Starting phenix.real_space_refine on Mon Aug 25 02:19:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hri_34974/08_2025/8hri_34974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hri_34974/08_2025/8hri_34974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hri_34974/08_2025/8hri_34974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hri_34974/08_2025/8hri_34974.map" model { file = "/net/cci-nas-00/data/ceres_data/8hri_34974/08_2025/8hri_34974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hri_34974/08_2025/8hri_34974.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.115 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 114 5.16 5 C 15711 2.51 5 N 4086 2.21 5 O 4620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24531 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Chain: "B" Number of atoms: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8191 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 8 Chain: "C" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Time building chain proxies: 5.37, per 1000 atoms: 0.22 Number of scatterers: 24531 At special positions: 0 Unit cell: (139.32, 151.36, 201.24, 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 114 16.00 O 4620 8.00 N 4086 7.00 C 15711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.02 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=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.5% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.891A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 4.051A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.945A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.656A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.538A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 806 removed outlier: 3.577A pdb=" N ILE A 805 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 806 " --> pdb=" O SER A 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 802 through 806' Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.033A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.201A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.656A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 4.066A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.077A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.626A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.871A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.608A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.051A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.570A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.557A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.539A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.384A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.582A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.675A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.226A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.575A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.847A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.540A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.565A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.722A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.528A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 937 removed outlier: 3.822A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.577A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.734A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.900A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.277A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.026A 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: 3.610A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.577A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.695A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.062A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.568A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.643A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.345A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.160A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.805A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 142 removed outlier: 7.615A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.098A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.721A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.547A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.119A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.471A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.692A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.240A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.601A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.611A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.544A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.224A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.639A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 1014 hydrogen bonds defined for protein. 2748 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: 5.24 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7684 1.34 - 1.46: 6283 1.46 - 1.59: 10990 1.59 - 1.72: 0 1.72 - 1.85: 141 Bond restraints: 25098 Sorted by residual: bond pdb=" N THR B 376 " pdb=" CA THR B 376 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.27e-02 6.20e+03 8.77e+00 bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.53e-02 4.27e+03 8.32e+00 bond pdb=" C PHE A 374 " pdb=" N PHE A 375 " ideal model delta sigma weight residual 1.331 1.300 0.031 1.23e-02 6.61e+03 6.38e+00 bond pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 1.452 1.480 -0.028 1.11e-02 8.12e+03 6.21e+00 bond pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.10e-02 8.26e+03 5.96e+00 ... (remaining 25093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 33787 2.57 - 5.14: 318 5.14 - 7.72: 20 7.72 - 10.29: 2 10.29 - 12.86: 2 Bond angle restraints: 34129 Sorted by residual: angle pdb=" CA PHE B 375 " pdb=" CB PHE B 375 " pdb=" CG PHE B 375 " ideal model delta sigma weight residual 113.80 120.94 -7.14 1.00e+00 1.00e+00 5.09e+01 angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 112.47 99.61 12.86 2.06e+00 2.36e-01 3.90e+01 angle pdb=" CA THR B 376 " pdb=" C THR B 376 " pdb=" O THR B 376 " ideal model delta sigma weight residual 121.88 115.73 6.15 1.13e+00 7.83e-01 2.96e+01 angle pdb=" N PRO B 373 " pdb=" CA PRO B 373 " pdb=" C PRO B 373 " ideal model delta sigma weight residual 112.47 101.82 10.65 2.06e+00 2.36e-01 2.67e+01 angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 113.41 107.87 5.54 1.22e+00 6.72e-01 2.06e+01 ... (remaining 34124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 13422 17.62 - 35.24: 1258 35.24 - 52.85: 251 52.85 - 70.47: 45 70.47 - 88.09: 23 Dihedral angle restraints: 14999 sinusoidal: 5882 harmonic: 9117 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 12.18 80.82 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 27.03 65.97 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 155.66 -62.66 1 1.00e+01 1.00e-02 5.19e+01 ... (remaining 14996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3059 0.052 - 0.104: 652 0.104 - 0.157: 151 0.157 - 0.209: 9 0.209 - 0.261: 2 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" C PRO A 373 " pdb=" CB PRO A 373 " both_signs ideal model delta sigma weight residual False 2.72 2.98 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LEU A 368 " pdb=" N LEU A 368 " pdb=" C LEU A 368 " pdb=" CB LEU A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LEU B 368 " pdb=" N LEU B 368 " pdb=" C LEU B 368 " pdb=" CB LEU B 368 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3870 not shown) Planarity restraints: 4411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 498 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO C 499 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 498 " -0.064 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO B 499 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " 0.063 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO A 322 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.051 5.00e-02 4.00e+02 ... (remaining 4408 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1917 2.74 - 3.28: 22777 3.28 - 3.82: 36706 3.82 - 4.36: 41437 4.36 - 4.90: 76836 Nonbonded interactions: 179673 Sorted by model distance: nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.240 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP A 40 " pdb=" NH1 ARG A 44 " model vdw 2.264 3.120 ... (remaining 179668 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' selection = (chain 'B' and (resid 15 through 827 or resid 848 through 1147)) selection = chain 'C' } 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: 9.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25140 Z= 0.157 Angle : 0.615 12.861 34213 Z= 0.341 Chirality : 0.046 0.261 3873 Planarity : 0.005 0.098 4411 Dihedral : 14.229 88.091 8993 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.95 % Favored : 94.76 % Rotamer: Outliers : 0.26 % Allowed : 0.33 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 3072 helix: 2.02 (0.21), residues: 679 sheet: 1.05 (0.19), residues: 682 loop : -1.55 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.018 0.001 TYR C 351 PHE 0.020 0.001 PHE A 486 TRP 0.015 0.001 TRP A 886 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00312 (25098) covalent geometry : angle 0.61098 (34129) SS BOND : bond 0.00601 ( 42) SS BOND : angle 1.54156 ( 84) hydrogen bonds : bond 0.12450 ( 1014) hydrogen bonds : angle 5.76938 ( 2748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 240 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.6914 (mtp) cc_final: 0.6618 (mtp) REVERT: A 725 GLU cc_start: 0.8549 (tt0) cc_final: 0.8216 (mt-10) REVERT: A 1107 ARG cc_start: 0.4894 (mpt-90) cc_final: 0.4470 (mtp180) REVERT: B 1019 ARG cc_start: 0.7518 (ttp-170) cc_final: 0.6983 (ttp-110) REVERT: C 676 THR cc_start: 0.3141 (OUTLIER) cc_final: 0.2922 (p) REVERT: C 773 GLU cc_start: 0.7413 (tt0) cc_final: 0.7158 (tt0) outliers start: 7 outliers final: 1 residues processed: 247 average time/residue: 0.5515 time to fit residues: 160.2421 Evaluate side-chains 104 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 676 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 487 ASN A 613 GLN A 914 ASN A1135 ASN B 81 ASN B 370 ASN B 450 ASN B 564 GLN B 675 GLN B 804 GLN B 824 ASN B 901 GLN B1101 HIS B1135 ASN C 658 ASN C 901 GLN C 914 ASN C1002 GLN C1083 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.288350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.231962 restraints weight = 32772.044| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 2.70 r_work: 0.3988 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 25140 Z= 0.313 Angle : 0.937 11.106 34213 Z= 0.505 Chirality : 0.056 0.392 3873 Planarity : 0.008 0.077 4411 Dihedral : 5.583 57.697 3352 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 1.97 % Allowed : 9.65 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3072 helix: 0.47 (0.19), residues: 697 sheet: 0.88 (0.19), residues: 652 loop : -1.93 (0.13), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 273 TYR 0.036 0.003 TYR A 796 PHE 0.033 0.003 PHE C 55 TRP 0.029 0.003 TRP C 886 HIS 0.012 0.002 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00689 (25098) covalent geometry : angle 0.92928 (34129) SS BOND : bond 0.00751 ( 42) SS BOND : angle 2.53394 ( 84) hydrogen bonds : bond 0.12406 ( 1014) hydrogen bonds : angle 6.19120 ( 2748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.904 Fit side-chains REVERT: A 786 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7427 (pmtt) REVERT: A 904 TYR cc_start: 0.7313 (m-10) cc_final: 0.7071 (m-10) REVERT: A 1031 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: A 1137 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8661 (t) REVERT: A 1138 TYR cc_start: 0.6625 (t80) cc_final: 0.5761 (m-80) REVERT: B 44 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.5292 (ptp-170) REVERT: B 153 MET cc_start: 0.0287 (tpp) cc_final: -0.0648 (ttp) REVERT: B 646 ARG cc_start: 0.7445 (mmp80) cc_final: 0.6828 (mpp80) REVERT: B 655 TYR cc_start: 0.6230 (t80) cc_final: 0.5906 (t80) REVERT: B 697 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7643 (mtm) REVERT: B 1019 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7833 (ttm-80) REVERT: C 661 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7768 (pt0) REVERT: C 676 THR cc_start: 0.3379 (OUTLIER) cc_final: 0.3175 (m) REVERT: C 1010 GLN cc_start: 0.8146 (mp10) cc_final: 0.7927 (mt0) REVERT: C 1074 ASN cc_start: 0.8100 (p0) cc_final: 0.7855 (p0) outliers start: 54 outliers final: 18 residues processed: 212 average time/residue: 0.5878 time to fit residues: 145.2690 Evaluate side-chains 125 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 150 optimal weight: 4.9990 chunk 220 optimal weight: 0.0000 chunk 100 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 779 GLN A 804 GLN A 935 GLN A1083 HIS B 644 GLN B 901 GLN B1101 HIS C 755 GLN C 901 GLN C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.289507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.233413 restraints weight = 33027.222| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 2.47 r_work: 0.4027 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25140 Z= 0.146 Angle : 0.598 8.547 34213 Z= 0.320 Chirality : 0.045 0.184 3873 Planarity : 0.005 0.065 4411 Dihedral : 4.704 53.537 3352 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 2.08 % Allowed : 13.12 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3072 helix: 1.63 (0.21), residues: 684 sheet: 0.58 (0.19), residues: 665 loop : -1.67 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 237 TYR 0.019 0.001 TYR C 265 PHE 0.016 0.001 PHE C 86 TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00290 (25098) covalent geometry : angle 0.59333 (34129) SS BOND : bond 0.00585 ( 42) SS BOND : angle 1.62100 ( 84) hydrogen bonds : bond 0.07544 ( 1014) hydrogen bonds : angle 5.36357 ( 2748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 1.057 Fit side-chains REVERT: A 968 SER cc_start: 0.8184 (m) cc_final: 0.7919 (p) REVERT: A 1117 THR cc_start: 0.7699 (m) cc_final: 0.7437 (p) REVERT: B 44 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.3652 (ptp-170) REVERT: B 153 MET cc_start: 0.0183 (tpp) cc_final: -0.0630 (ttp) REVERT: B 646 ARG cc_start: 0.7573 (mmp80) cc_final: 0.7095 (mpp80) REVERT: B 655 TYR cc_start: 0.6352 (t80) cc_final: 0.6131 (t80) REVERT: C 105 ILE cc_start: -0.0047 (OUTLIER) cc_final: -0.0266 (mp) REVERT: C 310 LYS cc_start: 0.6996 (ttpt) cc_final: 0.5998 (tptt) REVERT: C 709 ASN cc_start: 0.7210 (m-40) cc_final: 0.6976 (m110) REVERT: C 1010 GLN cc_start: 0.8236 (mp10) cc_final: 0.7897 (mt0) outliers start: 57 outliers final: 21 residues processed: 158 average time/residue: 0.6059 time to fit residues: 112.8365 Evaluate side-chains 106 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 914 ASN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 709 ASN B 901 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 564 GLN C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.269431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.205526 restraints weight = 31135.799| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.59 r_work: 0.3725 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 25140 Z= 0.307 Angle : 0.895 13.135 34213 Z= 0.485 Chirality : 0.055 0.317 3873 Planarity : 0.007 0.087 4411 Dihedral : 5.949 28.912 3349 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 3.43 % Allowed : 14.58 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.14), residues: 3072 helix: 0.74 (0.20), residues: 678 sheet: 0.33 (0.19), residues: 655 loop : -2.14 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C1107 TYR 0.056 0.003 TYR C 756 PHE 0.042 0.003 PHE B 377 TRP 0.033 0.003 TRP C 353 HIS 0.008 0.002 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00696 (25098) covalent geometry : angle 0.88660 (34129) SS BOND : bond 0.00835 ( 42) SS BOND : angle 2.68742 ( 84) hydrogen bonds : bond 0.14136 ( 1014) hydrogen bonds : angle 6.67211 ( 2748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 132 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 787 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: A 998 THR cc_start: 0.8154 (m) cc_final: 0.7798 (p) REVERT: A 1010 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: A 1031 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: A 1117 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8227 (p) REVERT: A 1138 TYR cc_start: 0.7161 (t80) cc_final: 0.6439 (m-80) REVERT: B 406 GLU cc_start: 0.3076 (OUTLIER) cc_final: 0.1982 (mm-30) REVERT: B 654 GLU cc_start: 0.7202 (tt0) cc_final: 0.6722 (tp30) REVERT: B 655 TYR cc_start: 0.7194 (t80) cc_final: 0.6592 (t80) REVERT: B 664 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7611 (mt) REVERT: B 796 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.5510 (p90) REVERT: B 976 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7654 (p) REVERT: B 1005 GLN cc_start: 0.8119 (mm110) cc_final: 0.7759 (mt0) REVERT: B 1138 TYR cc_start: 0.6787 (t80) cc_final: 0.6240 (m-80) REVERT: C 168 PHE cc_start: 0.6488 (t80) cc_final: 0.6239 (t80) REVERT: C 646 ARG cc_start: 0.7669 (mpt-90) cc_final: 0.7304 (mtt90) REVERT: C 664 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8343 (mt) REVERT: C 795 LYS cc_start: 0.7289 (mptm) cc_final: 0.6511 (mtpp) REVERT: C 814 LYS cc_start: 0.7895 (mmpt) cc_final: 0.6719 (tttp) REVERT: C 983 ARG cc_start: 0.7169 (ttp-170) cc_final: 0.6710 (mtm110) REVERT: C 1002 GLN cc_start: 0.8188 (mt0) cc_final: 0.7980 (tt0) REVERT: C 1010 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: C 1138 TYR cc_start: 0.7316 (t80) cc_final: 0.6682 (m-80) outliers start: 94 outliers final: 33 residues processed: 202 average time/residue: 0.6010 time to fit residues: 142.4632 Evaluate side-chains 144 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 796 TYR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 265 optimal weight: 0.7980 chunk 274 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 221 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 914 ASN B 49 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN C 49 HIS C 422 ASN C 641 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.274238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213429 restraints weight = 31565.027| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.73 r_work: 0.3814 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.7891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25140 Z= 0.164 Angle : 0.637 9.363 34213 Z= 0.341 Chirality : 0.046 0.233 3873 Planarity : 0.005 0.066 4411 Dihedral : 4.985 27.106 3349 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 2.27 % Allowed : 17.06 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.15), residues: 3072 helix: 1.48 (0.21), residues: 672 sheet: 0.48 (0.19), residues: 663 loop : -2.02 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.022 0.001 TYR C 265 PHE 0.022 0.001 PHE C 238 TRP 0.018 0.002 TRP C 353 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00328 (25098) covalent geometry : angle 0.63085 (34129) SS BOND : bond 0.00494 ( 42) SS BOND : angle 1.82990 ( 84) hydrogen bonds : bond 0.09178 ( 1014) hydrogen bonds : angle 5.73754 ( 2748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.5941 (p) cc_final: 0.5722 (t) REVERT: A 333 THR cc_start: 0.3221 (OUTLIER) cc_final: 0.2949 (t) REVERT: A 934 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7351 (tt) REVERT: A 973 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7748 (pt) REVERT: A 1010 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: A 1117 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 1138 TYR cc_start: 0.7080 (t80) cc_final: 0.6413 (m-80) REVERT: B 424 LYS cc_start: 0.5398 (OUTLIER) cc_final: 0.5070 (mmtp) REVERT: B 547 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7393 (mtpt) REVERT: B 654 GLU cc_start: 0.7031 (tt0) cc_final: 0.6697 (tp30) REVERT: B 655 TYR cc_start: 0.7071 (t80) cc_final: 0.6609 (t80) REVERT: B 664 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7594 (mt) REVERT: B 796 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.5447 (p90) REVERT: B 964 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7475 (tttp) REVERT: B 976 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7575 (p) REVERT: B 1005 GLN cc_start: 0.7765 (mm110) cc_final: 0.7530 (mt0) REVERT: B 1138 TYR cc_start: 0.6669 (t80) cc_final: 0.6278 (m-80) REVERT: C 101 ILE cc_start: -0.3531 (OUTLIER) cc_final: -0.3854 (pp) REVERT: C 646 ARG cc_start: 0.7619 (mpt-90) cc_final: 0.7319 (mtt90) REVERT: C 814 LYS cc_start: 0.7819 (mmpt) cc_final: 0.6776 (tttp) REVERT: C 1010 GLN cc_start: 0.8183 (mp10) cc_final: 0.7851 (mt0) outliers start: 62 outliers final: 23 residues processed: 166 average time/residue: 0.5665 time to fit residues: 111.6929 Evaluate side-chains 133 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 547 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 796 TYR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 181 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 210 optimal weight: 0.0870 chunk 138 optimal weight: 0.6980 chunk 161 optimal weight: 0.0470 chunk 120 optimal weight: 5.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN C 641 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.276069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.215957 restraints weight = 31844.222| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.49 r_work: 0.3871 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25140 Z= 0.137 Angle : 0.583 8.579 34213 Z= 0.310 Chirality : 0.044 0.302 3873 Planarity : 0.005 0.065 4411 Dihedral : 4.592 26.133 3349 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 1.90 % Allowed : 17.65 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.15), residues: 3072 helix: 1.67 (0.21), residues: 681 sheet: 0.51 (0.19), residues: 675 loop : -1.94 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.018 0.001 TYR C 265 PHE 0.023 0.001 PHE C 238 TRP 0.016 0.001 TRP C 353 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00261 (25098) covalent geometry : angle 0.57813 (34129) SS BOND : bond 0.00468 ( 42) SS BOND : angle 1.60920 ( 84) hydrogen bonds : bond 0.07835 ( 1014) hydrogen bonds : angle 5.42796 ( 2748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.1288 (OUTLIER) cc_final: 0.0282 (t) REVERT: A 934 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7311 (tt) REVERT: A 973 ILE cc_start: 0.8212 (tt) cc_final: 0.7427 (pt) REVERT: A 992 GLN cc_start: 0.5427 (OUTLIER) cc_final: 0.3859 (mm-40) REVERT: A 1010 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: A 1117 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 1138 TYR cc_start: 0.7143 (t80) cc_final: 0.6435 (m-80) REVERT: B 424 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5365 (mmtp) REVERT: B 654 GLU cc_start: 0.7135 (tt0) cc_final: 0.6656 (tp30) REVERT: B 655 TYR cc_start: 0.7201 (t80) cc_final: 0.6644 (t80) REVERT: B 664 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7622 (mt) REVERT: B 796 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.5371 (p90) REVERT: B 964 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7449 (tttp) REVERT: B 976 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7678 (p) REVERT: B 979 ASP cc_start: 0.6085 (t0) cc_final: 0.5794 (m-30) REVERT: B 1005 GLN cc_start: 0.7912 (mm110) cc_final: 0.7648 (mt0) REVERT: B 1138 TYR cc_start: 0.6688 (t80) cc_final: 0.6250 (m-80) REVERT: C 646 ARG cc_start: 0.7722 (mpt-90) cc_final: 0.7449 (mtt90) REVERT: C 814 LYS cc_start: 0.7846 (mmpt) cc_final: 0.6776 (tttp) REVERT: C 1010 GLN cc_start: 0.8296 (mp10) cc_final: 0.7893 (mt0) outliers start: 52 outliers final: 25 residues processed: 148 average time/residue: 0.5695 time to fit residues: 100.6823 Evaluate side-chains 134 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 796 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 17 optimal weight: 0.8980 chunk 169 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 233 optimal weight: 0.1980 chunk 299 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 641 ASN C 804 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.274871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.215483 restraints weight = 31680.003| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.57 r_work: 0.3849 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 25140 Z= 0.142 Angle : 0.579 17.170 34213 Z= 0.306 Chirality : 0.044 0.268 3873 Planarity : 0.005 0.065 4411 Dihedral : 4.411 24.592 3349 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 2.23 % Allowed : 17.87 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 3072 helix: 1.81 (0.21), residues: 686 sheet: 0.50 (0.20), residues: 654 loop : -1.87 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.017 0.001 TYR C1067 PHE 0.021 0.001 PHE C 238 TRP 0.013 0.001 TRP C 353 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00284 (25098) covalent geometry : angle 0.57521 (34129) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.42873 ( 84) hydrogen bonds : bond 0.07896 ( 1014) hydrogen bonds : angle 5.28861 ( 2748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 112 time to evaluate : 0.947 Fit side-chains REVERT: A 333 THR cc_start: 0.3394 (OUTLIER) cc_final: 0.3121 (t) REVERT: A 361 CYS cc_start: 0.1561 (OUTLIER) cc_final: 0.0600 (t) REVERT: A 808 ASP cc_start: 0.6346 (OUTLIER) cc_final: 0.5996 (m-30) REVERT: A 934 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7167 (tt) REVERT: A 973 ILE cc_start: 0.8205 (tt) cc_final: 0.7978 (pt) REVERT: A 1010 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: A 1138 TYR cc_start: 0.7115 (t80) cc_final: 0.6353 (m-80) REVERT: B 424 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5480 (mmtp) REVERT: B 549 THR cc_start: 0.8156 (m) cc_final: 0.7937 (t) REVERT: B 598 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7381 (pt) REVERT: B 654 GLU cc_start: 0.7142 (tt0) cc_final: 0.6651 (tp30) REVERT: B 655 TYR cc_start: 0.7217 (t80) cc_final: 0.6657 (t80) REVERT: B 664 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7663 (mt) REVERT: B 964 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7499 (tttp) REVERT: B 973 ILE cc_start: 0.5939 (OUTLIER) cc_final: 0.5654 (tt) REVERT: B 976 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 979 ASP cc_start: 0.6401 (t0) cc_final: 0.6177 (m-30) REVERT: B 1005 GLN cc_start: 0.7862 (mm110) cc_final: 0.7597 (mt0) REVERT: B 1134 ASN cc_start: 0.8518 (m-40) cc_final: 0.8308 (m110) REVERT: B 1138 TYR cc_start: 0.6702 (t80) cc_final: 0.6262 (m-80) REVERT: C 101 ILE cc_start: -0.3544 (OUTLIER) cc_final: -0.3795 (pp) REVERT: C 646 ARG cc_start: 0.7926 (mpt-90) cc_final: 0.7635 (mtt90) REVERT: C 795 LYS cc_start: 0.7198 (mptm) cc_final: 0.6194 (mtpp) REVERT: C 814 LYS cc_start: 0.7873 (mmpt) cc_final: 0.6765 (tttp) REVERT: C 981 PHE cc_start: 0.7937 (m-10) cc_final: 0.7729 (m-80) REVERT: C 1010 GLN cc_start: 0.8293 (mp10) cc_final: 0.7871 (mt0) outliers start: 61 outliers final: 30 residues processed: 161 average time/residue: 0.5050 time to fit residues: 98.4073 Evaluate side-chains 141 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 115 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 222 optimal weight: 0.0770 chunk 5 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.268093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.206354 restraints weight = 31070.912| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.46 r_work: 0.3755 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.8730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25140 Z= 0.199 Angle : 0.675 12.281 34213 Z= 0.364 Chirality : 0.047 0.301 3873 Planarity : 0.006 0.065 4411 Dihedral : 4.866 26.005 3349 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 2.45 % Allowed : 18.01 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.15), residues: 3072 helix: 1.39 (0.20), residues: 693 sheet: 0.53 (0.20), residues: 626 loop : -2.05 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 44 TYR 0.028 0.002 TYR C 279 PHE 0.027 0.002 PHE B 400 TRP 0.020 0.002 TRP C 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00416 (25098) covalent geometry : angle 0.66892 (34129) SS BOND : bond 0.00716 ( 42) SS BOND : angle 1.98184 ( 84) hydrogen bonds : bond 0.10778 ( 1014) hydrogen bonds : angle 5.69709 ( 2748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 111 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.3337 (OUTLIER) cc_final: 0.3051 (t) REVERT: A 361 CYS cc_start: 0.1556 (OUTLIER) cc_final: 0.0527 (t) REVERT: A 808 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.6122 (m-30) REVERT: A 934 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7375 (tt) REVERT: A 1010 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: A 1031 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 1138 TYR cc_start: 0.7076 (t80) cc_final: 0.6275 (m-80) REVERT: B 424 LYS cc_start: 0.6094 (OUTLIER) cc_final: 0.5700 (mmtp) REVERT: B 529 LYS cc_start: 0.6397 (mmpt) cc_final: 0.5190 (mmmt) REVERT: B 588 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7436 (p) REVERT: B 646 ARG cc_start: 0.7753 (mpp80) cc_final: 0.7494 (mtt90) REVERT: B 654 GLU cc_start: 0.7307 (tt0) cc_final: 0.6798 (tp30) REVERT: B 655 TYR cc_start: 0.7260 (t80) cc_final: 0.6644 (t80) REVERT: B 664 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7641 (mt) REVERT: B 751 ASN cc_start: 0.7953 (t0) cc_final: 0.7708 (t0) REVERT: B 964 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7750 (tttm) REVERT: B 1005 GLN cc_start: 0.8052 (mm110) cc_final: 0.7725 (mt0) REVERT: B 1138 TYR cc_start: 0.6795 (t80) cc_final: 0.6204 (m-80) REVERT: C 101 ILE cc_start: -0.3925 (OUTLIER) cc_final: -0.4196 (pp) REVERT: C 226 LEU cc_start: -0.0870 (OUTLIER) cc_final: -0.1322 (pt) REVERT: C 646 ARG cc_start: 0.8013 (mpt-90) cc_final: 0.7738 (mtt90) REVERT: C 795 LYS cc_start: 0.7255 (mptm) cc_final: 0.6188 (mtpp) REVERT: C 814 LYS cc_start: 0.7909 (mmpt) cc_final: 0.6765 (tttp) REVERT: C 1010 GLN cc_start: 0.8333 (mp10) cc_final: 0.7920 (mt0) outliers start: 67 outliers final: 36 residues processed: 165 average time/residue: 0.5266 time to fit residues: 104.8196 Evaluate side-chains 152 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 796 TYR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 224 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 284 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 300 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A 992 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.269304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.209057 restraints weight = 31215.882| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 2.58 r_work: 0.3779 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.8925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25140 Z= 0.161 Angle : 0.611 9.170 34213 Z= 0.328 Chirality : 0.045 0.190 3873 Planarity : 0.005 0.066 4411 Dihedral : 4.655 25.390 3349 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 1.72 % Allowed : 18.82 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 3072 helix: 1.71 (0.21), residues: 673 sheet: 0.50 (0.20), residues: 617 loop : -2.02 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1019 TYR 0.020 0.002 TYR C 351 PHE 0.021 0.001 PHE C 238 TRP 0.013 0.001 TRP B 436 HIS 0.009 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00329 (25098) covalent geometry : angle 0.60597 (34129) SS BOND : bond 0.00456 ( 42) SS BOND : angle 1.71104 ( 84) hydrogen bonds : bond 0.09094 ( 1014) hydrogen bonds : angle 5.49333 ( 2748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.941 Fit side-chains REVERT: A 333 THR cc_start: 0.3355 (OUTLIER) cc_final: 0.3068 (t) REVERT: A 361 CYS cc_start: 0.1676 (OUTLIER) cc_final: 0.0668 (t) REVERT: A 808 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6127 (m-30) REVERT: A 934 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7335 (tt) REVERT: A 1010 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8084 (mp10) REVERT: A 1138 TYR cc_start: 0.7179 (t80) cc_final: 0.6398 (m-80) REVERT: B 192 PHE cc_start: 0.4340 (m-80) cc_final: 0.3946 (m-80) REVERT: B 646 ARG cc_start: 0.7813 (mpp80) cc_final: 0.7461 (mtp180) REVERT: B 654 GLU cc_start: 0.7344 (tt0) cc_final: 0.6868 (tp30) REVERT: B 655 TYR cc_start: 0.7296 (t80) cc_final: 0.6678 (t80) REVERT: B 664 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7686 (mt) REVERT: B 751 ASN cc_start: 0.7983 (t0) cc_final: 0.7745 (t0) REVERT: B 964 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7601 (tttp) REVERT: B 1005 GLN cc_start: 0.8046 (mm110) cc_final: 0.7759 (mt0) REVERT: B 1138 TYR cc_start: 0.6835 (t80) cc_final: 0.6281 (m-80) REVERT: C 226 LEU cc_start: -0.0760 (OUTLIER) cc_final: -0.1156 (pt) REVERT: C 646 ARG cc_start: 0.8082 (mpt-90) cc_final: 0.7789 (mtt90) REVERT: C 795 LYS cc_start: 0.7281 (mptm) cc_final: 0.6490 (mtpp) REVERT: C 814 LYS cc_start: 0.7924 (mmpt) cc_final: 0.6701 (ttpp) REVERT: C 1010 GLN cc_start: 0.8355 (mp10) cc_final: 0.7917 (mt0) outliers start: 47 outliers final: 29 residues processed: 154 average time/residue: 0.4561 time to fit residues: 84.7556 Evaluate side-chains 146 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 180 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 268 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 198 optimal weight: 0.0060 chunk 102 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 115 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 519 HIS C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.272044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.211502 restraints weight = 31411.282| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 2.28 r_work: 0.3862 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.9007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25140 Z= 0.133 Angle : 0.565 9.676 34213 Z= 0.300 Chirality : 0.044 0.184 3873 Planarity : 0.005 0.067 4411 Dihedral : 4.343 24.053 3349 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.79 % Rotamer: Outliers : 1.46 % Allowed : 19.33 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 3072 helix: 1.98 (0.21), residues: 671 sheet: 0.48 (0.20), residues: 651 loop : -1.95 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.015 0.001 TYR C 265 PHE 0.022 0.001 PHE C 238 TRP 0.015 0.001 TRP B 436 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00262 (25098) covalent geometry : angle 0.56155 (34129) SS BOND : bond 0.00379 ( 42) SS BOND : angle 1.37336 ( 84) hydrogen bonds : bond 0.07432 ( 1014) hydrogen bonds : angle 5.23106 ( 2748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.3431 (OUTLIER) cc_final: 0.3139 (t) REVERT: A 361 CYS cc_start: 0.1694 (OUTLIER) cc_final: 0.0538 (t) REVERT: A 808 ASP cc_start: 0.6310 (OUTLIER) cc_final: 0.5984 (m-30) REVERT: A 904 TYR cc_start: 0.7536 (m-10) cc_final: 0.7174 (m-10) REVERT: A 1010 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: A 1138 TYR cc_start: 0.7156 (t80) cc_final: 0.6416 (m-80) REVERT: B 192 PHE cc_start: 0.4334 (m-80) cc_final: 0.3951 (m-80) REVERT: B 646 ARG cc_start: 0.7798 (mpp80) cc_final: 0.7468 (mtp180) REVERT: B 654 GLU cc_start: 0.7259 (tt0) cc_final: 0.6807 (tp30) REVERT: B 655 TYR cc_start: 0.7227 (t80) cc_final: 0.6647 (t80) REVERT: B 664 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7584 (mt) REVERT: B 751 ASN cc_start: 0.7919 (t0) cc_final: 0.7668 (t0) REVERT: B 964 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7392 (tttp) REVERT: B 1005 GLN cc_start: 0.7836 (mm110) cc_final: 0.7589 (mt0) REVERT: B 1138 TYR cc_start: 0.6675 (t80) cc_final: 0.6221 (m-80) REVERT: C 115 GLN cc_start: 0.2331 (OUTLIER) cc_final: 0.1599 (pm20) REVERT: C 226 LEU cc_start: -0.0956 (OUTLIER) cc_final: -0.1246 (pt) REVERT: C 646 ARG cc_start: 0.8030 (mpt-90) cc_final: 0.7743 (mtt90) REVERT: C 814 LYS cc_start: 0.7830 (mmpt) cc_final: 0.6692 (tmtp) REVERT: C 933 LYS cc_start: 0.6959 (mtpt) cc_final: 0.6656 (ttpt) REVERT: C 1010 GLN cc_start: 0.8238 (mp10) cc_final: 0.7786 (mt0) outliers start: 40 outliers final: 26 residues processed: 152 average time/residue: 0.4593 time to fit residues: 84.1175 Evaluate side-chains 143 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 172 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 11 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 149 optimal weight: 0.0980 chunk 212 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.271834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.212230 restraints weight = 31576.176| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 2.43 r_work: 0.3845 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.9020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.277 25140 Z= 0.198 Angle : 0.838 59.196 34213 Z= 0.464 Chirality : 0.065 2.744 3873 Planarity : 0.005 0.083 4411 Dihedral : 4.345 23.977 3349 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.11 % Favored : 94.82 % Rotamer: Outliers : 1.50 % Allowed : 19.33 % Favored : 79.17 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.15), residues: 3072 helix: 1.99 (0.21), residues: 671 sheet: 0.48 (0.20), residues: 651 loop : -1.95 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG B 567 TYR 0.016 0.001 TYR C 265 PHE 0.021 0.001 PHE C 238 TRP 0.014 0.001 TRP B 436 HIS 0.003 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00385 (25098) covalent geometry : angle 0.83682 (34129) SS BOND : bond 0.00368 ( 42) SS BOND : angle 1.33209 ( 84) hydrogen bonds : bond 0.07475 ( 1014) hydrogen bonds : angle 5.23433 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11722.42 seconds wall clock time: 199 minutes 38.13 seconds (11978.13 seconds total)