024, 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 108 16.00 O 4635 8.00 N 4003 7.00 C 15471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.99 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A 61 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1134 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 717 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B 61 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C1098 " Time building additional restraints: 11.16 Conformation dependent library (CDL) restraints added in 6.7 seconds 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5722 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 24.7% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.821A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.305A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.964A pdb=" N SER A 408 " --> pdb=" O ASN 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 737 through 743 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.799A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.105A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.766A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.018A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.552A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 442 removed outlier: 4.100A pdb=" N ASP B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.121A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.642A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (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 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.273A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.798A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.637A 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 365 through 370 removed outlier: 3.639A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.204A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.796A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.760A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.230A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.746A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.663A 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 966 removed outlier: 3.563A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 8.300A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.611A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.504A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.124A 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 removed outlier: 3.868A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 135 removed outlier: 7.406A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.101A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.587A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.622A 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 removed outlier: 4.012A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.854A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.688A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.688A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.768A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'B' and resid 23 through 30 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.056A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.725A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.772A pdb=" N SER B 205 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.467A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.138A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.840A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.740A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.378A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.378A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD6, first strand: chain 'C' and resid 23 through 30 removed outlier: 7.721A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.558A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.789A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.189A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.613A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.728A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.826A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.826A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.308A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1121 971 hydrogen bonds defined for protein. 2682 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: 22.18 Time building geometry restraints manager: 12.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5373 1.33 - 1.46: 6907 1.46 - 1.58: 12364 1.58 - 1.71: 0 1.71 - 1.84: 135 Bond restraints: 24779 Sorted by residual: bond pdb=" CA SER B 359 " pdb=" CB SER B 359 " ideal model delta sigma weight residual 1.534 1.469 0.064 1.76e-02 3.23e+03 1.34e+01 bond pdb=" N VAL B 576 " pdb=" CA VAL B 576 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.29e+01 bond pdb=" CA SER A 530 " pdb=" CB SER A 530 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.48e-02 4.57e+03 1.12e+01 bond pdb=" CA SER B 349 " pdb=" CB SER B 349 " ideal model delta sigma weight residual 1.529 1.478 0.051 1.65e-02 3.67e+03 9.38e+00 bond pdb=" CA SER B 530 " pdb=" CB SER B 530 " ideal model delta sigma weight residual 1.527 1.487 0.040 1.38e-02 5.25e+03 8.39e+00 ... (remaining 24774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 33175 2.35 - 4.69: 489 4.69 - 7.04: 46 7.04 - 9.38: 10 9.38 - 11.73: 1 Bond angle restraints: 33721 Sorted by residual: angle pdb=" N LEU B 582 " pdb=" CA LEU B 582 " pdb=" C LEU B 582 " ideal model delta sigma weight residual 112.93 105.92 7.01 1.12e+00 7.97e-01 3.91e+01 angle pdb=" C CYS B 525 " pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sigma weight residual 111.23 102.93 8.30 1.42e+00 4.96e-01 3.42e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 112.96 107.28 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" N GLN B 580 " pdb=" CA GLN B 580 " pdb=" C GLN B 580 " ideal model delta sigma weight residual 110.80 99.07 11.73 2.13e+00 2.20e-01 3.03e+01 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 111.77 106.24 5.53 1.04e+00 9.25e-01 2.83e+01 ... (remaining 33716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13839 17.84 - 35.68: 1029 35.68 - 53.51: 199 53.51 - 71.35: 48 71.35 - 89.19: 26 Dihedral angle restraints: 15141 sinusoidal: 6262 harmonic: 8879 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -0.82 -85.18 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.52 -83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CD ARG B 328 " pdb=" NE ARG B 328 " pdb=" CZ ARG B 328 " pdb=" NH1 ARG B 328 " ideal model delta sinusoidal sigma weight residual 0.00 79.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 ... (remaining 15138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3682 0.099 - 0.198: 209 0.198 - 0.297: 15 0.297 - 0.396: 2 0.396 - 0.495: 2 Chirality restraints: 3910 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 717 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ASN B 334 " pdb=" N ASN B 334 " pdb=" C ASN B 334 " pdb=" CB ASN B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3907 not shown) Planarity restraints: 4347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 328 " 1.079 9.50e-02 1.11e+02 4.84e-01 1.41e+02 pdb=" NE ARG B 328 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 328 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 328 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 328 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 577 " 0.951 9.50e-02 1.11e+02 4.26e-01 1.10e+02 pdb=" NE ARG B 577 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG B 577 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 577 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 577 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 355 " -0.921 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG B 355 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG B 355 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 355 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 355 " -0.024 2.00e-02 2.50e+03 ... (remaining 4344 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1985 2.74 - 3.28: 23722 3.28 - 3.82: 39728 3.82 - 4.36: 46585 4.36 - 4.90: 80966 Nonbonded interactions: 192986 Sorted by model distance: nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.202 3.040 nonbonded pdb=" NZ LYS C 535 " pdb=" OE2 GLU C 554 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.218 3.040 nonbonded pdb=" ND2 ASN B 125 " pdb=" O SER B 172 " model vdw 2.222 3.120 ... (remaining 192981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 21 through 69 or resid 82 through 141 or resid 155 through \ 177 or resid 189 through 197 or resid 201 through 243 or resid 264 through 620 \ or resid 641 through 676 or resid 691 through 1139 or resid 1301 through 1308)) selection = (chain 'B' and (resid 21 through 69 or resid 82 through 141 or resid 155 through \ 177 or resid 189 through 676 or resid 691 through 826 or resid 855 through 1139 \ or resid 1301 through 1308)) selection = (chain 'C' and (resid 21 through 197 or resid 201 through 243 or resid 264 throu \ gh 676 or resid 691 through 826 or resid 855 through 1139 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 90.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 104.480 Find NCS groups from input model: 3.410 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:5.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24843 Z= 0.216 Angle : 0.667 13.068 33876 Z= 0.382 Chirality : 0.049 0.495 3910 Planarity : 0.014 0.484 4320 Dihedral : 13.245 89.191 9308 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.97 % Favored : 95.69 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2995 helix: 2.70 (0.21), residues: 639 sheet: 0.54 (0.19), residues: 676 loop : -0.77 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.004 0.001 HIS A1048 PHE 0.015 0.001 PHE B 562 TYR 0.055 0.001 TYR C 756 ARG 0.010 0.000 ARG A1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 27) link_NAG-ASN : angle 3.11038 ( 81) hydrogen bonds : bond 0.18648 ( 956) hydrogen bonds : angle 7.73937 ( 2682) SS BOND : bond 0.00815 ( 37) SS BOND : angle 1.95666 ( 74) covalent geometry : bond 0.00382 (24779) covalent geometry : angle 0.64481 (33721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 811 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7870 (p0) cc_final: 0.7615 (p0) REVERT: A 41 LYS cc_start: 0.4495 (mmtt) cc_final: 0.3948 (mmtt) REVERT: A 101 ILE cc_start: 0.7999 (mt) cc_final: 0.7595 (mm) REVERT: A 113 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7426 (tmtt) REVERT: A 118 LEU cc_start: 0.7855 (tt) cc_final: 0.7606 (tt) REVERT: A 140 PHE cc_start: 0.6907 (p90) cc_final: 0.6251 (p90) REVERT: A 156 GLU cc_start: 0.7433 (tt0) cc_final: 0.7081 (tt0) REVERT: A 200 TYR cc_start: 0.6596 (m-80) cc_final: 0.6033 (m-80) REVERT: A 207 HIS cc_start: 0.7175 (m-70) cc_final: 0.6470 (m-70) REVERT: A 218 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6682 (mm-40) REVERT: A 224 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6462 (pt0) REVERT: A 269 TYR cc_start: 0.7825 (m-80) cc_final: 0.7608 (m-80) REVERT: A 287 ASP cc_start: 0.7339 (t0) cc_final: 0.7013 (t0) REVERT: A 298 GLU cc_start: 0.7459 (tt0) cc_final: 0.7138 (tt0) REVERT: A 304 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7579 (tppt) REVERT: A 307 THR cc_start: 0.7993 (m) cc_final: 0.7506 (p) REVERT: A 309 GLU cc_start: 0.6869 (mp0) cc_final: 0.6509 (mp0) REVERT: A 316 SER cc_start: 0.7524 (m) cc_final: 0.7170 (p) REVERT: A 347 PHE cc_start: 0.7124 (m-10) cc_final: 0.6885 (m-80) REVERT: A 385 THR cc_start: 0.7710 (p) cc_final: 0.7293 (t) REVERT: A 386 LYS cc_start: 0.7349 (mmpt) cc_final: 0.6894 (mmpt) REVERT: A 505 HIS cc_start: 0.6666 (m-70) cc_final: 0.6409 (m-70) REVERT: A 560 LEU cc_start: 0.7862 (mm) cc_final: 0.7638 (mt) REVERT: A 574 ASP cc_start: 0.6449 (t70) cc_final: 0.6226 (t0) REVERT: A 605 SER cc_start: 0.8041 (m) cc_final: 0.7816 (p) REVERT: A 645 THR cc_start: 0.7009 (m) cc_final: 0.6613 (p) REVERT: A 657 ASN cc_start: 0.8311 (m110) cc_final: 0.7980 (m-40) REVERT: A 658 ASN cc_start: 0.7677 (p0) cc_final: 0.7329 (p0) REVERT: A 691 SER cc_start: 0.7151 (m) cc_final: 0.6908 (p) REVERT: A 704 SER cc_start: 0.7555 (t) cc_final: 0.7316 (p) REVERT: A 714 ILE cc_start: 0.8025 (mm) cc_final: 0.7750 (mt) REVERT: A 718 PHE cc_start: 0.8163 (p90) cc_final: 0.7813 (p90) REVERT: A 790 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7406 (mtmm) REVERT: A 819 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6462 (mt-10) REVERT: A 872 GLN cc_start: 0.7285 (mt0) cc_final: 0.7042 (mt0) REVERT: A 895 GLN cc_start: 0.8077 (pt0) cc_final: 0.7689 (pm20) REVERT: A 935 GLN cc_start: 0.7104 (tt0) cc_final: 0.6837 (tp-100) REVERT: A 955 ASN cc_start: 0.7428 (m110) cc_final: 0.7163 (t0) REVERT: A 969 LYS cc_start: 0.7313 (mtmt) cc_final: 0.6923 (mmtp) REVERT: A 970 PHE cc_start: 0.8111 (m-80) cc_final: 0.7653 (m-10) REVERT: A 979 ASP cc_start: 0.7011 (t70) cc_final: 0.6754 (t70) REVERT: A 984 LEU cc_start: 0.7931 (mt) cc_final: 0.7662 (mm) REVERT: A 1010 GLN cc_start: 0.7633 (mt0) cc_final: 0.7171 (mm-40) REVERT: A 1072 GLU cc_start: 0.7999 (pt0) cc_final: 0.7772 (pm20) REVERT: A 1073 LYS cc_start: 0.7544 (mmmm) cc_final: 0.7242 (mmmm) REVERT: A 1107 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.6907 (mtt-85) REVERT: A 1138 TYR cc_start: 0.6809 (t80) cc_final: 0.6543 (t80) REVERT: B 87 ASN cc_start: 0.7819 (m-40) cc_final: 0.7083 (m-40) REVERT: B 95 THR cc_start: 0.7857 (t) cc_final: 0.7476 (m) REVERT: B 102 ARG cc_start: 0.7034 (mtt-85) cc_final: 0.6763 (ttm170) REVERT: B 126 VAL cc_start: 0.6872 (p) cc_final: 0.6452 (t) REVERT: B 129 LYS cc_start: 0.7096 (mtmm) cc_final: 0.6521 (mtmm) REVERT: B 194 PHE cc_start: 0.7741 (t80) cc_final: 0.7480 (t80) REVERT: B 210 ILE cc_start: 0.7629 (tp) cc_final: 0.7339 (pt) REVERT: B 236 THR cc_start: 0.7871 (t) cc_final: 0.7308 (p) REVERT: B 269 TYR cc_start: 0.7913 (m-80) cc_final: 0.7532 (m-80) REVERT: B 271 GLN cc_start: 0.7921 (mt0) cc_final: 0.7614 (mt0) REVERT: B 275 PHE cc_start: 0.7691 (m-80) cc_final: 0.7486 (m-80) REVERT: B 278 LYS cc_start: 0.7523 (ttmm) cc_final: 0.7104 (ttmm) REVERT: B 281 GLU cc_start: 0.7927 (mp0) cc_final: 0.7649 (mp0) REVERT: B 304 LYS cc_start: 0.7329 (mttm) cc_final: 0.7030 (mmmm) REVERT: B 318 PHE cc_start: 0.7622 (t80) cc_final: 0.7411 (t80) REVERT: B 324 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6912 (mp0) REVERT: B 339 HIS cc_start: 0.7799 (t70) cc_final: 0.7433 (t70) REVERT: B 532 ASN cc_start: 0.7870 (m-40) cc_final: 0.7595 (t0) REVERT: B 557 LYS cc_start: 0.7892 (mttp) cc_final: 0.7392 (mttp) REVERT: B 558 LYS cc_start: 0.7844 (mmmt) cc_final: 0.6916 (mmmt) REVERT: B 606 ASN cc_start: 0.8221 (m-40) cc_final: 0.7879 (m-40) REVERT: B 646 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7491 (ttp80) REVERT: B 654 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6746 (tm-30) REVERT: B 661 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7039 (mt-10) REVERT: B 697 MET cc_start: 0.7947 (ptm) cc_final: 0.7712 (ptp) REVERT: B 705 VAL cc_start: 0.7913 (t) cc_final: 0.7569 (m) REVERT: B 710 ASN cc_start: 0.7835 (p0) cc_final: 0.7275 (p0) REVERT: B 725 GLU cc_start: 0.7743 (tt0) cc_final: 0.7358 (tt0) REVERT: B 737 ASP cc_start: 0.6437 (t0) cc_final: 0.5828 (t0) REVERT: B 746 SER cc_start: 0.7284 (t) cc_final: 0.6768 (p) REVERT: B 748 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6224 (mt-10) REVERT: B 752 LEU cc_start: 0.7511 (tp) cc_final: 0.7304 (mp) REVERT: B 776 LYS cc_start: 0.6992 (ttpt) cc_final: 0.6729 (ttpt) REVERT: B 796 TYR cc_start: 0.7456 (t80) cc_final: 0.6982 (t80) REVERT: B 811 LYS cc_start: 0.7106 (ptpt) cc_final: 0.6821 (mtmm) REVERT: B 814 LYS cc_start: 0.6714 (mmtt) cc_final: 0.6272 (mmtt) REVERT: B 902 MET cc_start: 0.7424 (tpp) cc_final: 0.7106 (mmm) REVERT: B 935 GLN cc_start: 0.7730 (tp-100) cc_final: 0.7283 (tt0) REVERT: B 960 ASN cc_start: 0.7368 (t0) cc_final: 0.6963 (m-40) REVERT: B 964 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7389 (mtpp) REVERT: B 969 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7199 (mmtp) REVERT: B 1028 LYS cc_start: 0.7587 (mttm) cc_final: 0.7349 (mttm) REVERT: B 1031 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 1038 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7823 (mttp) REVERT: B 1045 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7781 (mtmt) REVERT: B 1050 MET cc_start: 0.8008 (ptp) cc_final: 0.7779 (ptm) REVERT: B 1071 GLN cc_start: 0.7878 (mt0) cc_final: 0.7483 (mt0) REVERT: B 1073 LYS cc_start: 0.7550 (tttt) cc_final: 0.7151 (tttt) REVERT: B 1126 CYS cc_start: 0.7318 (p) cc_final: 0.6835 (t) REVERT: B 1138 TYR cc_start: 0.7181 (t80) cc_final: 0.6836 (t80) REVERT: C 54 LEU cc_start: 0.7891 (mt) cc_final: 0.7556 (mt) REVERT: C 160 TYR cc_start: 0.6847 (p90) cc_final: 0.6303 (p90) REVERT: C 189 LEU cc_start: 0.7849 (mt) cc_final: 0.7519 (mp) REVERT: C 194 PHE cc_start: 0.8269 (m-80) cc_final: 0.7865 (m-10) REVERT: C 200 TYR cc_start: 0.6637 (m-80) cc_final: 0.5862 (m-80) REVERT: C 241 LEU cc_start: 0.8027 (mt) cc_final: 0.7531 (mp) REVERT: C 281 GLU cc_start: 0.7319 (pm20) cc_final: 0.6876 (pm20) REVERT: C 298 GLU cc_start: 0.6842 (tt0) cc_final: 0.6579 (tp30) REVERT: C 305 SER cc_start: 0.8437 (t) cc_final: 0.7925 (p) REVERT: C 307 THR cc_start: 0.8435 (t) cc_final: 0.8220 (p) REVERT: C 310 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7747 (ttpp) REVERT: C 319 ARG cc_start: 0.6556 (ttt90) cc_final: 0.6312 (ttt90) REVERT: C 320 VAL cc_start: 0.7865 (t) cc_final: 0.7589 (m) REVERT: C 356 LYS cc_start: 0.7844 (tmtt) cc_final: 0.7161 (tmtt) REVERT: C 357 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7088 (ttp-170) REVERT: C 358 ILE cc_start: 0.7794 (mp) cc_final: 0.7509 (mt) REVERT: C 360 ASN cc_start: 0.7471 (m110) cc_final: 0.6877 (p0) REVERT: C 375 PHE cc_start: 0.7542 (t80) cc_final: 0.7149 (t80) REVERT: C 382 VAL cc_start: 0.8000 (t) cc_final: 0.7668 (m) REVERT: C 420 ASP cc_start: 0.6253 (p0) cc_final: 0.5986 (p0) REVERT: C 422 ASN cc_start: 0.6963 (m-40) cc_final: 0.6707 (m110) REVERT: C 424 LYS cc_start: 0.7047 (tppt) cc_final: 0.6673 (tppt) REVERT: C 453 TYR cc_start: 0.6051 (p90) cc_final: 0.5390 (p90) REVERT: C 462 LYS cc_start: 0.7291 (mmtt) cc_final: 0.7036 (mmtt) REVERT: C 508 TYR cc_start: 0.6618 (m-80) cc_final: 0.6191 (m-80) REVERT: C 509 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6871 (mtt180) REVERT: C 511 VAL cc_start: 0.7525 (t) cc_final: 0.7296 (p) REVERT: C 512 VAL cc_start: 0.8063 (t) cc_final: 0.7666 (p) REVERT: C 525 CYS cc_start: 0.5614 (m) cc_final: 0.5222 (m) REVERT: C 528 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7378 (mtpp) REVERT: C 554 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6772 (mm-30) REVERT: C 564 GLN cc_start: 0.7597 (mm110) cc_final: 0.7255 (mm-40) REVERT: C 574 ASP cc_start: 0.6586 (m-30) cc_final: 0.6247 (t70) REVERT: C 578 ASP cc_start: 0.7687 (t0) cc_final: 0.7033 (t0) REVERT: C 581 THR cc_start: 0.7254 (p) cc_final: 0.6928 (p) REVERT: C 605 SER cc_start: 0.8471 (t) cc_final: 0.7946 (p) REVERT: C 656 VAL cc_start: 0.8396 (t) cc_final: 0.7987 (m) REVERT: C 664 ILE cc_start: 0.7403 (mt) cc_final: 0.7164 (mt) REVERT: C 673 SER cc_start: 0.7904 (t) cc_final: 0.7678 (t) REVERT: C 719 THR cc_start: 0.8292 (t) cc_final: 0.8061 (p) REVERT: C 725 GLU cc_start: 0.7557 (tt0) cc_final: 0.7122 (tt0) REVERT: C 737 ASP cc_start: 0.7341 (t0) cc_final: 0.7128 (t70) REVERT: C 773 GLU cc_start: 0.7062 (tt0) cc_final: 0.6732 (tt0) REVERT: C 779 GLN cc_start: 0.7661 (tt0) cc_final: 0.7379 (tm-30) REVERT: C 780 GLU cc_start: 0.7295 (tt0) cc_final: 0.7025 (tt0) REVERT: C 790 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7470 (ttpp) REVERT: C 824 ASN cc_start: 0.7592 (m-40) cc_final: 0.7358 (m-40) REVERT: C 859 THR cc_start: 0.7121 (m) cc_final: 0.6741 (p) REVERT: C 900 MET cc_start: 0.7682 (mtp) cc_final: 0.7392 (mtp) REVERT: C 904 TYR cc_start: 0.7514 (m-10) cc_final: 0.6645 (m-10) REVERT: C 952 VAL cc_start: 0.6583 (t) cc_final: 0.6326 (m) REVERT: C 964 LYS cc_start: 0.7700 (tmtt) cc_final: 0.7347 (mmtm) REVERT: C 1038 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8118 (mmtp) REVERT: C 1045 LYS cc_start: 0.8125 (tmtt) cc_final: 0.7659 (tmtt) REVERT: C 1055 SER cc_start: 0.8467 (t) cc_final: 0.7966 (p) REVERT: C 1073 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7555 (ttpt) REVERT: C 1092 GLU cc_start: 0.7340 (pm20) cc_final: 0.7044 (pm20) outliers start: 3 outliers final: 0 residues processed: 813 average time/residue: 0.4089 time to fit residues: 518.6322 Evaluate side-chains 658 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 0.0980 chunk 228 optimal weight: 0.9980 chunk 127 optimal weight: 0.0070 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 125 ASN A 196 ASN A 556 ASN A 606 ASN A 613 GLN A1101 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 658 ASN B 690 GLN B 779 GLN B1106 GLN C 66 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 804 GLN C 935 GLN C 955 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121151 restraints weight = 37581.139| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.48 r_work: 0.3385 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24843 Z= 0.189 Angle : 0.645 15.636 33876 Z= 0.337 Chirality : 0.048 0.449 3910 Planarity : 0.005 0.069 4320 Dihedral : 6.505 59.419 3825 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 2.44 % Allowed : 9.48 % Favored : 88.08 % 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: 0.46 (0.15), residues: 2995 helix: 2.64 (0.20), residues: 642 sheet: 0.72 (0.20), residues: 607 loop : -0.78 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.006 0.001 HIS B 207 PHE 0.024 0.002 PHE A 429 TYR 0.036 0.002 TYR C 756 ARG 0.009 0.001 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 27) link_NAG-ASN : angle 3.05378 ( 81) hydrogen bonds : bond 0.04830 ( 956) hydrogen bonds : angle 5.78226 ( 2682) SS BOND : bond 0.00665 ( 37) SS BOND : angle 2.84262 ( 74) covalent geometry : bond 0.00422 (24779) covalent geometry : angle 0.61475 (33721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 678 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5714 (mmtt) cc_final: 0.5439 (mmtt) REVERT: A 109 THR cc_start: 0.8545 (m) cc_final: 0.8177 (p) REVERT: A 140 PHE cc_start: 0.7341 (p90) cc_final: 0.7053 (p90) REVERT: A 170 TYR cc_start: 0.7951 (t80) cc_final: 0.7537 (t80) REVERT: A 200 TYR cc_start: 0.7014 (m-80) cc_final: 0.6804 (m-80) REVERT: A 218 GLN cc_start: 0.7332 (mm-40) cc_final: 0.7039 (mm-40) REVERT: A 298 GLU cc_start: 0.7857 (tt0) cc_final: 0.7576 (tt0) REVERT: A 304 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8520 (mttm) REVERT: A 307 THR cc_start: 0.8681 (m) cc_final: 0.8224 (p) REVERT: A 309 GLU cc_start: 0.7276 (mp0) cc_final: 0.7073 (mp0) REVERT: A 385 THR cc_start: 0.8472 (p) cc_final: 0.7799 (t) REVERT: A 386 LYS cc_start: 0.8275 (mmpt) cc_final: 0.7727 (mmpt) REVERT: A 436 TRP cc_start: 0.7712 (p90) cc_final: 0.7263 (p90) REVERT: A 464 PHE cc_start: 0.8208 (m-80) cc_final: 0.7957 (m-80) REVERT: A 493 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 560 LEU cc_start: 0.8661 (mm) cc_final: 0.8362 (mt) REVERT: A 574 ASP cc_start: 0.8004 (t70) cc_final: 0.7613 (t0) REVERT: A 581 THR cc_start: 0.7983 (m) cc_final: 0.7670 (p) REVERT: A 645 THR cc_start: 0.8127 (m) cc_final: 0.7896 (p) REVERT: A 654 GLU cc_start: 0.8009 (tt0) cc_final: 0.7780 (tt0) REVERT: A 655 TYR cc_start: 0.8536 (t80) cc_final: 0.8291 (t80) REVERT: A 657 ASN cc_start: 0.8652 (m110) cc_final: 0.8434 (m110) REVERT: A 658 ASN cc_start: 0.8144 (p0) cc_final: 0.7926 (p0) REVERT: A 714 ILE cc_start: 0.8572 (mm) cc_final: 0.8197 (mt) REVERT: A 779 GLN cc_start: 0.8187 (tp40) cc_final: 0.7963 (tp40) REVERT: A 819 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 875 SER cc_start: 0.8401 (p) cc_final: 0.8176 (m) REVERT: A 934 ILE cc_start: 0.8299 (tt) cc_final: 0.8076 (tt) REVERT: A 935 GLN cc_start: 0.7880 (tt0) cc_final: 0.7638 (tp-100) REVERT: A 974 SER cc_start: 0.8004 (p) cc_final: 0.7739 (t) REVERT: A 979 ASP cc_start: 0.7948 (t70) cc_final: 0.7674 (t70) REVERT: A 1019 ARG cc_start: 0.7829 (tpt90) cc_final: 0.7567 (tpt170) REVERT: A 1028 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8088 (mttp) REVERT: A 1107 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.7109 (mtt-85) REVERT: A 1138 TYR cc_start: 0.7273 (t80) cc_final: 0.7025 (t80) REVERT: B 126 VAL cc_start: 0.7887 (p) cc_final: 0.7671 (t) REVERT: B 129 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7547 (mtmm) REVERT: B 138 ASP cc_start: 0.7547 (t0) cc_final: 0.7317 (t0) REVERT: B 235 ILE cc_start: 0.8127 (mt) cc_final: 0.7926 (mt) REVERT: B 236 THR cc_start: 0.8776 (t) cc_final: 0.8472 (p) REVERT: B 275 PHE cc_start: 0.8578 (m-80) cc_final: 0.8233 (m-80) REVERT: B 281 GLU cc_start: 0.8083 (mp0) cc_final: 0.7873 (mp0) REVERT: B 310 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8321 (ttpt) REVERT: B 339 HIS cc_start: 0.7699 (t70) cc_final: 0.7257 (t70) REVERT: B 533 LEU cc_start: 0.8609 (mt) cc_final: 0.8369 (mt) REVERT: B 557 LYS cc_start: 0.8135 (mttp) cc_final: 0.7710 (mttp) REVERT: B 558 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7644 (mmmt) REVERT: B 574 ASP cc_start: 0.7944 (t0) cc_final: 0.7389 (t0) REVERT: B 581 THR cc_start: 0.8145 (p) cc_final: 0.7283 (t) REVERT: B 583 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 646 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8083 (ttp80) REVERT: B 697 MET cc_start: 0.8481 (ptm) cc_final: 0.8246 (ptp) REVERT: B 705 VAL cc_start: 0.8432 (t) cc_final: 0.8168 (m) REVERT: B 710 ASN cc_start: 0.8289 (p0) cc_final: 0.7796 (p0) REVERT: B 740 MET cc_start: 0.8061 (tpt) cc_final: 0.7854 (tpt) REVERT: B 764 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7806 (ttpt) REVERT: B 776 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7817 (ttpt) REVERT: B 811 LYS cc_start: 0.7797 (ptpt) cc_final: 0.7272 (mtmm) REVERT: B 814 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7048 (mmtt) REVERT: B 935 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7714 (tt0) REVERT: B 964 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8105 (mtpp) REVERT: B 984 LEU cc_start: 0.7820 (mm) cc_final: 0.7447 (mt) REVERT: B 1031 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 1045 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8449 (mtmt) REVERT: B 1073 LYS cc_start: 0.8138 (tttt) cc_final: 0.7912 (tttt) REVERT: B 1126 CYS cc_start: 0.7580 (p) cc_final: 0.7284 (t) REVERT: B 1138 TYR cc_start: 0.7759 (t80) cc_final: 0.7491 (t80) REVERT: C 160 TYR cc_start: 0.7003 (p90) cc_final: 0.6495 (p90) REVERT: C 198 ASP cc_start: 0.6537 (p0) cc_final: 0.6305 (p0) REVERT: C 200 TYR cc_start: 0.7488 (m-80) cc_final: 0.6380 (m-80) REVERT: C 241 LEU cc_start: 0.7852 (mt) cc_final: 0.7617 (mp) REVERT: C 281 GLU cc_start: 0.7970 (pm20) cc_final: 0.7385 (pm20) REVERT: C 298 GLU cc_start: 0.7984 (tt0) cc_final: 0.7767 (tp30) REVERT: C 302 THR cc_start: 0.8614 (t) cc_final: 0.8183 (p) REVERT: C 305 SER cc_start: 0.8988 (t) cc_final: 0.8622 (p) REVERT: C 307 THR cc_start: 0.8851 (t) cc_final: 0.8520 (p) REVERT: C 318 PHE cc_start: 0.8082 (t80) cc_final: 0.7796 (t80) REVERT: C 375 PHE cc_start: 0.7939 (t80) cc_final: 0.7689 (t80) REVERT: C 377 PHE cc_start: 0.8237 (t80) cc_final: 0.7743 (t80) REVERT: C 382 VAL cc_start: 0.8930 (t) cc_final: 0.8649 (m) REVERT: C 453 TYR cc_start: 0.6943 (p90) cc_final: 0.6664 (p90) REVERT: C 462 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7549 (mmtt) REVERT: C 493 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 525 CYS cc_start: 0.7034 (m) cc_final: 0.6739 (m) REVERT: C 528 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7875 (mtpp) REVERT: C 551 VAL cc_start: 0.8932 (p) cc_final: 0.8720 (t) REVERT: C 554 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7461 (mm-30) REVERT: C 578 ASP cc_start: 0.8339 (t0) cc_final: 0.8025 (t0) REVERT: C 656 VAL cc_start: 0.8749 (t) cc_final: 0.8535 (m) REVERT: C 737 ASP cc_start: 0.8098 (t0) cc_final: 0.7850 (t70) REVERT: C 740 MET cc_start: 0.8286 (ttt) cc_final: 0.8082 (ttt) REVERT: C 776 LYS cc_start: 0.8312 (tmmt) cc_final: 0.8047 (tttm) REVERT: C 780 GLU cc_start: 0.7977 (tt0) cc_final: 0.7731 (tt0) REVERT: C 824 ASN cc_start: 0.8104 (m-40) cc_final: 0.7816 (m110) REVERT: C 859 THR cc_start: 0.8422 (m) cc_final: 0.8104 (p) REVERT: C 900 MET cc_start: 0.8190 (mtp) cc_final: 0.7869 (mtp) REVERT: C 904 TYR cc_start: 0.7641 (m-10) cc_final: 0.6635 (m-10) REVERT: C 933 LYS cc_start: 0.7929 (mttp) cc_final: 0.7544 (mtmm) REVERT: C 952 VAL cc_start: 0.7978 (t) cc_final: 0.7634 (m) REVERT: C 969 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7774 (mmtp) REVERT: C 994 ASP cc_start: 0.7572 (t70) cc_final: 0.7349 (t0) REVERT: C 1045 LYS cc_start: 0.8457 (tmtt) cc_final: 0.8188 (mmmt) REVERT: C 1055 SER cc_start: 0.8421 (t) cc_final: 0.7981 (p) REVERT: C 1073 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7951 (ttpt) REVERT: C 1092 GLU cc_start: 0.7495 (pm20) cc_final: 0.7249 (pm20) REVERT: C 1116 THR cc_start: 0.8461 (m) cc_final: 0.7991 (t) outliers start: 65 outliers final: 41 residues processed: 715 average time/residue: 0.4161 time to fit residues: 457.1756 Evaluate side-chains 665 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 624 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 974 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 132 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 263 optimal weight: 0.5980 chunk 254 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 256 optimal weight: 0.5980 chunk 223 optimal weight: 0.0870 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS A 556 ASN A1101 HIS B 30 ASN B 271 GLN B 282 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN C 66 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120315 restraints weight = 37360.909| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.47 r_work: 0.3379 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24843 Z= 0.163 Angle : 0.609 12.158 33876 Z= 0.314 Chirality : 0.047 0.438 3910 Planarity : 0.005 0.060 4320 Dihedral : 6.084 58.027 3825 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.39 % Rotamer: Outliers : 2.70 % Allowed : 11.77 % Favored : 85.53 % 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: 0.41 (0.15), residues: 2995 helix: 2.51 (0.20), residues: 647 sheet: 0.68 (0.20), residues: 606 loop : -0.78 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.006 0.001 HIS A 207 PHE 0.025 0.002 PHE A 541 TYR 0.022 0.002 TYR C 756 ARG 0.015 0.001 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 27) link_NAG-ASN : angle 3.09159 ( 81) hydrogen bonds : bond 0.04708 ( 956) hydrogen bonds : angle 5.53504 ( 2682) SS BOND : bond 0.00354 ( 37) SS BOND : angle 1.63642 ( 74) covalent geometry : bond 0.00372 (24779) covalent geometry : angle 0.58582 (33721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 666 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8540 (m) cc_final: 0.8157 (p) REVERT: A 129 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8151 (mtmm) REVERT: A 140 PHE cc_start: 0.7323 (p90) cc_final: 0.7030 (p90) REVERT: A 169 GLU cc_start: 0.7598 (tp30) cc_final: 0.7363 (tp30) REVERT: A 238 PHE cc_start: 0.8151 (p90) cc_final: 0.7257 (p90) REVERT: A 240 THR cc_start: 0.8247 (m) cc_final: 0.7911 (t) REVERT: A 298 GLU cc_start: 0.7751 (tt0) cc_final: 0.7487 (tt0) REVERT: A 304 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8484 (mttm) REVERT: A 307 THR cc_start: 0.8637 (m) cc_final: 0.8185 (p) REVERT: A 385 THR cc_start: 0.8445 (p) cc_final: 0.7821 (t) REVERT: A 386 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7803 (mmpt) REVERT: A 436 TRP cc_start: 0.7726 (p90) cc_final: 0.7362 (p90) REVERT: A 453 TYR cc_start: 0.6987 (p90) cc_final: 0.6761 (p90) REVERT: A 464 PHE cc_start: 0.8074 (m-80) cc_final: 0.7743 (m-80) REVERT: A 508 TYR cc_start: 0.7279 (m-80) cc_final: 0.6861 (m-80) REVERT: A 560 LEU cc_start: 0.8627 (mm) cc_final: 0.8333 (mt) REVERT: A 574 ASP cc_start: 0.8049 (t70) cc_final: 0.7654 (t0) REVERT: A 581 THR cc_start: 0.8018 (m) cc_final: 0.7647 (p) REVERT: A 654 GLU cc_start: 0.8087 (tt0) cc_final: 0.7852 (tt0) REVERT: A 655 TYR cc_start: 0.8537 (t80) cc_final: 0.8166 (t80) REVERT: A 657 ASN cc_start: 0.8712 (m110) cc_final: 0.8481 (m110) REVERT: A 658 ASN cc_start: 0.8142 (p0) cc_final: 0.7868 (p0) REVERT: A 714 ILE cc_start: 0.8606 (mm) cc_final: 0.8248 (mt) REVERT: A 761 THR cc_start: 0.8102 (p) cc_final: 0.7800 (t) REVERT: A 779 GLN cc_start: 0.8264 (tp40) cc_final: 0.8061 (tt0) REVERT: A 819 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 875 SER cc_start: 0.8411 (p) cc_final: 0.8176 (m) REVERT: A 934 ILE cc_start: 0.8299 (tt) cc_final: 0.8024 (tt) REVERT: A 935 GLN cc_start: 0.7864 (tt0) cc_final: 0.7630 (tp-100) REVERT: A 974 SER cc_start: 0.8094 (p) cc_final: 0.7803 (t) REVERT: A 979 ASP cc_start: 0.7929 (t70) cc_final: 0.7674 (t70) REVERT: A 1019 ARG cc_start: 0.7805 (tpt90) cc_final: 0.7571 (tpt170) REVERT: A 1028 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8102 (mttp) REVERT: A 1107 ARG cc_start: 0.7599 (mtt-85) cc_final: 0.7179 (mtt-85) REVERT: B 126 VAL cc_start: 0.7995 (p) cc_final: 0.7744 (t) REVERT: B 129 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7723 (mmtm) REVERT: B 138 ASP cc_start: 0.7659 (t0) cc_final: 0.7320 (t0) REVERT: B 202 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7235 (ptpp) REVERT: B 204 TYR cc_start: 0.7832 (m-10) cc_final: 0.7603 (m-10) REVERT: B 235 ILE cc_start: 0.8143 (mt) cc_final: 0.7931 (mt) REVERT: B 236 THR cc_start: 0.8784 (t) cc_final: 0.8515 (p) REVERT: B 275 PHE cc_start: 0.8565 (m-80) cc_final: 0.8266 (m-80) REVERT: B 310 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8363 (ttpt) REVERT: B 328 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7298 (mtt-85) REVERT: B 339 HIS cc_start: 0.7481 (t70) cc_final: 0.7020 (t70) REVERT: B 533 LEU cc_start: 0.8677 (mt) cc_final: 0.8114 (mt) REVERT: B 557 LYS cc_start: 0.8129 (mttp) cc_final: 0.7887 (mttp) REVERT: B 574 ASP cc_start: 0.7924 (t0) cc_final: 0.7357 (t0) REVERT: B 578 ASP cc_start: 0.8283 (p0) cc_final: 0.8010 (p0) REVERT: B 581 THR cc_start: 0.8040 (p) cc_final: 0.7672 (p) REVERT: B 583 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 646 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8133 (ttp80) REVERT: B 705 VAL cc_start: 0.8459 (t) cc_final: 0.8254 (m) REVERT: B 710 ASN cc_start: 0.8235 (p0) cc_final: 0.7734 (p0) REVERT: B 776 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7779 (ttpt) REVERT: B 811 LYS cc_start: 0.7874 (ptpt) cc_final: 0.7351 (mtmm) REVERT: B 814 LYS cc_start: 0.7578 (mmtt) cc_final: 0.7045 (mmtt) REVERT: B 935 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7780 (tt0) REVERT: B 960 ASN cc_start: 0.8347 (t0) cc_final: 0.7977 (m-40) REVERT: B 964 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8166 (mtpp) REVERT: B 984 LEU cc_start: 0.7788 (mm) cc_final: 0.7464 (mt) REVERT: B 1045 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8489 (mtmt) REVERT: B 1126 CYS cc_start: 0.7608 (p) cc_final: 0.7391 (t) REVERT: B 1138 TYR cc_start: 0.7794 (t80) cc_final: 0.7542 (t80) REVERT: B 1139 ASP cc_start: 0.6735 (t0) cc_final: 0.6521 (t0) REVERT: C 160 TYR cc_start: 0.7018 (p90) cc_final: 0.6553 (p90) REVERT: C 190 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7992 (mtp85) REVERT: C 200 TYR cc_start: 0.7546 (m-80) cc_final: 0.6479 (m-80) REVERT: C 241 LEU cc_start: 0.7934 (mt) cc_final: 0.7603 (mp) REVERT: C 281 GLU cc_start: 0.8057 (pm20) cc_final: 0.7662 (pm20) REVERT: C 297 SER cc_start: 0.8415 (m) cc_final: 0.8152 (m) REVERT: C 298 GLU cc_start: 0.7992 (tt0) cc_final: 0.7786 (tt0) REVERT: C 302 THR cc_start: 0.8629 (t) cc_final: 0.8231 (p) REVERT: C 305 SER cc_start: 0.8976 (t) cc_final: 0.8578 (p) REVERT: C 307 THR cc_start: 0.8869 (t) cc_final: 0.8512 (p) REVERT: C 318 PHE cc_start: 0.8098 (t80) cc_final: 0.7786 (t80) REVERT: C 355 ARG cc_start: 0.8504 (mmm160) cc_final: 0.8185 (mtp85) REVERT: C 375 PHE cc_start: 0.7928 (t80) cc_final: 0.7685 (t80) REVERT: C 382 VAL cc_start: 0.8841 (t) cc_final: 0.8549 (m) REVERT: C 453 TYR cc_start: 0.7063 (p90) cc_final: 0.6715 (p90) REVERT: C 462 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7576 (mmtt) REVERT: C 493 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 525 CYS cc_start: 0.7011 (m) cc_final: 0.6760 (m) REVERT: C 528 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7984 (mtpp) REVERT: C 551 VAL cc_start: 0.9027 (p) cc_final: 0.8764 (t) REVERT: C 557 LYS cc_start: 0.7321 (ptpt) cc_final: 0.6920 (ptpp) REVERT: C 578 ASP cc_start: 0.8284 (t0) cc_final: 0.7993 (t0) REVERT: C 587 ILE cc_start: 0.8153 (pt) cc_final: 0.7913 (mt) REVERT: C 656 VAL cc_start: 0.8732 (t) cc_final: 0.8525 (m) REVERT: C 698 SER cc_start: 0.8681 (t) cc_final: 0.8062 (p) REVERT: C 737 ASP cc_start: 0.8159 (t0) cc_final: 0.7936 (t70) REVERT: C 740 MET cc_start: 0.8293 (ttt) cc_final: 0.7967 (ttt) REVERT: C 780 GLU cc_start: 0.8075 (tt0) cc_final: 0.7785 (tt0) REVERT: C 824 ASN cc_start: 0.8136 (m-40) cc_final: 0.7847 (m110) REVERT: C 859 THR cc_start: 0.8382 (m) cc_final: 0.8061 (p) REVERT: C 900 MET cc_start: 0.8121 (mtp) cc_final: 0.7856 (mtp) REVERT: C 904 TYR cc_start: 0.7611 (m-10) cc_final: 0.6549 (m-10) REVERT: C 952 VAL cc_start: 0.7992 (t) cc_final: 0.7658 (m) REVERT: C 1045 LYS cc_start: 0.8464 (tmtt) cc_final: 0.8180 (tmtt) REVERT: C 1055 SER cc_start: 0.8408 (t) cc_final: 0.7955 (p) REVERT: C 1073 LYS cc_start: 0.8251 (ttpt) cc_final: 0.8029 (ttpt) REVERT: C 1092 GLU cc_start: 0.7446 (pm20) cc_final: 0.7175 (pm20) REVERT: C 1116 THR cc_start: 0.8358 (m) cc_final: 0.7864 (t) outliers start: 72 outliers final: 56 residues processed: 704 average time/residue: 0.4884 time to fit residues: 533.7201 Evaluate side-chains 676 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 619 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 3 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 223 optimal weight: 0.0170 chunk 75 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 196 ASN A 556 ASN A1088 HIS A1101 HIS B 20 ASN B 30 ASN B 271 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 540 ASN C 784 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119019 restraints weight = 37308.159| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.47 r_work: 0.3354 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24843 Z= 0.189 Angle : 0.617 12.188 33876 Z= 0.319 Chirality : 0.048 0.447 3910 Planarity : 0.005 0.062 4320 Dihedral : 5.869 56.485 3825 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.57 % Favored : 95.39 % Rotamer: Outliers : 3.37 % Allowed : 13.08 % Favored : 83.55 % 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: 0.29 (0.15), residues: 2995 helix: 2.40 (0.20), residues: 651 sheet: 0.66 (0.19), residues: 629 loop : -0.91 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.005 0.001 HIS C 49 PHE 0.026 0.002 PHE A 541 TYR 0.019 0.002 TYR C 756 ARG 0.008 0.001 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 27) link_NAG-ASN : angle 3.16045 ( 81) hydrogen bonds : bond 0.04831 ( 956) hydrogen bonds : angle 5.38497 ( 2682) SS BOND : bond 0.00395 ( 37) SS BOND : angle 1.98252 ( 74) covalent geometry : bond 0.00430 (24779) covalent geometry : angle 0.59170 (33721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 673 time to evaluate : 5.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8596 (m) cc_final: 0.8266 (p) REVERT: A 129 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8147 (mtmm) REVERT: A 134 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6757 (tm-30) REVERT: A 140 PHE cc_start: 0.7359 (p90) cc_final: 0.7055 (p90) REVERT: A 170 TYR cc_start: 0.7941 (t80) cc_final: 0.7740 (t80) REVERT: A 196 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7984 (p0) REVERT: A 226 LEU cc_start: 0.8247 (mt) cc_final: 0.7964 (mp) REVERT: A 238 PHE cc_start: 0.8250 (p90) cc_final: 0.7476 (p90) REVERT: A 240 THR cc_start: 0.8283 (m) cc_final: 0.7978 (t) REVERT: A 298 GLU cc_start: 0.7778 (tt0) cc_final: 0.7561 (tt0) REVERT: A 304 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8471 (mttm) REVERT: A 307 THR cc_start: 0.8556 (m) cc_final: 0.8139 (p) REVERT: A 401 VAL cc_start: 0.8955 (m) cc_final: 0.8732 (p) REVERT: A 414 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6771 (tm-30) REVERT: A 436 TRP cc_start: 0.7783 (p90) cc_final: 0.7398 (p90) REVERT: A 508 TYR cc_start: 0.7347 (m-80) cc_final: 0.6924 (m-80) REVERT: A 509 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7859 (mtt180) REVERT: A 560 LEU cc_start: 0.8607 (mm) cc_final: 0.8326 (mt) REVERT: A 574 ASP cc_start: 0.8052 (t70) cc_final: 0.7657 (t0) REVERT: A 581 THR cc_start: 0.8116 (m) cc_final: 0.7639 (p) REVERT: A 583 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6894 (pm20) REVERT: A 654 GLU cc_start: 0.8052 (tt0) cc_final: 0.7811 (tt0) REVERT: A 655 TYR cc_start: 0.8515 (t80) cc_final: 0.8216 (t80) REVERT: A 657 ASN cc_start: 0.8768 (m110) cc_final: 0.8546 (m110) REVERT: A 658 ASN cc_start: 0.8146 (p0) cc_final: 0.7820 (p0) REVERT: A 761 THR cc_start: 0.8194 (p) cc_final: 0.7917 (t) REVERT: A 819 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7323 (mt-10) REVERT: A 875 SER cc_start: 0.8440 (p) cc_final: 0.8199 (m) REVERT: A 934 ILE cc_start: 0.8336 (tt) cc_final: 0.8040 (tt) REVERT: A 935 GLN cc_start: 0.7872 (tt0) cc_final: 0.7633 (tp-100) REVERT: A 974 SER cc_start: 0.8166 (p) cc_final: 0.7890 (t) REVERT: A 979 ASP cc_start: 0.7958 (t70) cc_final: 0.7696 (t70) REVERT: A 990 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 1028 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8116 (mttp) REVERT: A 1107 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7211 (mtt-85) REVERT: B 46 SER cc_start: 0.8734 (m) cc_final: 0.8434 (p) REVERT: B 126 VAL cc_start: 0.8102 (p) cc_final: 0.7877 (t) REVERT: B 129 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7731 (mmtm) REVERT: B 138 ASP cc_start: 0.7748 (t0) cc_final: 0.7435 (t0) REVERT: B 164 ASN cc_start: 0.6839 (p0) cc_final: 0.6405 (t0) REVERT: B 202 LYS cc_start: 0.8033 (ptpt) cc_final: 0.7105 (ptpp) REVERT: B 228 ASP cc_start: 0.7472 (t0) cc_final: 0.6706 (t0) REVERT: B 235 ILE cc_start: 0.8145 (mt) cc_final: 0.7888 (mm) REVERT: B 236 THR cc_start: 0.8814 (t) cc_final: 0.8530 (p) REVERT: B 275 PHE cc_start: 0.8611 (m-80) cc_final: 0.8254 (m-80) REVERT: B 339 HIS cc_start: 0.7330 (t70) cc_final: 0.6872 (t70) REVERT: B 557 LYS cc_start: 0.8120 (mttp) cc_final: 0.7901 (mttp) REVERT: B 646 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8138 (ttp80) REVERT: B 764 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7777 (ttpp) REVERT: B 772 VAL cc_start: 0.8359 (t) cc_final: 0.8135 (m) REVERT: B 776 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7814 (ttpt) REVERT: B 811 LYS cc_start: 0.7939 (ptpt) cc_final: 0.7433 (mtmm) REVERT: B 814 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7048 (mmtt) REVERT: B 935 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7838 (tt0) REVERT: B 960 ASN cc_start: 0.8366 (t0) cc_final: 0.8021 (m-40) REVERT: B 964 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8190 (mtpp) REVERT: B 973 ILE cc_start: 0.8860 (pt) cc_final: 0.8546 (pp) REVERT: B 1028 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8425 (mttp) REVERT: B 1045 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8491 (mtmt) REVERT: B 1138 TYR cc_start: 0.7860 (t80) cc_final: 0.7571 (t80) REVERT: C 160 TYR cc_start: 0.7074 (p90) cc_final: 0.6643 (p90) REVERT: C 191 GLU cc_start: 0.7660 (mp0) cc_final: 0.7280 (mp0) REVERT: C 200 TYR cc_start: 0.7603 (m-80) cc_final: 0.6531 (m-80) REVERT: C 241 LEU cc_start: 0.8010 (mt) cc_final: 0.7750 (mp) REVERT: C 281 GLU cc_start: 0.8080 (pm20) cc_final: 0.7705 (pm20) REVERT: C 297 SER cc_start: 0.8420 (m) cc_final: 0.8173 (m) REVERT: C 298 GLU cc_start: 0.8037 (tt0) cc_final: 0.7821 (tt0) REVERT: C 302 THR cc_start: 0.8619 (t) cc_final: 0.8252 (p) REVERT: C 305 SER cc_start: 0.8983 (t) cc_final: 0.8599 (p) REVERT: C 307 THR cc_start: 0.8874 (t) cc_final: 0.8514 (p) REVERT: C 310 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8455 (ttpt) REVERT: C 357 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7673 (ttm-80) REVERT: C 375 PHE cc_start: 0.7951 (t80) cc_final: 0.7732 (t80) REVERT: C 382 VAL cc_start: 0.8980 (t) cc_final: 0.8689 (m) REVERT: C 392 PHE cc_start: 0.7407 (m-80) cc_final: 0.7196 (m-80) REVERT: C 453 TYR cc_start: 0.7101 (p90) cc_final: 0.6111 (p90) REVERT: C 462 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7615 (mmtt) REVERT: C 493 GLN cc_start: 0.7825 (tm-30) cc_final: 0.6847 (tm-30) REVERT: C 525 CYS cc_start: 0.6994 (m) cc_final: 0.6787 (m) REVERT: C 528 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8106 (mtpp) REVERT: C 551 VAL cc_start: 0.9083 (p) cc_final: 0.8801 (t) REVERT: C 578 ASP cc_start: 0.8327 (t0) cc_final: 0.8055 (t0) REVERT: C 644 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7879 (tp40) REVERT: C 656 VAL cc_start: 0.8717 (t) cc_final: 0.8489 (m) REVERT: C 698 SER cc_start: 0.8694 (t) cc_final: 0.8047 (p) REVERT: C 737 ASP cc_start: 0.8278 (t0) cc_final: 0.8061 (t70) REVERT: C 740 MET cc_start: 0.8144 (ttt) cc_final: 0.7920 (tpp) REVERT: C 780 GLU cc_start: 0.8132 (tt0) cc_final: 0.7843 (tt0) REVERT: C 820 ASP cc_start: 0.7844 (t0) cc_final: 0.7459 (m-30) REVERT: C 824 ASN cc_start: 0.8186 (m-40) cc_final: 0.7868 (m110) REVERT: C 859 THR cc_start: 0.8444 (m) cc_final: 0.8093 (p) REVERT: C 900 MET cc_start: 0.8135 (mtp) cc_final: 0.7858 (mtp) REVERT: C 904 TYR cc_start: 0.7657 (m-10) cc_final: 0.6557 (m-10) REVERT: C 952 VAL cc_start: 0.8053 (t) cc_final: 0.7736 (m) REVERT: C 1055 SER cc_start: 0.8449 (t) cc_final: 0.7982 (p) REVERT: C 1092 GLU cc_start: 0.7426 (pm20) cc_final: 0.7161 (pm20) REVERT: C 1116 THR cc_start: 0.8347 (m) cc_final: 0.7871 (t) outliers start: 90 outliers final: 67 residues processed: 717 average time/residue: 0.5565 time to fit residues: 620.1502 Evaluate side-chains 708 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 638 time to evaluate : 7.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 186 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 257 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 224 optimal weight: 0.6980 chunk 173 optimal weight: 0.3980 chunk 199 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 505 HIS A 556 ASN A1101 HIS B 30 ASN B 218 GLN B 282 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118839 restraints weight = 37417.707| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.46 r_work: 0.3361 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24843 Z= 0.147 Angle : 0.596 11.783 33876 Z= 0.306 Chirality : 0.047 0.445 3910 Planarity : 0.004 0.063 4320 Dihedral : 5.750 59.934 3825 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 3.37 % Allowed : 14.36 % Favored : 82.27 % 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: 0.30 (0.15), residues: 2995 helix: 2.51 (0.20), residues: 645 sheet: 0.59 (0.19), residues: 631 loop : -0.90 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS A 207 PHE 0.028 0.001 PHE A 541 TYR 0.018 0.001 TYR B 396 ARG 0.006 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 27) link_NAG-ASN : angle 3.18024 ( 81) hydrogen bonds : bond 0.04533 ( 956) hydrogen bonds : angle 5.31195 ( 2682) SS BOND : bond 0.00333 ( 37) SS BOND : angle 1.75060 ( 74) covalent geometry : bond 0.00335 (24779) covalent geometry : angle 0.57133 (33721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 662 time to evaluate : 3.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5998 (mmtt) cc_final: 0.4784 (mmmt) REVERT: A 109 THR cc_start: 0.8541 (m) cc_final: 0.8229 (p) REVERT: A 134 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6706 (tm-30) REVERT: A 140 PHE cc_start: 0.7344 (p90) cc_final: 0.7038 (p90) REVERT: A 170 TYR cc_start: 0.7921 (t80) cc_final: 0.7593 (t80) REVERT: A 226 LEU cc_start: 0.8193 (mt) cc_final: 0.7910 (mp) REVERT: A 240 THR cc_start: 0.8292 (m) cc_final: 0.7982 (t) REVERT: A 298 GLU cc_start: 0.7699 (tt0) cc_final: 0.7461 (tt0) REVERT: A 304 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8456 (mttm) REVERT: A 307 THR cc_start: 0.8570 (m) cc_final: 0.8151 (p) REVERT: A 401 VAL cc_start: 0.8967 (m) cc_final: 0.8738 (p) REVERT: A 436 TRP cc_start: 0.7779 (p90) cc_final: 0.7351 (p90) REVERT: A 508 TYR cc_start: 0.7278 (m-80) cc_final: 0.6872 (m-80) REVERT: A 509 ARG cc_start: 0.8251 (mtt180) cc_final: 0.7807 (mtt180) REVERT: A 533 LEU cc_start: 0.8427 (tt) cc_final: 0.8152 (pp) REVERT: A 560 LEU cc_start: 0.8562 (mm) cc_final: 0.8276 (mt) REVERT: A 574 ASP cc_start: 0.8051 (t70) cc_final: 0.7658 (t0) REVERT: A 581 THR cc_start: 0.8105 (m) cc_final: 0.7611 (p) REVERT: A 583 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: A 654 GLU cc_start: 0.8072 (tt0) cc_final: 0.7837 (tt0) REVERT: A 655 TYR cc_start: 0.8477 (t80) cc_final: 0.8115 (t80) REVERT: A 657 ASN cc_start: 0.8761 (m110) cc_final: 0.8533 (m110) REVERT: A 658 ASN cc_start: 0.8154 (p0) cc_final: 0.7801 (p0) REVERT: A 714 ILE cc_start: 0.8611 (mm) cc_final: 0.8297 (mt) REVERT: A 726 ILE cc_start: 0.8592 (mp) cc_final: 0.8363 (mt) REVERT: A 761 THR cc_start: 0.8153 (p) cc_final: 0.7830 (t) REVERT: A 819 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 875 SER cc_start: 0.8416 (p) cc_final: 0.8173 (m) REVERT: A 933 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7906 (mtmm) REVERT: A 934 ILE cc_start: 0.8342 (tt) cc_final: 0.8028 (tt) REVERT: A 935 GLN cc_start: 0.7823 (tt0) cc_final: 0.7596 (tp-100) REVERT: A 974 SER cc_start: 0.8194 (p) cc_final: 0.7920 (t) REVERT: A 979 ASP cc_start: 0.7967 (t70) cc_final: 0.7703 (t70) REVERT: A 1107 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7181 (mtt-85) REVERT: B 46 SER cc_start: 0.8741 (m) cc_final: 0.8433 (p) REVERT: B 102 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7523 (ttm110) REVERT: B 126 VAL cc_start: 0.8148 (p) cc_final: 0.7938 (t) REVERT: B 138 ASP cc_start: 0.7770 (t0) cc_final: 0.7442 (t0) REVERT: B 164 ASN cc_start: 0.6808 (p0) cc_final: 0.6350 (t0) REVERT: B 202 LYS cc_start: 0.8042 (ptpt) cc_final: 0.7124 (ptpp) REVERT: B 235 ILE cc_start: 0.8118 (mt) cc_final: 0.7889 (mm) REVERT: B 236 THR cc_start: 0.8793 (t) cc_final: 0.8504 (p) REVERT: B 275 PHE cc_start: 0.8575 (m-80) cc_final: 0.8241 (m-80) REVERT: B 339 HIS cc_start: 0.7223 (t70) cc_final: 0.6754 (t70) REVERT: B 533 LEU cc_start: 0.8701 (mt) cc_final: 0.8353 (mt) REVERT: B 557 LYS cc_start: 0.8101 (mttp) cc_final: 0.7882 (mttp) REVERT: B 646 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8189 (ttp80) REVERT: B 710 ASN cc_start: 0.8227 (p0) cc_final: 0.7930 (p0) REVERT: B 776 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7817 (ttpt) REVERT: B 811 LYS cc_start: 0.7955 (ptpt) cc_final: 0.7453 (mtmm) REVERT: B 814 LYS cc_start: 0.7574 (mmtt) cc_final: 0.7080 (mmtt) REVERT: B 935 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7880 (tt0) REVERT: B 960 ASN cc_start: 0.8367 (t0) cc_final: 0.8026 (m-40) REVERT: B 964 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8143 (mtpp) REVERT: B 1028 LYS cc_start: 0.8662 (mmtp) cc_final: 0.8447 (mttp) REVERT: B 1072 GLU cc_start: 0.8167 (pm20) cc_final: 0.7955 (pm20) REVERT: B 1138 TYR cc_start: 0.7876 (t80) cc_final: 0.7569 (t80) REVERT: C 160 TYR cc_start: 0.7088 (p90) cc_final: 0.6715 (p90) REVERT: C 190 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7845 (mtt-85) REVERT: C 200 TYR cc_start: 0.7612 (m-80) cc_final: 0.6523 (m-80) REVERT: C 241 LEU cc_start: 0.7988 (mt) cc_final: 0.7717 (mp) REVERT: C 281 GLU cc_start: 0.8089 (pm20) cc_final: 0.7704 (pm20) REVERT: C 297 SER cc_start: 0.8422 (m) cc_final: 0.8172 (m) REVERT: C 302 THR cc_start: 0.8629 (t) cc_final: 0.8250 (p) REVERT: C 305 SER cc_start: 0.8982 (t) cc_final: 0.8604 (p) REVERT: C 307 THR cc_start: 0.8881 (t) cc_final: 0.8522 (p) REVERT: C 357 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: C 375 PHE cc_start: 0.7927 (t80) cc_final: 0.7719 (t80) REVERT: C 382 VAL cc_start: 0.8965 (t) cc_final: 0.8704 (m) REVERT: C 392 PHE cc_start: 0.7348 (m-80) cc_final: 0.7124 (m-80) REVERT: C 453 TYR cc_start: 0.7079 (p90) cc_final: 0.6685 (p90) REVERT: C 462 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7601 (mmtt) REVERT: C 528 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8208 (mtpp) REVERT: C 551 VAL cc_start: 0.9101 (p) cc_final: 0.8817 (t) REVERT: C 578 ASP cc_start: 0.8271 (t0) cc_final: 0.8004 (t0) REVERT: C 698 SER cc_start: 0.8593 (t) cc_final: 0.7984 (p) REVERT: C 737 ASP cc_start: 0.8251 (t0) cc_final: 0.8046 (t0) REVERT: C 740 MET cc_start: 0.8144 (ttt) cc_final: 0.7856 (tpp) REVERT: C 780 GLU cc_start: 0.8101 (tt0) cc_final: 0.7811 (tt0) REVERT: C 820 ASP cc_start: 0.7812 (t0) cc_final: 0.7484 (m-30) REVERT: C 824 ASN cc_start: 0.8155 (m-40) cc_final: 0.7859 (m110) REVERT: C 859 THR cc_start: 0.8429 (m) cc_final: 0.8089 (p) REVERT: C 900 MET cc_start: 0.8087 (mtp) cc_final: 0.7803 (mtp) REVERT: C 904 TYR cc_start: 0.7623 (m-10) cc_final: 0.6551 (m-10) REVERT: C 952 VAL cc_start: 0.8039 (t) cc_final: 0.7720 (m) REVERT: C 1055 SER cc_start: 0.8439 (t) cc_final: 0.8040 (p) REVERT: C 1092 GLU cc_start: 0.7423 (pm20) cc_final: 0.7132 (pm20) REVERT: C 1116 THR cc_start: 0.8314 (m) cc_final: 0.7866 (t) outliers start: 90 outliers final: 64 residues processed: 706 average time/residue: 0.4412 time to fit residues: 487.5903 Evaluate side-chains 698 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 633 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 57 optimal weight: 0.3980 chunk 272 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 155 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 784 GLN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118625 restraints weight = 37113.207| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.48 r_work: 0.3356 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24843 Z= 0.155 Angle : 0.599 11.928 33876 Z= 0.307 Chirality : 0.047 0.439 3910 Planarity : 0.004 0.071 4320 Dihedral : 5.518 55.518 3825 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 3.41 % Allowed : 15.59 % Favored : 81.00 % 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: 0.25 (0.15), residues: 2995 helix: 2.39 (0.20), residues: 659 sheet: 0.52 (0.19), residues: 642 loop : -0.91 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.004 0.001 HIS A 207 PHE 0.028 0.002 PHE A 541 TYR 0.018 0.001 TYR B 396 ARG 0.008 0.000 ARG B1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 27) link_NAG-ASN : angle 3.10500 ( 81) hydrogen bonds : bond 0.04526 ( 956) hydrogen bonds : angle 5.28599 ( 2682) SS BOND : bond 0.00398 ( 37) SS BOND : angle 1.78841 ( 74) covalent geometry : bond 0.00355 (24779) covalent geometry : angle 0.57502 (33721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 640 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5963 (mmtt) cc_final: 0.4673 (mmmt) REVERT: A 134 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6668 (tm-30) REVERT: A 140 PHE cc_start: 0.7366 (p90) cc_final: 0.7033 (p90) REVERT: A 170 TYR cc_start: 0.8000 (t80) cc_final: 0.7667 (t80) REVERT: A 238 PHE cc_start: 0.8273 (p90) cc_final: 0.7548 (p90) REVERT: A 240 THR cc_start: 0.8289 (m) cc_final: 0.8021 (t) REVERT: A 298 GLU cc_start: 0.7743 (tt0) cc_final: 0.7455 (tt0) REVERT: A 304 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8444 (mttm) REVERT: A 307 THR cc_start: 0.8539 (m) cc_final: 0.8121 (p) REVERT: A 401 VAL cc_start: 0.8968 (m) cc_final: 0.8738 (p) REVERT: A 436 TRP cc_start: 0.7773 (p90) cc_final: 0.7503 (p90) REVERT: A 493 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 508 TYR cc_start: 0.7294 (m-80) cc_final: 0.6882 (m-80) REVERT: A 560 LEU cc_start: 0.8615 (mm) cc_final: 0.8328 (mt) REVERT: A 574 ASP cc_start: 0.8038 (t70) cc_final: 0.7641 (t0) REVERT: A 581 THR cc_start: 0.8103 (m) cc_final: 0.7550 (p) REVERT: A 583 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: A 645 THR cc_start: 0.8467 (t) cc_final: 0.8165 (p) REVERT: A 654 GLU cc_start: 0.8088 (tt0) cc_final: 0.7840 (tt0) REVERT: A 655 TYR cc_start: 0.8482 (t80) cc_final: 0.8131 (t80) REVERT: A 657 ASN cc_start: 0.8760 (m110) cc_final: 0.8542 (m110) REVERT: A 658 ASN cc_start: 0.8162 (p0) cc_final: 0.7793 (p0) REVERT: A 726 ILE cc_start: 0.8584 (mp) cc_final: 0.8359 (mt) REVERT: A 761 THR cc_start: 0.8178 (p) cc_final: 0.7818 (t) REVERT: A 776 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7980 (ttmm) REVERT: A 819 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7425 (mt-10) REVERT: A 875 SER cc_start: 0.8421 (p) cc_final: 0.8168 (m) REVERT: A 933 LYS cc_start: 0.8336 (ttpp) cc_final: 0.8115 (mtpp) REVERT: A 934 ILE cc_start: 0.8304 (tt) cc_final: 0.7999 (tt) REVERT: A 935 GLN cc_start: 0.7810 (tt0) cc_final: 0.7567 (tp-100) REVERT: A 974 SER cc_start: 0.8236 (p) cc_final: 0.7957 (t) REVERT: A 979 ASP cc_start: 0.7987 (t70) cc_final: 0.7715 (t70) REVERT: A 1107 ARG cc_start: 0.7610 (mtt-85) cc_final: 0.7241 (mtt-85) REVERT: B 46 SER cc_start: 0.8755 (m) cc_final: 0.8449 (p) REVERT: B 102 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7539 (ttm110) REVERT: B 126 VAL cc_start: 0.8216 (p) cc_final: 0.7989 (t) REVERT: B 138 ASP cc_start: 0.7748 (t0) cc_final: 0.7430 (t0) REVERT: B 164 ASN cc_start: 0.6807 (p0) cc_final: 0.6389 (t0) REVERT: B 202 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7061 (ptpp) REVERT: B 235 ILE cc_start: 0.8132 (mt) cc_final: 0.7899 (mm) REVERT: B 236 THR cc_start: 0.8794 (t) cc_final: 0.8499 (p) REVERT: B 275 PHE cc_start: 0.8594 (m-80) cc_final: 0.8232 (m-80) REVERT: B 339 HIS cc_start: 0.7186 (t70) cc_final: 0.6716 (t70) REVERT: B 557 LYS cc_start: 0.8098 (mttp) cc_final: 0.7885 (mttp) REVERT: B 577 ARG cc_start: 0.8711 (ttm170) cc_final: 0.8509 (ptp-170) REVERT: B 646 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8213 (ttp80) REVERT: B 710 ASN cc_start: 0.8265 (p0) cc_final: 0.7933 (p0) REVERT: B 772 VAL cc_start: 0.8323 (t) cc_final: 0.8071 (m) REVERT: B 776 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7790 (ttpt) REVERT: B 811 LYS cc_start: 0.7988 (ptpt) cc_final: 0.7520 (mtmm) REVERT: B 814 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7056 (mmtt) REVERT: B 904 TYR cc_start: 0.7592 (m-10) cc_final: 0.7232 (m-10) REVERT: B 935 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7887 (tt0) REVERT: B 960 ASN cc_start: 0.8405 (t0) cc_final: 0.8048 (m-40) REVERT: B 964 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8150 (mtpp) REVERT: B 966 LEU cc_start: 0.8976 (tp) cc_final: 0.8551 (tt) REVERT: B 979 ASP cc_start: 0.8210 (t70) cc_final: 0.7793 (t0) REVERT: B 1028 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8424 (mttp) REVERT: B 1045 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8383 (mtmt) REVERT: B 1138 TYR cc_start: 0.7915 (t80) cc_final: 0.7596 (t80) REVERT: C 160 TYR cc_start: 0.7111 (p90) cc_final: 0.6739 (p90) REVERT: C 191 GLU cc_start: 0.7630 (mp0) cc_final: 0.7233 (mp0) REVERT: C 200 TYR cc_start: 0.7660 (m-80) cc_final: 0.6557 (m-80) REVERT: C 241 LEU cc_start: 0.7974 (mt) cc_final: 0.7703 (mp) REVERT: C 266 TYR cc_start: 0.7513 (m-80) cc_final: 0.7045 (m-80) REVERT: C 281 GLU cc_start: 0.8084 (pm20) cc_final: 0.7727 (pm20) REVERT: C 297 SER cc_start: 0.8392 (m) cc_final: 0.8121 (m) REVERT: C 302 THR cc_start: 0.8629 (t) cc_final: 0.8234 (p) REVERT: C 305 SER cc_start: 0.8979 (t) cc_final: 0.8607 (p) REVERT: C 307 THR cc_start: 0.8862 (t) cc_final: 0.8492 (p) REVERT: C 310 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8413 (tttt) REVERT: C 375 PHE cc_start: 0.7975 (t80) cc_final: 0.7746 (t80) REVERT: C 382 VAL cc_start: 0.8948 (t) cc_final: 0.8673 (m) REVERT: C 392 PHE cc_start: 0.7358 (m-80) cc_final: 0.7140 (m-80) REVERT: C 453 TYR cc_start: 0.7080 (p90) cc_final: 0.6673 (p90) REVERT: C 462 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7621 (mmtt) REVERT: C 528 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8222 (mtpp) REVERT: C 551 VAL cc_start: 0.9076 (p) cc_final: 0.8791 (t) REVERT: C 578 ASP cc_start: 0.8290 (t0) cc_final: 0.8009 (t0) REVERT: C 698 SER cc_start: 0.8598 (t) cc_final: 0.7913 (p) REVERT: C 737 ASP cc_start: 0.8272 (t0) cc_final: 0.8048 (t0) REVERT: C 740 MET cc_start: 0.8162 (ttt) cc_final: 0.7876 (tpp) REVERT: C 747 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.7185 (p) REVERT: C 780 GLU cc_start: 0.8047 (tt0) cc_final: 0.7761 (tt0) REVERT: C 820 ASP cc_start: 0.7787 (t0) cc_final: 0.7492 (t70) REVERT: C 824 ASN cc_start: 0.8173 (m-40) cc_final: 0.7816 (m110) REVERT: C 859 THR cc_start: 0.8470 (m) cc_final: 0.8084 (p) REVERT: C 900 MET cc_start: 0.8089 (mtp) cc_final: 0.7796 (mtp) REVERT: C 904 TYR cc_start: 0.7613 (m-10) cc_final: 0.6546 (m-10) REVERT: C 952 VAL cc_start: 0.8009 (t) cc_final: 0.7698 (m) REVERT: C 1092 GLU cc_start: 0.7408 (pm20) cc_final: 0.7092 (pm20) REVERT: C 1116 THR cc_start: 0.8270 (m) cc_final: 0.7818 (t) outliers start: 91 outliers final: 74 residues processed: 686 average time/residue: 0.4827 time to fit residues: 515.2406 Evaluate side-chains 712 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 636 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 183 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 49 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 196 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A1101 HIS B 30 ASN B 66 HIS B 218 GLN B 787 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118620 restraints weight = 37334.756| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.45 r_work: 0.3356 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24843 Z= 0.168 Angle : 0.611 12.450 33876 Z= 0.313 Chirality : 0.047 0.441 3910 Planarity : 0.004 0.060 4320 Dihedral : 5.394 54.802 3825 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 3.75 % Allowed : 15.93 % Favored : 80.32 % 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: 0.20 (0.15), residues: 2995 helix: 2.35 (0.20), residues: 654 sheet: 0.49 (0.19), residues: 648 loop : -0.94 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS B 207 PHE 0.028 0.002 PHE A 541 TYR 0.019 0.001 TYR B 660 ARG 0.012 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 27) link_NAG-ASN : angle 3.15734 ( 81) hydrogen bonds : bond 0.04602 ( 956) hydrogen bonds : angle 5.29676 ( 2682) SS BOND : bond 0.00392 ( 37) SS BOND : angle 2.05672 ( 74) covalent geometry : bond 0.00386 (24779) covalent geometry : angle 0.58427 (33721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 653 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 140 PHE cc_start: 0.7349 (p90) cc_final: 0.7024 (p90) REVERT: A 170 TYR cc_start: 0.7992 (t80) cc_final: 0.7764 (t80) REVERT: A 238 PHE cc_start: 0.8286 (p90) cc_final: 0.7633 (p90) REVERT: A 240 THR cc_start: 0.8262 (m) cc_final: 0.8040 (t) REVERT: A 298 GLU cc_start: 0.7703 (tt0) cc_final: 0.7443 (tt0) REVERT: A 304 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8456 (mttm) REVERT: A 307 THR cc_start: 0.8547 (m) cc_final: 0.8120 (p) REVERT: A 401 VAL cc_start: 0.8945 (m) cc_final: 0.8743 (p) REVERT: A 436 TRP cc_start: 0.7839 (p90) cc_final: 0.7521 (p90) REVERT: A 464 PHE cc_start: 0.8250 (m-80) cc_final: 0.8017 (m-80) REVERT: A 493 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 508 TYR cc_start: 0.7347 (m-80) cc_final: 0.6914 (m-80) REVERT: A 560 LEU cc_start: 0.8685 (mm) cc_final: 0.8374 (mt) REVERT: A 574 ASP cc_start: 0.8033 (t70) cc_final: 0.7617 (t0) REVERT: A 581 THR cc_start: 0.8117 (m) cc_final: 0.7515 (p) REVERT: A 583 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: A 654 GLU cc_start: 0.8105 (tt0) cc_final: 0.7874 (tt0) REVERT: A 655 TYR cc_start: 0.8481 (t80) cc_final: 0.8114 (t80) REVERT: A 657 ASN cc_start: 0.8780 (m110) cc_final: 0.8554 (m110) REVERT: A 658 ASN cc_start: 0.8171 (p0) cc_final: 0.7809 (p0) REVERT: A 726 ILE cc_start: 0.8591 (mp) cc_final: 0.8378 (mt) REVERT: A 761 THR cc_start: 0.8134 (p) cc_final: 0.7845 (t) REVERT: A 763 LEU cc_start: 0.8377 (mt) cc_final: 0.8173 (mp) REVERT: A 819 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 875 SER cc_start: 0.8447 (p) cc_final: 0.8186 (m) REVERT: A 934 ILE cc_start: 0.8337 (tt) cc_final: 0.8032 (tt) REVERT: A 935 GLN cc_start: 0.7806 (tt0) cc_final: 0.7570 (tp-100) REVERT: A 1028 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8283 (mttp) REVERT: A 1107 ARG cc_start: 0.7599 (mtt-85) cc_final: 0.7214 (mtt-85) REVERT: B 126 VAL cc_start: 0.8251 (p) cc_final: 0.8046 (t) REVERT: B 138 ASP cc_start: 0.7749 (t0) cc_final: 0.7457 (t0) REVERT: B 164 ASN cc_start: 0.6748 (p0) cc_final: 0.6402 (t0) REVERT: B 202 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7056 (ptpp) REVERT: B 235 ILE cc_start: 0.8107 (mt) cc_final: 0.7883 (mm) REVERT: B 236 THR cc_start: 0.8792 (t) cc_final: 0.8504 (p) REVERT: B 275 PHE cc_start: 0.8593 (m-80) cc_final: 0.8225 (m-80) REVERT: B 339 HIS cc_start: 0.7088 (t70) cc_final: 0.6635 (t70) REVERT: B 465 GLU cc_start: 0.7860 (tp30) cc_final: 0.7555 (tp30) REVERT: B 537 LYS cc_start: 0.8339 (mtpp) cc_final: 0.8050 (mtpt) REVERT: B 557 LYS cc_start: 0.8054 (mttp) cc_final: 0.7846 (mttp) REVERT: B 583 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 646 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8200 (ttp80) REVERT: B 710 ASN cc_start: 0.8270 (p0) cc_final: 0.7923 (p0) REVERT: B 762 GLN cc_start: 0.8072 (mt0) cc_final: 0.7850 (mt0) REVERT: B 772 VAL cc_start: 0.8367 (t) cc_final: 0.8140 (m) REVERT: B 776 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7840 (ttpt) REVERT: B 811 LYS cc_start: 0.8027 (ptpt) cc_final: 0.7548 (mtmm) REVERT: B 814 LYS cc_start: 0.7591 (mmtt) cc_final: 0.7096 (mmtt) REVERT: B 935 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7858 (tt0) REVERT: B 960 ASN cc_start: 0.8383 (t0) cc_final: 0.8031 (m-40) REVERT: B 964 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8147 (mtpp) REVERT: B 966 LEU cc_start: 0.8991 (tp) cc_final: 0.8778 (tt) REVERT: B 979 ASP cc_start: 0.8208 (t70) cc_final: 0.7801 (t0) REVERT: B 1028 LYS cc_start: 0.8656 (mmtp) cc_final: 0.8331 (mmtp) REVERT: B 1045 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8382 (mtmt) REVERT: B 1138 TYR cc_start: 0.7948 (t80) cc_final: 0.7608 (t80) REVERT: C 160 TYR cc_start: 0.7158 (p90) cc_final: 0.6777 (p90) REVERT: C 190 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7831 (mtt-85) REVERT: C 200 TYR cc_start: 0.7680 (m-80) cc_final: 0.6618 (m-80) REVERT: C 241 LEU cc_start: 0.7983 (mt) cc_final: 0.7749 (mp) REVERT: C 266 TYR cc_start: 0.7499 (m-80) cc_final: 0.7108 (m-80) REVERT: C 271 GLN cc_start: 0.8360 (mt0) cc_final: 0.8033 (mt0) REVERT: C 281 GLU cc_start: 0.8066 (pm20) cc_final: 0.7747 (pm20) REVERT: C 297 SER cc_start: 0.8388 (m) cc_final: 0.8102 (m) REVERT: C 302 THR cc_start: 0.8629 (t) cc_final: 0.8242 (p) REVERT: C 305 SER cc_start: 0.8994 (t) cc_final: 0.8613 (p) REVERT: C 307 THR cc_start: 0.8858 (t) cc_final: 0.8484 (p) REVERT: C 310 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8301 (ttpt) REVERT: C 375 PHE cc_start: 0.8027 (t80) cc_final: 0.7824 (t80) REVERT: C 382 VAL cc_start: 0.8930 (t) cc_final: 0.8685 (m) REVERT: C 453 TYR cc_start: 0.7130 (p90) cc_final: 0.6726 (p90) REVERT: C 462 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7638 (mmtt) REVERT: C 528 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8185 (mtpp) REVERT: C 578 ASP cc_start: 0.8237 (t0) cc_final: 0.7959 (t0) REVERT: C 663 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6067 (t70) REVERT: C 698 SER cc_start: 0.8604 (t) cc_final: 0.7932 (p) REVERT: C 737 ASP cc_start: 0.8270 (t0) cc_final: 0.8046 (t0) REVERT: C 740 MET cc_start: 0.8113 (ttt) cc_final: 0.7817 (tpp) REVERT: C 747 THR cc_start: 0.7452 (OUTLIER) cc_final: 0.7234 (p) REVERT: C 780 GLU cc_start: 0.8037 (tt0) cc_final: 0.7771 (tt0) REVERT: C 820 ASP cc_start: 0.7826 (t0) cc_final: 0.7521 (t70) REVERT: C 824 ASN cc_start: 0.8174 (m-40) cc_final: 0.7810 (m110) REVERT: C 856 ASN cc_start: 0.8005 (t0) cc_final: 0.7796 (t0) REVERT: C 859 THR cc_start: 0.8499 (m) cc_final: 0.8092 (p) REVERT: C 900 MET cc_start: 0.8115 (mtp) cc_final: 0.7814 (mtp) REVERT: C 904 TYR cc_start: 0.7624 (m-10) cc_final: 0.6503 (m-10) REVERT: C 952 VAL cc_start: 0.8037 (t) cc_final: 0.7731 (m) REVERT: C 1012 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8170 (mt) REVERT: C 1073 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7949 (mtpt) REVERT: C 1092 GLU cc_start: 0.7435 (pm20) cc_final: 0.7135 (pm20) REVERT: C 1116 THR cc_start: 0.8293 (m) cc_final: 0.7844 (t) outliers start: 100 outliers final: 80 residues processed: 701 average time/residue: 0.3736 time to fit residues: 404.2728 Evaluate side-chains 715 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 631 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 218 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 175 optimal weight: 0.3980 chunk 249 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 211 optimal weight: 0.0980 chunk 289 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 30 ASN B 218 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119621 restraints weight = 37261.547| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.48 r_work: 0.3369 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24843 Z= 0.128 Angle : 0.596 12.282 33876 Z= 0.306 Chirality : 0.046 0.438 3910 Planarity : 0.004 0.081 4320 Dihedral : 5.220 55.060 3825 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 3.37 % Allowed : 16.87 % Favored : 79.76 % 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: 0.30 (0.15), residues: 2995 helix: 2.37 (0.20), residues: 659 sheet: 0.60 (0.19), residues: 640 loop : -0.88 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 PHE 0.029 0.001 PHE A 541 TYR 0.022 0.001 TYR B 660 ARG 0.008 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 27) link_NAG-ASN : angle 3.06867 ( 81) hydrogen bonds : bond 0.04300 ( 956) hydrogen bonds : angle 5.22993 ( 2682) SS BOND : bond 0.00461 ( 37) SS BOND : angle 2.03925 ( 74) covalent geometry : bond 0.00292 (24779) covalent geometry : angle 0.57049 (33721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 638 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5918 (mmtt) cc_final: 0.4685 (mmmt) REVERT: A 113 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8107 (mppt) REVERT: A 134 GLN cc_start: 0.7112 (tm-30) cc_final: 0.6754 (tm-30) REVERT: A 140 PHE cc_start: 0.7344 (p90) cc_final: 0.7004 (p90) REVERT: A 170 TYR cc_start: 0.7972 (t80) cc_final: 0.7706 (t80) REVERT: A 238 PHE cc_start: 0.8280 (p90) cc_final: 0.7612 (p90) REVERT: A 240 THR cc_start: 0.8281 (m) cc_final: 0.8064 (t) REVERT: A 298 GLU cc_start: 0.7738 (tt0) cc_final: 0.7456 (tt0) REVERT: A 304 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8432 (mttm) REVERT: A 307 THR cc_start: 0.8517 (m) cc_final: 0.8107 (p) REVERT: A 401 VAL cc_start: 0.8947 (m) cc_final: 0.8730 (p) REVERT: A 436 TRP cc_start: 0.7788 (p90) cc_final: 0.7465 (p90) REVERT: A 493 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 508 TYR cc_start: 0.7314 (m-80) cc_final: 0.6893 (m-80) REVERT: A 560 LEU cc_start: 0.8688 (mm) cc_final: 0.8368 (mt) REVERT: A 574 ASP cc_start: 0.8024 (t70) cc_final: 0.7603 (t0) REVERT: A 581 THR cc_start: 0.8093 (m) cc_final: 0.7491 (p) REVERT: A 583 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: A 654 GLU cc_start: 0.8106 (tt0) cc_final: 0.7861 (tt0) REVERT: A 655 TYR cc_start: 0.8470 (t80) cc_final: 0.8063 (t80) REVERT: A 657 ASN cc_start: 0.8771 (m110) cc_final: 0.8548 (m110) REVERT: A 658 ASN cc_start: 0.8157 (p0) cc_final: 0.7838 (p0) REVERT: A 726 ILE cc_start: 0.8598 (mp) cc_final: 0.8378 (mt) REVERT: A 761 THR cc_start: 0.8087 (p) cc_final: 0.7767 (t) REVERT: A 763 LEU cc_start: 0.8362 (mt) cc_final: 0.8156 (mp) REVERT: A 776 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7936 (ttmm) REVERT: A 819 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 869 MET cc_start: 0.8260 (mtt) cc_final: 0.8051 (mtp) REVERT: A 875 SER cc_start: 0.8447 (p) cc_final: 0.8171 (m) REVERT: A 933 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8132 (mtpp) REVERT: A 934 ILE cc_start: 0.8290 (tt) cc_final: 0.7986 (tt) REVERT: A 935 GLN cc_start: 0.7800 (tt0) cc_final: 0.7521 (tp-100) REVERT: A 979 ASP cc_start: 0.7924 (t70) cc_final: 0.7646 (t70) REVERT: A 1107 ARG cc_start: 0.7615 (mtt-85) cc_final: 0.7219 (mtt-85) REVERT: B 126 VAL cc_start: 0.8276 (p) cc_final: 0.8060 (t) REVERT: B 138 ASP cc_start: 0.7763 (t0) cc_final: 0.7481 (t0) REVERT: B 164 ASN cc_start: 0.6655 (p0) cc_final: 0.6379 (t0) REVERT: B 202 LYS cc_start: 0.7988 (ptpt) cc_final: 0.6911 (ptpp) REVERT: B 235 ILE cc_start: 0.8097 (mt) cc_final: 0.7870 (mm) REVERT: B 236 THR cc_start: 0.8796 (t) cc_final: 0.8509 (p) REVERT: B 275 PHE cc_start: 0.8587 (m-80) cc_final: 0.8232 (m-80) REVERT: B 310 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8249 (tttt) REVERT: B 339 HIS cc_start: 0.7050 (t70) cc_final: 0.6627 (t70) REVERT: B 396 TYR cc_start: 0.7521 (m-80) cc_final: 0.7268 (m-80) REVERT: B 423 TYR cc_start: 0.8150 (t80) cc_final: 0.7373 (t80) REVERT: B 429 PHE cc_start: 0.7409 (t80) cc_final: 0.7160 (t80) REVERT: B 537 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8063 (mtpp) REVERT: B 557 LYS cc_start: 0.8058 (mttp) cc_final: 0.7830 (mttp) REVERT: B 577 ARG cc_start: 0.8684 (ttm170) cc_final: 0.8452 (ptp-170) REVERT: B 583 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 646 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8196 (ttp80) REVERT: B 762 GLN cc_start: 0.8048 (mt0) cc_final: 0.7815 (mt0) REVERT: B 772 VAL cc_start: 0.8316 (t) cc_final: 0.8057 (m) REVERT: B 776 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7784 (ttpt) REVERT: B 811 LYS cc_start: 0.7998 (ptpt) cc_final: 0.7537 (mtmm) REVERT: B 814 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7065 (mmtt) REVERT: B 935 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7853 (tt0) REVERT: B 960 ASN cc_start: 0.8403 (t0) cc_final: 0.8019 (m-40) REVERT: B 964 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8134 (mtpp) REVERT: B 979 ASP cc_start: 0.8188 (t70) cc_final: 0.7783 (t0) REVERT: B 1045 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8389 (mtmt) REVERT: B 1138 TYR cc_start: 0.7907 (t80) cc_final: 0.7597 (t80) REVERT: C 160 TYR cc_start: 0.7146 (p90) cc_final: 0.6821 (p90) REVERT: C 190 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7972 (mtt-85) REVERT: C 191 GLU cc_start: 0.7614 (mp0) cc_final: 0.7221 (mp0) REVERT: C 200 TYR cc_start: 0.7631 (m-80) cc_final: 0.6513 (m-80) REVERT: C 241 LEU cc_start: 0.7935 (mt) cc_final: 0.7682 (mp) REVERT: C 266 TYR cc_start: 0.7446 (m-80) cc_final: 0.7056 (m-80) REVERT: C 271 GLN cc_start: 0.8366 (mt0) cc_final: 0.7998 (mt0) REVERT: C 281 GLU cc_start: 0.8088 (pm20) cc_final: 0.7730 (pm20) REVERT: C 297 SER cc_start: 0.8347 (m) cc_final: 0.8067 (m) REVERT: C 302 THR cc_start: 0.8612 (t) cc_final: 0.8228 (p) REVERT: C 305 SER cc_start: 0.8986 (t) cc_final: 0.8634 (p) REVERT: C 310 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8395 (ttpt) REVERT: C 375 PHE cc_start: 0.8056 (t80) cc_final: 0.7834 (t80) REVERT: C 382 VAL cc_start: 0.8915 (t) cc_final: 0.8672 (m) REVERT: C 453 TYR cc_start: 0.7094 (p90) cc_final: 0.6498 (p90) REVERT: C 462 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7636 (mmtt) REVERT: C 493 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7311 (tm-30) REVERT: C 528 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8218 (mtpp) REVERT: C 578 ASP cc_start: 0.8238 (t0) cc_final: 0.7940 (t0) REVERT: C 698 SER cc_start: 0.8566 (t) cc_final: 0.7866 (p) REVERT: C 725 GLU cc_start: 0.7910 (tt0) cc_final: 0.7658 (tt0) REVERT: C 737 ASP cc_start: 0.8276 (t0) cc_final: 0.8041 (t0) REVERT: C 740 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7803 (tpp) REVERT: C 747 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7173 (p) REVERT: C 780 GLU cc_start: 0.8005 (tt0) cc_final: 0.7728 (tt0) REVERT: C 819 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6958 (mt-10) REVERT: C 820 ASP cc_start: 0.7795 (t0) cc_final: 0.7318 (m-30) REVERT: C 824 ASN cc_start: 0.8154 (m-40) cc_final: 0.7855 (m110) REVERT: C 859 THR cc_start: 0.8489 (m) cc_final: 0.8062 (p) REVERT: C 900 MET cc_start: 0.8121 (mtp) cc_final: 0.7833 (mtp) REVERT: C 904 TYR cc_start: 0.7630 (m-10) cc_final: 0.6575 (m-10) REVERT: C 952 VAL cc_start: 0.7970 (t) cc_final: 0.7666 (m) REVERT: C 1012 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8002 (mp) REVERT: C 1055 SER cc_start: 0.8540 (t) cc_final: 0.7928 (p) REVERT: C 1073 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7919 (mtpt) REVERT: C 1092 GLU cc_start: 0.7445 (pm20) cc_final: 0.7144 (pm20) REVERT: C 1116 THR cc_start: 0.8254 (m) cc_final: 0.7774 (t) outliers start: 90 outliers final: 74 residues processed: 686 average time/residue: 0.3749 time to fit residues: 397.7047 Evaluate side-chains 715 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 637 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 126 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 155 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.0010 chunk 265 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A1101 HIS B 30 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 787 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 784 GLN C 935 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119472 restraints weight = 37292.751| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.45 r_work: 0.3372 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24843 Z= 0.141 Angle : 0.602 12.490 33876 Z= 0.309 Chirality : 0.046 0.435 3910 Planarity : 0.004 0.085 4320 Dihedral : 5.158 54.275 3825 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 3.15 % Allowed : 17.43 % Favored : 79.42 % 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: 0.28 (0.15), residues: 2995 helix: 2.38 (0.20), residues: 653 sheet: 0.59 (0.19), residues: 642 loop : -0.90 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS B 207 PHE 0.028 0.001 PHE A 541 TYR 0.019 0.001 TYR B 660 ARG 0.007 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 27) link_NAG-ASN : angle 3.03667 ( 81) hydrogen bonds : bond 0.04351 ( 956) hydrogen bonds : angle 5.21972 ( 2682) SS BOND : bond 0.00356 ( 37) SS BOND : angle 1.92831 ( 74) covalent geometry : bond 0.00324 (24779) covalent geometry : angle 0.57734 (33721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 640 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.5948 (mmtt) cc_final: 0.4712 (mmmt) REVERT: A 113 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8110 (mppt) REVERT: A 134 GLN cc_start: 0.7033 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 140 PHE cc_start: 0.7301 (p90) cc_final: 0.7010 (p90) REVERT: A 238 PHE cc_start: 0.8301 (p90) cc_final: 0.7690 (p90) REVERT: A 298 GLU cc_start: 0.7712 (tt0) cc_final: 0.7437 (tt0) REVERT: A 304 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8425 (mttm) REVERT: A 307 THR cc_start: 0.8509 (m) cc_final: 0.8104 (p) REVERT: A 375 PHE cc_start: 0.8300 (t80) cc_final: 0.7834 (t80) REVERT: A 436 TRP cc_start: 0.7800 (p90) cc_final: 0.7480 (p90) REVERT: A 493 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7578 (tm-30) REVERT: A 508 TYR cc_start: 0.7297 (m-80) cc_final: 0.6901 (m-80) REVERT: A 560 LEU cc_start: 0.8723 (mm) cc_final: 0.8407 (mt) REVERT: A 574 ASP cc_start: 0.8033 (t70) cc_final: 0.7611 (t0) REVERT: A 581 THR cc_start: 0.8112 (m) cc_final: 0.7540 (p) REVERT: A 583 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: A 654 GLU cc_start: 0.8086 (tt0) cc_final: 0.7848 (tt0) REVERT: A 655 TYR cc_start: 0.8455 (t80) cc_final: 0.8033 (t80) REVERT: A 657 ASN cc_start: 0.8759 (m110) cc_final: 0.8532 (m110) REVERT: A 658 ASN cc_start: 0.8167 (p0) cc_final: 0.7858 (p0) REVERT: A 726 ILE cc_start: 0.8598 (mp) cc_final: 0.8370 (mt) REVERT: A 761 THR cc_start: 0.8081 (p) cc_final: 0.7771 (t) REVERT: A 763 LEU cc_start: 0.8374 (mt) cc_final: 0.8156 (mp) REVERT: A 819 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 875 SER cc_start: 0.8463 (p) cc_final: 0.8169 (m) REVERT: A 933 LYS cc_start: 0.8381 (ttpp) cc_final: 0.8165 (mtpp) REVERT: A 934 ILE cc_start: 0.8333 (tt) cc_final: 0.8029 (tt) REVERT: A 935 GLN cc_start: 0.7795 (tt0) cc_final: 0.7555 (tp-100) REVERT: A 977 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8096 (mp) REVERT: A 979 ASP cc_start: 0.7898 (t70) cc_final: 0.7645 (t70) REVERT: A 1107 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7231 (mtt-85) REVERT: B 126 VAL cc_start: 0.8287 (p) cc_final: 0.8081 (t) REVERT: B 138 ASP cc_start: 0.7735 (t0) cc_final: 0.7482 (t0) REVERT: B 164 ASN cc_start: 0.6635 (p0) cc_final: 0.6414 (t0) REVERT: B 202 LYS cc_start: 0.7993 (ptpt) cc_final: 0.7326 (ptpp) REVERT: B 235 ILE cc_start: 0.8091 (mt) cc_final: 0.7881 (mm) REVERT: B 236 THR cc_start: 0.8784 (t) cc_final: 0.8504 (p) REVERT: B 275 PHE cc_start: 0.8589 (m-80) cc_final: 0.8227 (m-80) REVERT: B 310 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8228 (tttt) REVERT: B 324 GLU cc_start: 0.8123 (pm20) cc_final: 0.7789 (pm20) REVERT: B 339 HIS cc_start: 0.6989 (t70) cc_final: 0.6598 (t70) REVERT: B 396 TYR cc_start: 0.7516 (m-80) cc_final: 0.7258 (m-80) REVERT: B 423 TYR cc_start: 0.8199 (t80) cc_final: 0.7445 (t80) REVERT: B 429 PHE cc_start: 0.7393 (t80) cc_final: 0.7153 (t80) REVERT: B 537 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8085 (mtpp) REVERT: B 577 ARG cc_start: 0.8673 (ttm170) cc_final: 0.8394 (ptp-170) REVERT: B 646 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8169 (ttp80) REVERT: B 702 GLU cc_start: 0.7754 (tp30) cc_final: 0.7475 (tp30) REVERT: B 762 GLN cc_start: 0.8031 (mt0) cc_final: 0.7815 (mt0) REVERT: B 772 VAL cc_start: 0.8336 (t) cc_final: 0.8085 (m) REVERT: B 776 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7809 (ttpt) REVERT: B 779 GLN cc_start: 0.8354 (tp40) cc_final: 0.7975 (tt0) REVERT: B 814 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7296 (mmtt) REVERT: B 819 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 935 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7855 (tt0) REVERT: B 960 ASN cc_start: 0.8406 (t0) cc_final: 0.8039 (m-40) REVERT: B 964 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8117 (mtpp) REVERT: B 979 ASP cc_start: 0.8196 (t70) cc_final: 0.7808 (t0) REVERT: B 1045 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8366 (mtmt) REVERT: B 1077 THR cc_start: 0.8649 (t) cc_final: 0.8414 (t) REVERT: B 1082 CYS cc_start: 0.8148 (t) cc_final: 0.7901 (t) REVERT: B 1138 TYR cc_start: 0.7914 (t80) cc_final: 0.7610 (t80) REVERT: C 160 TYR cc_start: 0.7151 (p90) cc_final: 0.6825 (p90) REVERT: C 190 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7956 (mtt-85) REVERT: C 191 GLU cc_start: 0.7593 (mp0) cc_final: 0.7208 (mp0) REVERT: C 200 TYR cc_start: 0.7571 (m-80) cc_final: 0.6492 (m-80) REVERT: C 241 LEU cc_start: 0.7926 (mt) cc_final: 0.7675 (mp) REVERT: C 266 TYR cc_start: 0.7436 (m-80) cc_final: 0.7077 (m-80) REVERT: C 271 GLN cc_start: 0.8353 (mt0) cc_final: 0.8009 (mt0) REVERT: C 281 GLU cc_start: 0.8074 (pm20) cc_final: 0.7748 (pm20) REVERT: C 302 THR cc_start: 0.8609 (t) cc_final: 0.8234 (p) REVERT: C 305 SER cc_start: 0.8993 (t) cc_final: 0.8638 (p) REVERT: C 382 VAL cc_start: 0.8932 (t) cc_final: 0.8683 (m) REVERT: C 453 TYR cc_start: 0.7122 (p90) cc_final: 0.6547 (p90) REVERT: C 462 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7664 (mmtt) REVERT: C 493 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 528 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8229 (mtpp) REVERT: C 558 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7024 (mmtt) REVERT: C 577 ARG cc_start: 0.8741 (ttm-80) cc_final: 0.8403 (ttm-80) REVERT: C 578 ASP cc_start: 0.8219 (t0) cc_final: 0.7918 (t0) REVERT: C 646 ARG cc_start: 0.7831 (mtm180) cc_final: 0.7596 (mtm180) REVERT: C 698 SER cc_start: 0.8536 (t) cc_final: 0.7834 (p) REVERT: C 737 ASP cc_start: 0.8237 (t0) cc_final: 0.8015 (t0) REVERT: C 740 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7759 (tpp) REVERT: C 747 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.7187 (p) REVERT: C 780 GLU cc_start: 0.8032 (tt0) cc_final: 0.7751 (tt0) REVERT: C 819 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6956 (mt-10) REVERT: C 820 ASP cc_start: 0.7792 (t0) cc_final: 0.7330 (m-30) REVERT: C 824 ASN cc_start: 0.8164 (m-40) cc_final: 0.7860 (m110) REVERT: C 900 MET cc_start: 0.8126 (mtp) cc_final: 0.7888 (mtp) REVERT: C 904 TYR cc_start: 0.7641 (m-10) cc_final: 0.6598 (m-10) REVERT: C 952 VAL cc_start: 0.8000 (t) cc_final: 0.7706 (m) REVERT: C 1012 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8173 (mt) REVERT: C 1055 SER cc_start: 0.8524 (t) cc_final: 0.7905 (p) REVERT: C 1073 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7947 (mtpt) REVERT: C 1092 GLU cc_start: 0.7445 (pm20) cc_final: 0.7195 (pm20) REVERT: C 1116 THR cc_start: 0.8287 (m) cc_final: 0.7807 (t) outliers start: 84 outliers final: 74 residues processed: 683 average time/residue: 0.4059 time to fit residues: 433.0674 Evaluate side-chains 697 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 618 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 169 optimal weight: 0.0050 chunk 194 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 189 optimal weight: 0.6980 chunk 178 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1101 HIS B 30 ASN B 99 ASN B 218 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 804 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119075 restraints weight = 37332.353| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.46 r_work: 0.3369 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24843 Z= 0.143 Angle : 0.604 12.505 33876 Z= 0.310 Chirality : 0.046 0.436 3910 Planarity : 0.005 0.088 4320 Dihedral : 5.132 54.103 3825 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 3.30 % Allowed : 17.92 % Favored : 78.79 % 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: 0.25 (0.15), residues: 2995 helix: 2.35 (0.20), residues: 654 sheet: 0.54 (0.19), residues: 649 loop : -0.91 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.008 0.001 HIS B 207 PHE 0.028 0.002 PHE C 515 TYR 0.023 0.001 TYR B 660 ARG 0.013 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 27) link_NAG-ASN : angle 3.04238 ( 81) hydrogen bonds : bond 0.04340 ( 956) hydrogen bonds : angle 5.21432 ( 2682) SS BOND : bond 0.00356 ( 37) SS BOND : angle 1.89430 ( 74) covalent geometry : bond 0.00330 (24779) covalent geometry : angle 0.57950 (33721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 624 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6001 (mmtt) cc_final: 0.4797 (mmmt) REVERT: A 113 LYS cc_start: 0.8400 (mtpp) cc_final: 0.8120 (mppt) REVERT: A 134 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 140 PHE cc_start: 0.7364 (p90) cc_final: 0.7023 (p90) REVERT: A 170 TYR cc_start: 0.8002 (t80) cc_final: 0.7644 (t80) REVERT: A 238 PHE cc_start: 0.8304 (p90) cc_final: 0.7684 (p90) REVERT: A 298 GLU cc_start: 0.7710 (tt0) cc_final: 0.7440 (tt0) REVERT: A 304 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8403 (mttm) REVERT: A 307 THR cc_start: 0.8505 (m) cc_final: 0.8102 (p) REVERT: A 375 PHE cc_start: 0.8296 (t80) cc_final: 0.7826 (t80) REVERT: A 436 TRP cc_start: 0.7815 (p90) cc_final: 0.7536 (p90) REVERT: A 493 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 508 TYR cc_start: 0.7286 (m-80) cc_final: 0.6912 (m-80) REVERT: A 560 LEU cc_start: 0.8726 (mm) cc_final: 0.8406 (mt) REVERT: A 574 ASP cc_start: 0.8027 (t70) cc_final: 0.7605 (t0) REVERT: A 581 THR cc_start: 0.8095 (m) cc_final: 0.7516 (p) REVERT: A 583 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: A 654 GLU cc_start: 0.8054 (tt0) cc_final: 0.7807 (tt0) REVERT: A 655 TYR cc_start: 0.8455 (t80) cc_final: 0.8031 (t80) REVERT: A 657 ASN cc_start: 0.8761 (m110) cc_final: 0.8532 (m110) REVERT: A 658 ASN cc_start: 0.8153 (p0) cc_final: 0.7840 (p0) REVERT: A 726 ILE cc_start: 0.8596 (mp) cc_final: 0.8370 (mt) REVERT: A 761 THR cc_start: 0.8094 (p) cc_final: 0.7783 (t) REVERT: A 763 LEU cc_start: 0.8384 (mt) cc_final: 0.8171 (mp) REVERT: A 819 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7368 (mt-10) REVERT: A 869 MET cc_start: 0.8304 (mtp) cc_final: 0.8097 (mtt) REVERT: A 875 SER cc_start: 0.8462 (p) cc_final: 0.8178 (m) REVERT: A 933 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8144 (mtpp) REVERT: A 934 ILE cc_start: 0.8301 (tt) cc_final: 0.7990 (tt) REVERT: A 935 GLN cc_start: 0.7799 (tt0) cc_final: 0.7536 (tp-100) REVERT: A 977 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 979 ASP cc_start: 0.7910 (t70) cc_final: 0.7652 (t70) REVERT: A 1107 ARG cc_start: 0.7609 (mtt-85) cc_final: 0.7234 (mtt-85) REVERT: B 126 VAL cc_start: 0.8303 (p) cc_final: 0.8098 (t) REVERT: B 138 ASP cc_start: 0.7756 (t0) cc_final: 0.7505 (t0) REVERT: B 202 LYS cc_start: 0.7988 (ptpt) cc_final: 0.7320 (ptpp) REVERT: B 235 ILE cc_start: 0.8092 (mt) cc_final: 0.7875 (mm) REVERT: B 236 THR cc_start: 0.8787 (t) cc_final: 0.8496 (p) REVERT: B 275 PHE cc_start: 0.8607 (m-80) cc_final: 0.8242 (m-80) REVERT: B 310 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8218 (tttt) REVERT: B 324 GLU cc_start: 0.8114 (pm20) cc_final: 0.7774 (pm20) REVERT: B 339 HIS cc_start: 0.6963 (t70) cc_final: 0.6583 (t70) REVERT: B 360 ASN cc_start: 0.7818 (m-40) cc_final: 0.7402 (t0) REVERT: B 396 TYR cc_start: 0.7518 (m-80) cc_final: 0.7237 (m-80) REVERT: B 423 TYR cc_start: 0.8175 (t80) cc_final: 0.7410 (t80) REVERT: B 429 PHE cc_start: 0.7421 (t80) cc_final: 0.7179 (t80) REVERT: B 537 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8064 (mtpp) REVERT: B 557 LYS cc_start: 0.8095 (mttp) cc_final: 0.7840 (mttp) REVERT: B 646 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8172 (ttp80) REVERT: B 702 GLU cc_start: 0.7738 (tp30) cc_final: 0.7457 (tp30) REVERT: B 710 ASN cc_start: 0.8318 (p0) cc_final: 0.7963 (p0) REVERT: B 762 GLN cc_start: 0.8035 (mt0) cc_final: 0.7832 (mt0) REVERT: B 772 VAL cc_start: 0.8326 (t) cc_final: 0.8075 (m) REVERT: B 776 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7813 (ttpt) REVERT: B 779 GLN cc_start: 0.8340 (tp40) cc_final: 0.7973 (tt0) REVERT: B 814 LYS cc_start: 0.7574 (mmtt) cc_final: 0.7293 (mmtt) REVERT: B 819 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 935 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7841 (tt0) REVERT: B 960 ASN cc_start: 0.8428 (t0) cc_final: 0.8044 (m-40) REVERT: B 964 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8112 (mtpp) REVERT: B 979 ASP cc_start: 0.8207 (t70) cc_final: 0.7813 (t0) REVERT: B 1045 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8350 (mtmt) REVERT: B 1077 THR cc_start: 0.8649 (t) cc_final: 0.8420 (t) REVERT: B 1138 TYR cc_start: 0.7925 (t80) cc_final: 0.7629 (t80) REVERT: C 160 TYR cc_start: 0.7104 (p90) cc_final: 0.6784 (p90) REVERT: C 190 ARG cc_start: 0.8195 (mtt-85) cc_final: 0.7992 (mtt-85) REVERT: C 191 GLU cc_start: 0.7568 (mp0) cc_final: 0.7177 (mp0) REVERT: C 200 TYR cc_start: 0.7601 (m-80) cc_final: 0.6559 (m-80) REVERT: C 241 LEU cc_start: 0.7921 (mt) cc_final: 0.7676 (mp) REVERT: C 266 TYR cc_start: 0.7449 (m-80) cc_final: 0.7089 (m-80) REVERT: C 271 GLN cc_start: 0.8362 (mt0) cc_final: 0.8029 (mt0) REVERT: C 281 GLU cc_start: 0.8112 (pm20) cc_final: 0.7778 (pm20) REVERT: C 302 THR cc_start: 0.8613 (t) cc_final: 0.8253 (p) REVERT: C 305 SER cc_start: 0.8980 (t) cc_final: 0.8619 (p) REVERT: C 357 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7568 (ttm-80) REVERT: C 382 VAL cc_start: 0.8923 (t) cc_final: 0.8677 (m) REVERT: C 453 TYR cc_start: 0.7103 (p90) cc_final: 0.6516 (p90) REVERT: C 462 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7700 (mmtt) REVERT: C 493 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 528 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8225 (mtpp) REVERT: C 558 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7062 (mmtt) REVERT: C 578 ASP cc_start: 0.8227 (t0) cc_final: 0.7937 (t0) REVERT: C 646 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7597 (mtm180) REVERT: C 698 SER cc_start: 0.8539 (t) cc_final: 0.7828 (p) REVERT: C 737 ASP cc_start: 0.8237 (t0) cc_final: 0.8020 (t0) REVERT: C 740 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7777 (tpp) REVERT: C 776 LYS cc_start: 0.8385 (tmmt) cc_final: 0.8031 (tttm) REVERT: C 780 GLU cc_start: 0.7984 (tt0) cc_final: 0.7732 (tt0) REVERT: C 819 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6954 (mt-10) REVERT: C 820 ASP cc_start: 0.7785 (t0) cc_final: 0.7309 (m-30) REVERT: C 824 ASN cc_start: 0.8160 (m-40) cc_final: 0.7842 (m110) REVERT: C 900 MET cc_start: 0.8122 (mtp) cc_final: 0.7859 (mtp) REVERT: C 904 TYR cc_start: 0.7624 (m-10) cc_final: 0.6499 (m-10) REVERT: C 952 VAL cc_start: 0.7989 (t) cc_final: 0.7698 (m) REVERT: C 969 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7775 (mmtp) REVERT: C 1012 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8169 (mt) REVERT: C 1045 LYS cc_start: 0.8409 (tmtt) cc_final: 0.8115 (mmmm) REVERT: C 1055 SER cc_start: 0.8529 (t) cc_final: 0.7910 (p) REVERT: C 1073 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7937 (mtpt) REVERT: C 1092 GLU cc_start: 0.7450 (pm20) cc_final: 0.7199 (pm20) REVERT: C 1116 THR cc_start: 0.8254 (m) cc_final: 0.7771 (t) outliers start: 88 outliers final: 76 residues processed: 670 average time/residue: 0.3629 time to fit residues: 375.8632 Evaluate side-chains 702 residues out of total 2668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 622 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.3279 > 50: distance: 57 - 81: 4.706 distance: 63 - 93: 3.740 distance: 75 - 81: 4.764 distance: 81 - 82: 13.451 distance: 82 - 83: 15.376 distance: 82 - 85: 17.103 distance: 83 - 84: 21.440 distance: 83 - 93: 6.227 distance: 85 - 86: 13.498 distance: 86 - 87: 11.952 distance: 86 - 88: 5.754 distance: 90 - 91: 3.906 distance: 91 - 92: 4.441 distance: 94 - 95: 11.488 distance: 94 - 97: 5.533 distance: 95 - 96: 7.514 distance: 95 - 101: 11.027 distance: 97 - 98: 8.450 distance: 98 - 99: 6.203 distance: 98 - 100: 4.670 distance: 101 - 102: 7.970 distance: 102 - 103: 4.983 distance: 102 - 105: 7.656 distance: 103 - 104: 24.790 distance: 103 - 113: 21.853 distance: 105 - 106: 5.431 distance: 106 - 107: 5.256 distance: 106 - 108: 6.399 distance: 107 - 109: 5.494 distance: 109 - 111: 5.070 distance: 110 - 111: 4.929 distance: 111 - 112: 5.801 distance: 113 - 114: 24.164 distance: 114 - 115: 41.817 distance: 114 - 117: 20.793 distance: 115 - 116: 17.854 distance: 115 - 122: 46.402 distance: 117 - 118: 8.349 distance: 118 - 119: 3.782 distance: 119 - 120: 8.201 distance: 120 - 121: 12.421 distance: 122 - 123: 4.917 distance: 123 - 124: 28.973 distance: 123 - 126: 9.674 distance: 124 - 125: 16.991 distance: 124 - 130: 15.229 distance: 126 - 127: 14.286 distance: 127 - 128: 7.768 distance: 127 - 129: 11.093 distance: 130 - 131: 7.902 distance: 130 - 136: 6.281 distance: 131 - 132: 5.192 distance: 131 - 134: 7.223 distance: 132 - 133: 10.602 distance: 132 - 137: 6.584 distance: 134 - 135: 10.823 distance: 135 - 136: 13.624 distance: 137 - 138: 16.283 distance: 138 - 139: 21.967 distance: 138 - 141: 20.590 distance: 139 - 140: 33.296 distance: 139 - 145: 13.613 distance: 141 - 142: 9.174 distance: 142 - 143: 14.536 distance: 142 - 144: 4.897 distance: 145 - 146: 34.773 distance: 146 - 147: 39.149 distance: 146 - 149: 48.953 distance: 147 - 148: 13.531 distance: 147 - 153: 12.243 distance: 149 - 150: 48.278 distance: 150 - 151: 28.342 distance: 150 - 152: 18.139 distance: 153 - 154: 9.189 distance: 154 - 155: 7.786 distance: 154 - 157: 12.692 distance: 155 - 156: 27.911 distance: 155 - 164: 11.413 distance: 157 - 158: 7.399 distance: 158 - 159: 8.181 distance: 158 - 160: 5.594 distance: 159 - 161: 5.056 distance: 160 - 162: 6.548 distance: 161 - 163: 5.095 distance: 162 - 163: 5.176 distance: 164 - 165: 11.202 distance: 165 - 166: 6.760 distance: 165 - 168: 34.461 distance: 166 - 167: 20.020 distance: 166 - 171: 18.607 distance: 168 - 169: 9.675 distance: 168 - 170: 18.453