Starting phenix.real_space_refine on Sat Jun 21 07:57:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hri_34974/06_2025/8hri_34974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hri_34974/06_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_34974/06_2025/8hri_34974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hri_34974/06_2025/8hri_34974.map" model { file = "/net/cci-nas-00/data/ceres_data/8hri_34974/06_2025/8hri_34974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hri_34974/06_2025/8hri_34974.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.115 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.56, per 1000 atoms: 0.63 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: 6.07 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.71 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: 10.78 Time building geometry restraints manager: 7.20 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: 12.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 58.980 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (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 TRP 0.015 0.001 TRP A 886 HIS 0.002 0.000 HIS C1088 PHE 0.020 0.001 PHE A 486 TYR 0.018 0.001 TYR C 351 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd hydrogen bonds : bond 0.12450 ( 1014) hydrogen bonds : angle 5.76938 ( 2748) SS BOND : bond 0.00601 ( 42) SS BOND : angle 1.54156 ( 84) covalent geometry : bond 0.00312 (25098) covalent geometry : angle 0.61098 (34129) *********************** 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 : 2.418 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: 1.2425 time to fit residues: 362.2739 Evaluate side-chains 105 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 3.174 ------------------------------------------------------------------------------- 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 263 optimal weight: 0.0870 chunk 236 optimal weight: 0.0270 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 283 optimal weight: 0.8980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 613 GLN A 644 GLN A1083 HIS ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 450 ASN B 564 GLN B 675 GLN B 804 GLN B 824 ASN C 165 ASN C 658 ASN C1002 GLN C1083 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5106 r_free = 0.5106 target = 0.309672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.268896 restraints weight = 35629.840| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 3.06 r_work: 0.4337 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 25140 Z= 0.176 Angle : 0.657 10.740 34213 Z= 0.348 Chirality : 0.046 0.189 3873 Planarity : 0.006 0.077 4411 Dihedral : 4.591 58.072 3352 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 1.42 % Allowed : 8.77 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3072 helix: 1.71 (0.20), residues: 701 sheet: 0.86 (0.19), residues: 709 loop : -1.61 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.005 0.001 HIS B1064 PHE 0.027 0.002 PHE B 275 TYR 0.025 0.002 TYR C 453 ARG 0.008 0.001 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.06290 ( 1014) hydrogen bonds : angle 5.13644 ( 2748) SS BOND : bond 0.00595 ( 42) SS BOND : angle 1.55018 ( 84) covalent geometry : bond 0.00372 (25098) covalent geometry : angle 0.65367 (34129) *********************** 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 173 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 2.420 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.7491 (mtp) cc_final: 0.7279 (mtp) REVERT: A 786 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7237 (pmtt) REVERT: A 869 MET cc_start: 0.7458 (mtt) cc_final: 0.6786 (mtt) REVERT: A 916 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7506 (tt) REVERT: B 44 ARG cc_start: 0.5228 (OUTLIER) cc_final: 0.4532 (ptp-170) REVERT: B 153 MET cc_start: 0.0136 (tpp) cc_final: -0.0849 (tmm) REVERT: B 921 LYS cc_start: 0.5702 (mtpp) cc_final: 0.5300 (pttm) outliers start: 39 outliers final: 12 residues processed: 167 average time/residue: 1.2149 time to fit residues: 238.9114 Evaluate side-chains 106 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 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 368 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 283 optimal weight: 0.0270 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A1101 HIS A1135 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 675 GLN B 901 GLN B1101 HIS C 901 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.282896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.225380 restraints weight = 31953.720| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.70 r_work: 0.3892 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 25140 Z= 0.260 Angle : 0.830 9.498 34213 Z= 0.449 Chirality : 0.053 0.658 3873 Planarity : 0.007 0.086 4411 Dihedral : 5.413 45.540 3351 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.11 % Rotamer: Outliers : 2.37 % Allowed : 13.01 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3072 helix: 0.74 (0.19), residues: 692 sheet: 0.72 (0.19), residues: 662 loop : -1.80 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 886 HIS 0.008 0.002 HIS C1101 PHE 0.041 0.003 PHE B 338 TYR 0.033 0.003 TYR C 91 ARG 0.010 0.001 ARG C 273 Details of bonding type rmsd hydrogen bonds : bond 0.12415 ( 1014) hydrogen bonds : angle 6.11474 ( 2748) SS BOND : bond 0.00697 ( 42) SS BOND : angle 2.38676 ( 84) covalent geometry : bond 0.00548 (25098) covalent geometry : angle 0.82216 (34129) *********************** 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 233 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 168 time to evaluate : 2.707 Fit side-chains revert: symmetry clash REVERT: A 619 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: A 646 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7284 (mpp80) REVERT: A 904 TYR cc_start: 0.7446 (m-10) cc_final: 0.7138 (m-10) REVERT: A 1031 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: A 1113 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: A 1138 TYR cc_start: 0.6955 (t80) cc_final: 0.6180 (m-80) REVERT: B 153 MET cc_start: 0.0457 (tpp) cc_final: -0.0977 (pmm) REVERT: B 646 ARG cc_start: 0.7363 (mmp80) cc_final: 0.7148 (mpp80) REVERT: B 1138 TYR cc_start: 0.6638 (t80) cc_final: 0.6412 (m-80) REVERT: C 61 ASN cc_start: 0.3035 (OUTLIER) cc_final: 0.2073 (p0) REVERT: C 310 LYS cc_start: 0.7105 (ttpt) cc_final: 0.6078 (tptt) REVERT: C 644 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6783 (tt0) REVERT: C 814 LYS cc_start: 0.7531 (mmpt) cc_final: 0.6748 (tttp) REVERT: C 851 CYS cc_start: 0.5700 (OUTLIER) cc_final: 0.5495 (p) outliers start: 65 outliers final: 16 residues processed: 219 average time/residue: 1.2686 time to fit residues: 330.7382 Evaluate side-chains 130 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 851 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 89 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 278 optimal weight: 0.0050 chunk 3 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 644 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 901 GLN A 935 GLN A 965 GLN A1101 HIS ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1101 HIS C 49 HIS C 52 GLN C 965 GLN C1058 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.277628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.218134 restraints weight = 31864.401| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.62 r_work: 0.3839 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 25140 Z= 0.212 Angle : 0.711 9.915 34213 Z= 0.380 Chirality : 0.049 0.256 3873 Planarity : 0.006 0.081 4411 Dihedral : 5.037 34.920 3349 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 2.74 % Allowed : 14.87 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3072 helix: 1.28 (0.20), residues: 688 sheet: 0.58 (0.19), residues: 672 loop : -1.90 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 353 HIS 0.006 0.001 HIS A1088 PHE 0.043 0.002 PHE A 275 TYR 0.027 0.002 TYR A 796 ARG 0.009 0.001 ARG A1107 Details of bonding type rmsd hydrogen bonds : bond 0.09790 ( 1014) hydrogen bonds : angle 5.73842 ( 2748) SS BOND : bond 0.01017 ( 42) SS BOND : angle 1.86817 ( 84) covalent geometry : bond 0.00465 (25098) covalent geometry : angle 0.70601 (34129) *********************** 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 199 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 124 time to evaluate : 2.509 Fit side-chains REVERT: A 646 ARG cc_start: 0.8285 (tpp80) cc_final: 0.8000 (tpp80) REVERT: A 1010 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: A 1113 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: A 1117 THR cc_start: 0.8393 (m) cc_final: 0.8158 (p) REVERT: A 1138 TYR cc_start: 0.7067 (t80) cc_final: 0.6313 (m-80) REVERT: B 278 LYS cc_start: 0.5961 (OUTLIER) cc_final: 0.5531 (tmtt) REVERT: B 654 GLU cc_start: 0.6926 (tt0) cc_final: 0.6525 (tp30) REVERT: B 755 GLN cc_start: 0.8141 (mt0) cc_final: 0.7904 (mt0) REVERT: B 957 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: C 61 ASN cc_start: 0.3060 (OUTLIER) cc_final: 0.2071 (p0) REVERT: C 644 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7299 (tp40) REVERT: C 646 ARG cc_start: 0.7572 (mmt180) cc_final: 0.7254 (mtt90) REVERT: C 751 ASN cc_start: 0.8133 (t0) cc_final: 0.7925 (t0) REVERT: C 814 LYS cc_start: 0.7759 (mmpt) cc_final: 0.6765 (tttp) outliers start: 75 outliers final: 22 residues processed: 177 average time/residue: 1.1374 time to fit residues: 243.0130 Evaluate side-chains 123 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 644 GLN 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 Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 198 optimal weight: 0.0040 chunk 147 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 270 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 293 optimal weight: 0.5980 chunk 235 optimal weight: 0.2980 chunk 260 optimal weight: 0.0670 chunk 200 optimal weight: 0.8980 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN B 914 ASN C 196 ASN C 641 ASN C 709 ASN C1058 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.281794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.224273 restraints weight = 32127.607| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.61 r_work: 0.3917 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25140 Z= 0.134 Angle : 0.576 11.773 34213 Z= 0.307 Chirality : 0.044 0.187 3873 Planarity : 0.005 0.065 4411 Dihedral : 4.469 26.553 3349 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.57 % Rotamer: Outliers : 1.72 % Allowed : 16.99 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3072 helix: 1.79 (0.21), residues: 680 sheet: 0.60 (0.19), residues: 691 loop : -1.80 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.002 0.000 HIS A1088 PHE 0.017 0.001 PHE C 375 TYR 0.018 0.001 TYR C 265 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.07233 ( 1014) hydrogen bonds : angle 5.29337 ( 2748) SS BOND : bond 0.00437 ( 42) SS BOND : angle 2.04629 ( 84) covalent geometry : bond 0.00254 (25098) covalent geometry : angle 0.56731 (34129) *********************** 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 152 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 2.620 Fit side-chains REVERT: A 233 ILE cc_start: 0.1580 (OUTLIER) cc_final: 0.0664 (mm) REVERT: A 646 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7985 (tpp80) REVERT: A 992 GLN cc_start: 0.4314 (OUTLIER) cc_final: 0.4088 (mt0) REVERT: A 1010 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: A 1113 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: A 1117 THR cc_start: 0.8338 (m) cc_final: 0.8118 (p) REVERT: A 1138 TYR cc_start: 0.7120 (t80) cc_final: 0.6261 (m-80) REVERT: B 278 LYS cc_start: 0.5700 (OUTLIER) cc_final: 0.5473 (ptmm) REVERT: B 654 GLU cc_start: 0.7025 (tt0) cc_final: 0.6547 (tp30) REVERT: B 655 TYR cc_start: 0.6761 (t80) cc_final: 0.6366 (t80) REVERT: B 663 ASP cc_start: 0.7772 (t70) cc_final: 0.7458 (t70) REVERT: B 664 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7476 (mt) REVERT: B 957 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: B 1134 ASN cc_start: 0.8388 (m-40) cc_final: 0.8160 (m110) REVERT: C 61 ASN cc_start: 0.3077 (OUTLIER) cc_final: 0.2110 (p0) REVERT: C 130 VAL cc_start: 0.4044 (m) cc_final: 0.3753 (t) REVERT: C 646 ARG cc_start: 0.7602 (mmt180) cc_final: 0.7211 (mtt90) REVERT: C 709 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6917 (m-40) REVERT: C 814 LYS cc_start: 0.7758 (mmpt) cc_final: 0.6731 (tttp) REVERT: C 1115 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.7798 (mt) outliers start: 47 outliers final: 20 residues processed: 144 average time/residue: 1.2532 time to fit residues: 218.2818 Evaluate side-chains 126 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 LYS 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 914 ASN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 934 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 219 optimal weight: 0.2980 chunk 276 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 239 optimal weight: 0.0980 chunk 171 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 709 ASN C 978 ASN C1058 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.280347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.221937 restraints weight = 32046.176| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.64 r_work: 0.3900 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25140 Z= 0.134 Angle : 0.561 7.151 34213 Z= 0.298 Chirality : 0.044 0.196 3873 Planarity : 0.005 0.063 4411 Dihedral : 4.347 25.550 3349 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 1.94 % Allowed : 17.14 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3072 helix: 1.82 (0.21), residues: 686 sheet: 0.52 (0.19), residues: 711 loop : -1.76 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.015 0.001 PHE B 565 TYR 0.019 0.001 TYR B 904 ARG 0.003 0.000 ARG C 237 Details of bonding type rmsd hydrogen bonds : bond 0.07484 ( 1014) hydrogen bonds : angle 5.18783 ( 2748) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.40629 ( 84) covalent geometry : bond 0.00263 (25098) covalent geometry : angle 0.55686 (34129) *********************** 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 154 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 3.453 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.1569 (OUTLIER) cc_final: 0.0682 (mm) REVERT: A 333 THR cc_start: 0.3535 (OUTLIER) cc_final: 0.3304 (t) REVERT: A 646 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8068 (tpp80) REVERT: A 934 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7181 (tt) REVERT: A 992 GLN cc_start: 0.4295 (OUTLIER) cc_final: 0.4028 (mt0) REVERT: A 1010 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: A 1113 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: A 1117 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8247 (p) REVERT: A 1138 TYR cc_start: 0.7074 (t80) cc_final: 0.6232 (m-80) REVERT: B 278 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.5519 (ptmm) REVERT: B 654 GLU cc_start: 0.7048 (tt0) cc_final: 0.6555 (tp30) REVERT: B 655 TYR cc_start: 0.6790 (t80) cc_final: 0.6396 (t80) REVERT: B 663 ASP cc_start: 0.7792 (t70) cc_final: 0.7463 (t70) REVERT: B 664 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7525 (mt) REVERT: B 731 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7636 (mtp) REVERT: B 1134 ASN cc_start: 0.8385 (m-40) cc_final: 0.8159 (m110) REVERT: C 61 ASN cc_start: 0.3081 (OUTLIER) cc_final: 0.2102 (p0) REVERT: C 130 VAL cc_start: 0.4211 (m) cc_final: 0.3966 (t) REVERT: C 644 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6019 (tt0) REVERT: C 748 GLU cc_start: 0.5930 (mp0) cc_final: 0.5705 (mp0) REVERT: C 814 LYS cc_start: 0.7795 (mmpt) cc_final: 0.6720 (tttp) outliers start: 53 outliers final: 25 residues processed: 143 average time/residue: 1.1249 time to fit residues: 193.5781 Evaluate side-chains 125 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS 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 992 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 565 PHE 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 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR 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 Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 206 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 0.0980 chunk 154 optimal weight: 0.5980 chunk 168 optimal weight: 0.0970 chunk 285 optimal weight: 0.9990 chunk 197 optimal weight: 0.0980 chunk 235 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS B 901 GLN B 914 ASN C 422 ASN C 901 GLN C 935 GLN C1058 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.283217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.225020 restraints weight = 32351.292| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.33 r_work: 0.3982 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25140 Z= 0.112 Angle : 0.520 8.102 34213 Z= 0.273 Chirality : 0.043 0.168 3873 Planarity : 0.005 0.063 4411 Dihedral : 4.077 24.646 3349 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 1.42 % Allowed : 18.09 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3072 helix: 2.01 (0.21), residues: 688 sheet: 0.55 (0.19), residues: 689 loop : -1.65 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A1088 PHE 0.017 0.001 PHE C 562 TYR 0.014 0.001 TYR A1067 ARG 0.004 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.05992 ( 1014) hydrogen bonds : angle 4.95066 ( 2748) SS BOND : bond 0.00331 ( 42) SS BOND : angle 1.10090 ( 84) covalent geometry : bond 0.00217 (25098) covalent geometry : angle 0.51732 (34129) *********************** 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 137 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 4.016 Fit side-chains REVERT: A 233 ILE cc_start: 0.1598 (OUTLIER) cc_final: 0.0830 (mt) REVERT: A 1010 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: A 1113 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: A 1138 TYR cc_start: 0.7103 (t80) cc_final: 0.6308 (m-80) REVERT: B 278 LYS cc_start: 0.5665 (ptmm) cc_final: 0.5465 (ptmm) REVERT: B 654 GLU cc_start: 0.6976 (tt0) cc_final: 0.6529 (tp30) REVERT: B 655 TYR cc_start: 0.6738 (t80) cc_final: 0.6390 (t80) REVERT: B 663 ASP cc_start: 0.7719 (t70) cc_final: 0.7412 (t70) REVERT: B 664 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7492 (mt) REVERT: B 754 LEU cc_start: 0.7968 (pt) cc_final: 0.7607 (mt) REVERT: C 130 VAL cc_start: 0.4110 (m) cc_final: 0.3892 (t) REVERT: C 576 VAL cc_start: 0.3993 (OUTLIER) cc_final: 0.3592 (m) REVERT: C 646 ARG cc_start: 0.7575 (mmt180) cc_final: 0.7198 (mtt90) REVERT: C 748 GLU cc_start: 0.5944 (mp0) cc_final: 0.5733 (mp0) REVERT: C 814 LYS cc_start: 0.7748 (mmpt) cc_final: 0.6728 (tttp) outliers start: 39 outliers final: 20 residues processed: 132 average time/residue: 1.4327 time to fit residues: 230.8007 Evaluate side-chains 111 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 565 PHE 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 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR 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 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 154 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 675 GLN B 755 GLN B 901 GLN C 519 HIS 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 = 0.4788 r_free = 0.4788 target = 0.267084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.204073 restraints weight = 30870.283| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.56 r_work: 0.3719 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.8563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 25140 Z= 0.285 Angle : 0.796 9.887 34213 Z= 0.430 Chirality : 0.052 0.274 3873 Planarity : 0.006 0.063 4411 Dihedral : 5.228 25.637 3349 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.75 % Rotamer: Outliers : 2.08 % Allowed : 18.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3072 helix: 1.18 (0.20), residues: 680 sheet: 0.45 (0.20), residues: 630 loop : -1.98 (0.13), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 353 HIS 0.013 0.002 HIS A1048 PHE 0.055 0.003 PHE C 194 TYR 0.037 0.003 TYR C 279 ARG 0.012 0.001 ARG B1000 Details of bonding type rmsd hydrogen bonds : bond 0.12911 ( 1014) hydrogen bonds : angle 6.03098 ( 2748) SS BOND : bond 0.00600 ( 42) SS BOND : angle 2.11769 ( 84) covalent geometry : bond 0.00625 (25098) covalent geometry : angle 0.79020 (34129) *********************** 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 185 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 128 time to evaluate : 2.972 Fit side-chains revert: symmetry clash REVERT: A 333 THR cc_start: 0.3382 (OUTLIER) cc_final: 0.3119 (t) REVERT: A 934 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7397 (tt) REVERT: A 992 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5997 (mt0) REVERT: A 1010 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: A 1113 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: A 1138 TYR cc_start: 0.7223 (t80) cc_final: 0.6306 (m-80) REVERT: B 278 LYS cc_start: 0.5820 (OUTLIER) cc_final: 0.5551 (tttm) REVERT: B 529 LYS cc_start: 0.6383 (mmpt) cc_final: 0.6090 (mmmm) REVERT: B 654 GLU cc_start: 0.7284 (tt0) cc_final: 0.6779 (tp30) REVERT: B 655 TYR cc_start: 0.7099 (t80) cc_final: 0.6535 (t80) REVERT: B 663 ASP cc_start: 0.7831 (t70) cc_final: 0.7592 (t0) REVERT: B 664 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7581 (mt) REVERT: B 964 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8235 (ttpp) REVERT: B 979 ASP cc_start: 0.6663 (t0) cc_final: 0.6351 (m-30) REVERT: B 1138 TYR cc_start: 0.6612 (t80) cc_final: 0.6205 (m-80) REVERT: C 61 ASN cc_start: 0.3116 (OUTLIER) cc_final: 0.2069 (p0) REVERT: C 130 VAL cc_start: 0.5305 (m) cc_final: 0.4824 (t) REVERT: C 168 PHE cc_start: 0.6742 (t80) cc_final: 0.3115 (m-80) REVERT: C 646 ARG cc_start: 0.8105 (mmt180) cc_final: 0.7751 (mtt90) REVERT: C 751 ASN cc_start: 0.8455 (t0) cc_final: 0.8144 (t0) REVERT: C 795 LYS cc_start: 0.7322 (mptm) cc_final: 0.6395 (mtpp) REVERT: C 814 LYS cc_start: 0.7950 (mmpt) cc_final: 0.6602 (ttpp) outliers start: 57 outliers final: 26 residues processed: 174 average time/residue: 1.2386 time to fit residues: 256.7236 Evaluate side-chains 143 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 796 TYR 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 992 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 382 VAL 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 914 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS 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 991 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 264 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 263 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** B 675 GLN C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.268898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.207613 restraints weight = 31163.563| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.57 r_work: 0.3760 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.8854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25140 Z= 0.188 Angle : 0.660 11.891 34213 Z= 0.354 Chirality : 0.047 0.203 3873 Planarity : 0.006 0.066 4411 Dihedral : 4.881 25.114 3349 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 1.57 % Allowed : 18.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3072 helix: 1.46 (0.20), residues: 677 sheet: 0.44 (0.20), residues: 624 loop : -2.05 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.012 0.001 HIS A1083 PHE 0.031 0.002 PHE B 377 TYR 0.027 0.002 TYR B 904 ARG 0.006 0.000 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.09897 ( 1014) hydrogen bonds : angle 5.63240 ( 2748) SS BOND : bond 0.00467 ( 42) SS BOND : angle 1.73759 ( 84) covalent geometry : bond 0.00398 (25098) covalent geometry : angle 0.65507 (34129) *********************** 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 159 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 2.723 Fit side-chains REVERT: A 333 THR cc_start: 0.3395 (OUTLIER) cc_final: 0.3153 (t) REVERT: A 362 VAL cc_start: 0.1222 (OUTLIER) cc_final: 0.0849 (m) REVERT: A 655 TYR cc_start: 0.7819 (t80) cc_final: 0.7466 (t80) REVERT: A 934 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7337 (tt) REVERT: A 1010 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: A 1113 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: A 1138 TYR cc_start: 0.7208 (t80) cc_final: 0.6354 (m-80) REVERT: B 192 PHE cc_start: 0.4405 (m-80) cc_final: 0.3971 (m-80) REVERT: B 532 ASN cc_start: 0.6693 (m-40) cc_final: 0.6299 (m110) REVERT: B 654 GLU cc_start: 0.7375 (tt0) cc_final: 0.6892 (tp30) REVERT: B 655 TYR cc_start: 0.7268 (t80) cc_final: 0.6699 (t80) REVERT: B 663 ASP cc_start: 0.7894 (t70) cc_final: 0.7661 (t0) REVERT: B 664 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7584 (mt) REVERT: B 779 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7554 (tp40) REVERT: B 964 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7790 (tttp) REVERT: B 979 ASP cc_start: 0.6799 (t0) cc_final: 0.6594 (m-30) REVERT: B 1138 TYR cc_start: 0.6645 (t80) cc_final: 0.6287 (m-80) REVERT: C 61 ASN cc_start: 0.3115 (OUTLIER) cc_final: 0.1750 (p0) REVERT: C 226 LEU cc_start: -0.0634 (OUTLIER) cc_final: -0.1265 (pp) REVERT: C 646 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7768 (mtt90) REVERT: C 751 ASN cc_start: 0.8439 (t0) cc_final: 0.7844 (m-40) REVERT: C 795 LYS cc_start: 0.7312 (mptm) cc_final: 0.6576 (mtpp) REVERT: C 814 LYS cc_start: 0.7917 (mmpt) cc_final: 0.6635 (ttpp) outliers start: 43 outliers final: 24 residues processed: 150 average time/residue: 1.0827 time to fit residues: 198.0602 Evaluate side-chains 138 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP 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 779 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 226 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 914 ASN Chi-restraints excluded: chain C residue 991 VAL 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 174 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 137 optimal weight: 0.0050 chunk 68 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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** B 675 GLN B 755 GLN B 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.267084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.215151 restraints weight = 31005.784| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.72 r_work: 0.3795 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.9372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25140 Z= 0.183 Angle : 0.651 9.869 34213 Z= 0.350 Chirality : 0.047 0.207 3873 Planarity : 0.006 0.065 4411 Dihedral : 4.804 26.286 3349 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 1.42 % Allowed : 19.40 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3072 helix: 1.56 (0.21), residues: 677 sheet: 0.35 (0.20), residues: 624 loop : -2.02 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 353 HIS 0.004 0.001 HIS C1048 PHE 0.040 0.002 PHE B 377 TYR 0.032 0.002 TYR B 904 ARG 0.007 0.001 ARG A1107 Details of bonding type rmsd hydrogen bonds : bond 0.09866 ( 1014) hydrogen bonds : angle 5.60827 ( 2748) SS BOND : bond 0.00421 ( 42) SS BOND : angle 1.66841 ( 84) covalent geometry : bond 0.00374 (25098) covalent geometry : angle 0.64700 (34129) ********************** 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 160 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 2.625 Fit side-chains REVERT: A 233 ILE cc_start: 0.2226 (OUTLIER) cc_final: 0.1576 (tp) REVERT: A 333 THR cc_start: 0.3346 (OUTLIER) cc_final: 0.3081 (t) REVERT: A 362 VAL cc_start: 0.0768 (OUTLIER) cc_final: 0.0339 (m) REVERT: A 934 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7419 (tt) REVERT: A 1010 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: A 1031 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: A 1113 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: A 1138 TYR cc_start: 0.7263 (t80) cc_final: 0.6584 (m-80) REVERT: B 278 LYS cc_start: 0.6184 (ptmm) cc_final: 0.5941 (tttm) REVERT: B 529 LYS cc_start: 0.6980 (mmpt) cc_final: 0.5909 (mmmt) REVERT: B 532 ASN cc_start: 0.7078 (m-40) cc_final: 0.6719 (m-40) REVERT: B 646 ARG cc_start: 0.7893 (mpp80) cc_final: 0.7560 (mtt180) REVERT: B 654 GLU cc_start: 0.7148 (tt0) cc_final: 0.6863 (tp30) REVERT: B 655 TYR cc_start: 0.7202 (t80) cc_final: 0.6661 (t80) REVERT: B 664 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7614 (mt) REVERT: B 751 ASN cc_start: 0.8152 (t0) cc_final: 0.7883 (t0) REVERT: B 964 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7772 (tttp) REVERT: B 1138 TYR cc_start: 0.6693 (t80) cc_final: 0.6482 (m-80) REVERT: C 61 ASN cc_start: 0.2843 (OUTLIER) cc_final: 0.1655 (p0) REVERT: C 646 ARG cc_start: 0.8111 (mmt180) cc_final: 0.7864 (mtt90) REVERT: C 751 ASN cc_start: 0.8485 (t0) cc_final: 0.8077 (m-40) REVERT: C 814 LYS cc_start: 0.7862 (mmpt) cc_final: 0.6830 (tttp) outliers start: 39 outliers final: 25 residues processed: 153 average time/residue: 1.1076 time to fit residues: 203.6640 Evaluate side-chains 140 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 389 ASP 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 975 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS 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 991 VAL 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 309 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 293 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** B 394 ASN B 675 GLN B 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.265662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.228523 restraints weight = 31028.551| |-----------------------------------------------------------------------------| r_work (start): 0.4469 rms_B_bonded: 2.18 r_work: 0.4053 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.9676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25140 Z= 0.179 Angle : 0.648 9.557 34213 Z= 0.348 Chirality : 0.046 0.177 3873 Planarity : 0.006 0.067 4411 Dihedral : 4.809 25.318 3349 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 1.46 % Allowed : 19.73 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3072 helix: 1.57 (0.21), residues: 673 sheet: 0.21 (0.20), residues: 601 loop : -2.03 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 353 HIS 0.004 0.001 HIS C 519 PHE 0.034 0.002 PHE B 377 TYR 0.040 0.002 TYR B 904 ARG 0.005 0.000 ARG A1107 Details of bonding type rmsd hydrogen bonds : bond 0.09819 ( 1014) hydrogen bonds : angle 5.58015 ( 2748) SS BOND : bond 0.00518 ( 42) SS BOND : angle 1.78187 ( 84) covalent geometry : bond 0.00372 (25098) covalent geometry : angle 0.64295 (34129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21095.11 seconds wall clock time: 367 minutes 36.58 seconds (22056.58 seconds total)