Starting phenix.real_space_refine on Mon Sep 30 06:27:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/09_2024/8hri_34974.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/09_2024/8hri_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/09_2024/8hri_34974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/09_2024/8hri_34974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/09_2024/8hri_34974.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hri_34974/09_2024/8hri_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 16.96, per 1000 atoms: 0.69 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: 5.29 Conformation dependent library (CDL) restraints added in 3.0 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: 3.08 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: 10.70 Time building geometry restraints manager: 6.36 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: 19.450 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 55.850 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.480 ------------------------------------------------------------------------------- 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 25098 Z= 0.205 Angle : 0.611 12.861 34129 Z= 0.339 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 *********************** 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 fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 2.665 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: 1.1715 time to fit residues: 341.1831 Evaluate side-chains 105 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4738 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 25098 Z= 0.247 Angle : 0.654 10.740 34129 Z= 0.346 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 *********************** 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 fitting. rotamer outliers: 39 poor density : 134 time to evaluate : 2.499 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.7464 (mtp) cc_final: 0.7214 (mtp) REVERT: A 786 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6974 (pmtt) REVERT: A 869 MET cc_start: 0.6910 (mtt) cc_final: 0.6141 (mtt) REVERT: A 916 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7200 (tt) REVERT: B 44 ARG cc_start: 0.4918 (OUTLIER) cc_final: 0.4693 (ptp-170) REVERT: B 153 MET cc_start: 0.0293 (tpp) cc_final: -0.0827 (tmm) REVERT: B 921 LYS cc_start: 0.5555 (mtpp) cc_final: 0.5142 (pttm) REVERT: C 1010 GLN cc_start: 0.7666 (mp10) cc_final: 0.7431 (mt0) outliers start: 39 outliers final: 12 residues processed: 167 average time/residue: 1.2278 time to fit residues: 241.5477 Evaluate side-chains 107 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 157 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 0.0020 chunk 192 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 306 optimal weight: 0.6980 chunk 252 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 644 GLN A1101 HIS A1135 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 675 GLN B1083 HIS C 49 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1101 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5074 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.223 25098 Z= 0.206 Angle : 0.569 8.042 34129 Z= 0.303 Chirality : 0.044 0.242 3873 Planarity : 0.005 0.086 4411 Dihedral : 4.192 42.907 3351 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 1.64 % Allowed : 11.91 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3072 helix: 2.08 (0.21), residues: 687 sheet: 0.81 (0.19), residues: 668 loop : -1.47 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 886 HIS 0.004 0.001 HIS A1101 PHE 0.039 0.001 PHE C 43 TYR 0.016 0.001 TYR C1067 ARG 0.007 0.000 ARG C 44 *********************** 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 176 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 131 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 646 ARG cc_start: 0.6618 (tpp80) cc_final: 0.5909 (mmp-170) REVERT: A 711 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8492 (t) REVERT: A 869 MET cc_start: 0.6945 (mtt) cc_final: 0.6253 (mtt) REVERT: B 44 ARG cc_start: 0.5177 (ptp-170) cc_final: 0.4363 (ptp-170) REVERT: B 646 ARG cc_start: 0.6853 (mmp80) cc_final: 0.6176 (mpp80) REVERT: B 904 TYR cc_start: 0.6935 (m-10) cc_final: 0.6653 (m-10) REVERT: B 955 ASN cc_start: 0.6672 (t0) cc_final: 0.6449 (m-40) REVERT: C 61 ASN cc_start: 0.2565 (OUTLIER) cc_final: 0.1556 (p0) REVERT: C 1071 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7414 (mt0) outliers start: 45 outliers final: 17 residues processed: 168 average time/residue: 1.1333 time to fit residues: 227.2538 Evaluate side-chains 115 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 130 VAL 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 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1122 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 280 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 914 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 603 ASN B 675 GLN C 755 GLN C 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 25098 Z= 0.222 Angle : 0.615 7.685 34129 Z= 0.328 Chirality : 0.046 0.209 3873 Planarity : 0.005 0.078 4411 Dihedral : 4.285 22.736 3349 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 1.97 % Allowed : 13.88 % Favored : 84.14 % 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: -0.30 (0.15), residues: 3072 helix: 1.92 (0.21), residues: 682 sheet: 0.73 (0.19), residues: 667 loop : -1.56 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 886 HIS 0.003 0.001 HIS C1064 PHE 0.019 0.001 PHE C 201 TYR 0.039 0.002 TYR C 756 ARG 0.011 0.000 ARG C 44 *********************** 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 177 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 123 time to evaluate : 2.278 Fit side-chains REVERT: A 619 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: A 711 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8915 (t) REVERT: A 869 MET cc_start: 0.7319 (mtt) cc_final: 0.6715 (mtt) REVERT: A 1113 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: B 153 MET cc_start: 0.0514 (tpp) cc_final: -0.0562 (ttp) REVERT: B 646 ARG cc_start: 0.7093 (mmp80) cc_final: 0.6839 (mpp80) REVERT: C 310 LYS cc_start: 0.6860 (ttpt) cc_final: 0.6014 (tptt) REVERT: C 851 CYS cc_start: 0.5411 (OUTLIER) cc_final: 0.5204 (p) REVERT: C 969 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6688 (tppp) outliers start: 54 outliers final: 24 residues processed: 168 average time/residue: 1.0343 time to fit residues: 210.2197 Evaluate side-chains 121 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1096 VAL 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 394 ASN Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 664 ILE 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 934 ILE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.3980 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 A 804 GLN A 901 GLN A 914 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 709 ASN B 901 GLN B 957 GLN B1101 HIS C 52 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 25098 Z= 0.317 Angle : 0.720 10.471 34129 Z= 0.390 Chirality : 0.049 0.264 3873 Planarity : 0.006 0.075 4411 Dihedral : 4.868 24.767 3349 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.43 % 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: -0.58 (0.15), residues: 3072 helix: 1.33 (0.20), residues: 683 sheet: 0.73 (0.20), residues: 663 loop : -1.65 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.006 0.001 HIS C1058 PHE 0.050 0.002 PHE A 275 TYR 0.039 0.002 TYR C 756 ARG 0.008 0.001 ARG B 408 *********************** 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 195 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 128 time to evaluate : 2.512 Fit side-chains REVERT: A 646 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7702 (tpp80) REVERT: A 1010 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: A 1031 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: A 1138 TYR cc_start: 0.6782 (t80) cc_final: 0.6395 (m-80) REVERT: B 612 TYR cc_start: 0.6572 (m-10) cc_final: 0.6308 (m-10) REVERT: B 755 GLN cc_start: 0.8010 (mt0) cc_final: 0.7776 (mt0) REVERT: B 1005 GLN cc_start: 0.7023 (mm110) cc_final: 0.6794 (mt0) REVERT: C 644 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7315 (tp40) REVERT: C 664 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8124 (mt) REVERT: C 740 MET cc_start: 0.8272 (mmm) cc_final: 0.8069 (ttt) REVERT: C 814 LYS cc_start: 0.7350 (mmpt) cc_final: 0.6399 (tttp) REVERT: C 1115 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7933 (mt) outliers start: 67 outliers final: 22 residues processed: 186 average time/residue: 1.0381 time to fit residues: 231.9498 Evaluate side-chains 124 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain 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 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 223 LEU 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 664 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 139 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 99 optimal weight: 0.0170 chunk 158 optimal weight: 10.0000 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 965 GLN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 709 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1071 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25098 Z= 0.165 Angle : 0.556 7.792 34129 Z= 0.296 Chirality : 0.044 0.212 3873 Planarity : 0.005 0.062 4411 Dihedral : 4.255 23.538 3349 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 1.68 % Allowed : 16.88 % Favored : 81.44 % 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: -0.39 (0.15), residues: 3072 helix: 1.79 (0.21), residues: 687 sheet: 0.65 (0.19), residues: 692 loop : -1.62 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.003 0.000 HIS A1088 PHE 0.015 0.001 PHE C 201 TYR 0.019 0.001 TYR A 796 ARG 0.008 0.000 ARG B 983 *********************** 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 152 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 106 time to evaluate : 2.356 Fit side-chains REVERT: A 233 ILE cc_start: 0.0643 (OUTLIER) cc_final: 0.0134 (mt) REVERT: A 646 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7557 (tpp80) REVERT: A 1138 TYR cc_start: 0.6779 (t80) cc_final: 0.6368 (m-80) REVERT: B 723 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7469 (p) REVERT: B 755 GLN cc_start: 0.7916 (mt0) cc_final: 0.7700 (mt0) REVERT: B 957 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: C 202 LYS cc_start: 0.4516 (OUTLIER) cc_final: 0.3816 (ttmm) REVERT: C 814 LYS cc_start: 0.7359 (mmpt) cc_final: 0.6406 (tttp) REVERT: C 1010 GLN cc_start: 0.7737 (mm110) cc_final: 0.7226 (mt0) REVERT: C 1115 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7734 (mt) outliers start: 46 outliers final: 18 residues processed: 142 average time/residue: 1.0470 time to fit residues: 180.2697 Evaluate side-chains 118 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 1096 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS 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 738 CYS Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 755 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 138 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 B 675 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 641 ASN C 644 GLN C 709 ASN C1058 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25098 Z= 0.251 Angle : 0.626 7.618 34129 Z= 0.336 Chirality : 0.046 0.195 3873 Planarity : 0.005 0.061 4411 Dihedral : 4.562 23.838 3349 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 1.90 % Allowed : 17.46 % Favored : 80.64 % 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: -0.59 (0.15), residues: 3072 helix: 1.53 (0.20), residues: 693 sheet: 0.59 (0.20), residues: 659 loop : -1.71 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 353 HIS 0.005 0.001 HIS A1048 PHE 0.019 0.002 PHE B 377 TYR 0.024 0.002 TYR C 756 ARG 0.009 0.001 ARG B 408 *********************** 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 166 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 114 time to evaluate : 2.756 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.1139 (OUTLIER) cc_final: 0.0561 (pp) REVERT: A 646 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7932 (tpp80) REVERT: A 1010 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: A 1031 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: A 1138 TYR cc_start: 0.6825 (t80) cc_final: 0.6470 (m-80) REVERT: B 663 ASP cc_start: 0.7741 (t70) cc_final: 0.7538 (t0) REVERT: B 664 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7808 (mt) REVERT: B 723 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7533 (p) REVERT: B 755 GLN cc_start: 0.8122 (mt0) cc_final: 0.7901 (mt0) REVERT: B 957 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: B 964 LYS cc_start: 0.7339 (ttmm) cc_final: 0.7003 (tttm) REVERT: B 1005 GLN cc_start: 0.7045 (mm110) cc_final: 0.6765 (mt0) REVERT: C 748 GLU cc_start: 0.5843 (mp0) cc_final: 0.5596 (mp0) REVERT: C 795 LYS cc_start: 0.7220 (mptm) cc_final: 0.6537 (mtpp) REVERT: C 804 GLN cc_start: 0.8289 (mt0) cc_final: 0.8083 (mt0) REVERT: C 814 LYS cc_start: 0.7499 (mmpt) cc_final: 0.6450 (tttp) REVERT: C 1010 GLN cc_start: 0.7817 (mm110) cc_final: 0.7278 (mt0) outliers start: 52 outliers final: 24 residues processed: 158 average time/residue: 1.1764 time to fit residues: 222.0672 Evaluate side-chains 138 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 655 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS 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 785 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 957 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 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 0.2980 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 606 ASN A 914 ASN B 675 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 564 GLN C 641 ASN C 709 ASN C1058 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.7987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25098 Z= 0.214 Angle : 0.595 10.278 34129 Z= 0.320 Chirality : 0.045 0.227 3873 Planarity : 0.005 0.064 4411 Dihedral : 4.475 23.654 3349 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 1.83 % Allowed : 17.98 % Favored : 80.20 % 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: -0.59 (0.15), residues: 3072 helix: 1.76 (0.21), residues: 678 sheet: 0.52 (0.20), residues: 671 loop : -1.77 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.029 0.001 PHE B 464 TYR 0.029 0.002 TYR C 707 ARG 0.012 0.000 ARG B 328 *********************** 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 169 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 119 time to evaluate : 2.866 Fit side-chains revert: symmetry clash REVERT: A 233 ILE cc_start: 0.1326 (OUTLIER) cc_final: 0.0798 (pp) REVERT: A 646 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7984 (tpp80) REVERT: A 1010 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: A 1019 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7116 (ttp80) REVERT: A 1031 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: A 1138 TYR cc_start: 0.6866 (t80) cc_final: 0.6506 (m-80) REVERT: B 655 TYR cc_start: 0.6637 (t80) cc_final: 0.6410 (t80) REVERT: B 664 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7737 (mt) REVERT: B 723 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7558 (p) REVERT: B 731 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7624 (ttp) REVERT: B 755 GLN cc_start: 0.8278 (mt0) cc_final: 0.8009 (mt0) REVERT: B 964 LYS cc_start: 0.7191 (ttmm) cc_final: 0.6971 (tttp) REVERT: B 1005 GLN cc_start: 0.7172 (mm110) cc_final: 0.6899 (mt0) REVERT: C 709 ASN cc_start: 0.6928 (OUTLIER) cc_final: 0.6710 (m110) REVERT: C 748 GLU cc_start: 0.5969 (mp0) cc_final: 0.5751 (mp0) REVERT: C 751 ASN cc_start: 0.8102 (t0) cc_final: 0.7829 (t0) REVERT: C 795 LYS cc_start: 0.7203 (mptm) cc_final: 0.6509 (mtpp) REVERT: C 814 LYS cc_start: 0.7499 (mmpt) cc_final: 0.6459 (tttp) REVERT: C 1010 GLN cc_start: 0.7786 (mm110) cc_final: 0.7268 (mt0) outliers start: 50 outliers final: 27 residues processed: 159 average time/residue: 1.1640 time to fit residues: 221.2145 Evaluate side-chains 140 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 581 THR 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 785 VAL Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 747 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 253 optimal weight: 0.7980 chunk 265 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 C 61 ASN C 641 ASN C 709 ASN C 901 GLN C1058 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.8291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25098 Z= 0.211 Angle : 0.598 9.091 34129 Z= 0.320 Chirality : 0.045 0.188 3873 Planarity : 0.005 0.063 4411 Dihedral : 4.465 23.520 3349 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.82 % Rotamer: Outliers : 1.68 % Allowed : 18.71 % Favored : 79.61 % 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: -0.65 (0.15), residues: 3072 helix: 1.71 (0.21), residues: 679 sheet: 0.61 (0.20), residues: 622 loop : -1.80 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 353 HIS 0.004 0.001 HIS C1064 PHE 0.020 0.001 PHE C 562 TYR 0.021 0.002 TYR C 707 ARG 0.005 0.000 ARG B 328 *********************** 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 165 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 119 time to evaluate : 2.388 Fit side-chains REVERT: A 233 ILE cc_start: 0.1665 (OUTLIER) cc_final: 0.1160 (pp) REVERT: A 646 ARG cc_start: 0.8299 (tpp80) cc_final: 0.8073 (tpp80) REVERT: A 1010 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: A 1019 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7196 (ttp-110) REVERT: A 1031 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: A 1138 TYR cc_start: 0.6920 (t80) cc_final: 0.6550 (m-80) REVERT: B 655 TYR cc_start: 0.6718 (t80) cc_final: 0.6459 (t80) REVERT: B 664 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7759 (mt) REVERT: B 723 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7560 (p) REVERT: B 755 GLN cc_start: 0.8338 (mt0) cc_final: 0.8072 (mt0) REVERT: B 796 TYR cc_start: 0.6043 (OUTLIER) cc_final: 0.4840 (p90) REVERT: B 964 LYS cc_start: 0.7367 (ttmm) cc_final: 0.7110 (tttp) REVERT: B 1005 GLN cc_start: 0.7165 (mm110) cc_final: 0.6874 (mt0) REVERT: C 751 ASN cc_start: 0.8045 (t0) cc_final: 0.7762 (t0) REVERT: C 795 LYS cc_start: 0.7232 (mptm) cc_final: 0.6519 (mtpp) REVERT: C 814 LYS cc_start: 0.7530 (mmpt) cc_final: 0.6444 (tttp) REVERT: C 1010 GLN cc_start: 0.7795 (mm110) cc_final: 0.7267 (mt0) REVERT: C 1123 SER cc_start: 0.9233 (t) cc_final: 0.8878 (m) outliers start: 46 outliers final: 28 residues processed: 158 average time/residue: 1.0734 time to fit residues: 204.8025 Evaluate side-chains 145 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR 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 591 SER Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 796 TYR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 599 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 C 709 ASN C 901 GLN C1058 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.8755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25098 Z= 0.234 Angle : 0.627 10.827 34129 Z= 0.336 Chirality : 0.046 0.173 3873 Planarity : 0.006 0.107 4411 Dihedral : 4.602 23.732 3349 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 1.46 % Allowed : 19.04 % Favored : 79.50 % 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: -0.73 (0.15), residues: 3072 helix: 1.65 (0.21), residues: 678 sheet: 0.57 (0.20), residues: 628 loop : -1.88 (0.13), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.014 0.001 HIS A1083 PHE 0.019 0.002 PHE A 490 TYR 0.020 0.002 TYR C 265 ARG 0.009 0.001 ARG C 983 ********************** 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 167 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 2.699 Fit side-chains REVERT: A 233 ILE cc_start: 0.1897 (OUTLIER) cc_final: 0.1327 (tp) REVERT: A 646 ARG cc_start: 0.8351 (tpp80) cc_final: 0.8124 (tpp80) REVERT: A 1010 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: A 1031 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6593 (mt-10) REVERT: A 1138 TYR cc_start: 0.6976 (t80) cc_final: 0.6618 (m-80) REVERT: B 529 LYS cc_start: 0.6618 (mmpt) cc_final: 0.5616 (mmmt) REVERT: B 655 TYR cc_start: 0.6777 (t80) cc_final: 0.6504 (t80) REVERT: B 664 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7665 (mt) REVERT: B 723 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7554 (p) REVERT: B 751 ASN cc_start: 0.7675 (t0) cc_final: 0.7437 (t0) REVERT: B 755 GLN cc_start: 0.8316 (mt0) cc_final: 0.8062 (mt0) REVERT: B 796 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.4918 (p90) REVERT: B 964 LYS cc_start: 0.7421 (ttmm) cc_final: 0.7192 (tttm) REVERT: B 1005 GLN cc_start: 0.7319 (mm110) cc_final: 0.6995 (mt0) REVERT: C 226 LEU cc_start: 0.0186 (OUTLIER) cc_final: -0.0394 (pp) REVERT: C 751 ASN cc_start: 0.8052 (t0) cc_final: 0.7422 (m-40) REVERT: C 795 LYS cc_start: 0.7263 (mptm) cc_final: 0.6528 (mtpp) REVERT: C 814 LYS cc_start: 0.7493 (mmpt) cc_final: 0.6410 (tttp) REVERT: C 1010 GLN cc_start: 0.7747 (mm110) cc_final: 0.7253 (mt0) REVERT: C 1123 SER cc_start: 0.9227 (t) cc_final: 0.8860 (m) outliers start: 40 outliers final: 27 residues processed: 161 average time/residue: 1.0632 time to fit residues: 205.5287 Evaluate side-chains 140 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR 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 591 SER Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 796 TYR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 226 LEU 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 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 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 196 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 228 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 103 optimal weight: 0.0170 chunk 254 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN C 901 GLN C1058 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.273049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214084 restraints weight = 31442.211| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.60 r_work: 0.3844 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.8869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25098 Z= 0.176 Angle : 0.566 9.366 34129 Z= 0.302 Chirality : 0.044 0.157 3873 Planarity : 0.005 0.065 4411 Dihedral : 4.296 23.026 3349 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 1.21 % Allowed : 19.62 % 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: -0.62 (0.15), residues: 3072 helix: 1.92 (0.21), residues: 672 sheet: 0.42 (0.21), residues: 606 loop : -1.74 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 353 HIS 0.004 0.001 HIS B 49 PHE 0.019 0.001 PHE C 562 TYR 0.016 0.001 TYR A 904 ARG 0.004 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6828.12 seconds wall clock time: 121 minutes 55.22 seconds (7315.22 seconds total)