Starting phenix.real_space_refine on Mon Aug 25 02:20:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hrj_34975/08_2025/8hrj_34975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hrj_34975/08_2025/8hrj_34975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hrj_34975/08_2025/8hrj_34975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hrj_34975/08_2025/8hrj_34975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hrj_34975/08_2025/8hrj_34975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hrj_34975/08_2025/8hrj_34975.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 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 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24531 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Chain: "B" Number of atoms: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8191 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 53, 'TRANS': 990} Chain breaks: 8 Chain: "C" Number of atoms: 8170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8170 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 53, 'TRANS': 987} Chain breaks: 8 Time building chain proxies: 4.65, per 1000 atoms: 0.19 Number of scatterers: 24531 At special positions: 0 Unit cell: (147.06, 149.64, 200.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4620 8.00 N 4086 7.00 C 15711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.5% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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: 3.946A 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: 3.588A 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: 3.815A 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: 3.657A 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: 4.399A 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: 3.609A 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: 3.571A 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: 3.538A 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: 3.574A 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: 3.836A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.578A 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: 3.899A 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: 8.278A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.889A 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: 7.163A 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: 3.609A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.026A 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: 5.856A 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: 8.709A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.451A 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: 6.859A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.725A 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: 4.644A 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: 8.344A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.109A 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: 3.913A 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: 6.565A 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: 3.546A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.673A 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: 6.120A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.233A 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: 6.470A 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: 8.584A 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) removed outlier: 9.543A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.239A 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: 6.983A 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: 6.168A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.803A 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: 4.25 Time building geometry restraints manager: 2.34 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: 7718 1.34 - 1.46: 6266 1.46 - 1.59: 10973 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 1.492 -0.038 1.27e-02 6.20e+03 9.05e+00 bond pdb=" CA SER A 366 " pdb=" CB SER A 366 " ideal model delta sigma weight residual 1.532 1.489 0.043 1.53e-02 4.27e+03 8.03e+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 6.26e+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 6.20e+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 5.85e+00 ... (remaining 25093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 33787 2.57 - 5.15: 318 5.15 - 7.72: 20 7.72 - 10.29: 2 10.29 - 12.87: 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 113.80 120.89 -7.09 1.00e+00 1.00e+00 5.03e+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 99.60 12.87 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 121.88 115.74 6.14 1.13e+00 7.83e-01 2.95e+01 angle pdb=" N PRO B 373 " pdb=" CA PRO B 373 " pdb=" C PRO B 373 " ideal model delta sigma weight residual 112.47 101.81 10.66 2.06e+00 2.36e-01 2.68e+01 angle pdb=" N SER A 366 " pdb=" CA SER A 366 " pdb=" C SER A 366 " ideal model delta sigma weight residual 113.41 107.90 5.51 1.22e+00 6.72e-01 2.04e+01 ... (remaining 34124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 13420 17.62 - 35.24: 1260 35.24 - 52.86: 251 52.86 - 70.48: 45 70.48 - 88.10: 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 12.19 80.81 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 27.02 65.98 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 93.00 155.67 -62.67 1 1.00e+01 1.00e-02 5.19e+01 ... (remaining 14996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3074 0.053 - 0.106: 648 0.106 - 0.158: 141 0.158 - 0.211: 8 0.211 - 0.264: 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 1.74e+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 1.23e+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 1.06e+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 9.79e-02 1.53e+01 pdb=" N PRO C 499 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.052 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 9.73e-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: 1909 2.74 - 3.28: 22779 3.28 - 3.82: 36704 3.82 - 4.36: 41451 4.36 - 4.90: 76839 Nonbonded interactions: 179682 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 2.222 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.239 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 2.263 3.120 ... (remaining 179677 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: 11.080 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.170 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25140 Z= 0.159 Angle : 0.616 12.865 34213 Z= 0.341 Chirality : 0.045 0.264 3873 Planarity : 0.005 0.098 4411 Dihedral : 14.229 88.095 8993 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.95 % Favored : 94.76 % Rotamer: Outliers : 0.26 % Allowed : 0.33 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 3072 helix: 2.02 (0.21), residues: 679 sheet: 1.05 (0.19), residues: 682 loop : -1.55 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 493 TYR 0.018 0.001 TYR C 351 PHE 0.020 0.001 PHE A 486 TRP 0.015 0.001 TRP A 886 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00314 (25098) covalent geometry : angle 0.61152 (34129) SS BOND : bond 0.00602 ( 42) SS BOND : angle 1.54216 ( 84) hydrogen bonds : bond 0.12448 ( 1014) hydrogen bonds : angle 5.76899 ( 2748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 313 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 1019 ARG cc_start: 0.8007 (ttp80) cc_final: 0.6341 (ptm160) REVERT: C 934 ILE cc_start: 0.8041 (tt) cc_final: 0.7829 (mm) REVERT: C 955 ASN cc_start: 0.6969 (t0) cc_final: 0.6656 (m-40) outliers start: 7 outliers final: 1 residues processed: 320 average time/residue: 0.1499 time to fit residues: 75.9338 Evaluate side-chains 158 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 613 GLN A 690 GLN A 804 GLN A 935 GLN A1010 GLN A1135 ASN B 49 HIS B 81 ASN B 370 ASN B 422 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 606 ASN B 658 ASN B 762 GLN B 901 GLN B1083 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 777 ASN C 901 GLN C 965 GLN C1002 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.267418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.224146 restraints weight = 39843.981| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 3.29 r_work: 0.4092 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 25140 Z= 0.252 Angle : 0.824 18.787 34213 Z= 0.440 Chirality : 0.052 0.357 3873 Planarity : 0.007 0.086 4411 Dihedral : 5.199 58.801 3351 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 2.19 % Allowed : 9.54 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3072 helix: 1.00 (0.20), residues: 690 sheet: 0.64 (0.19), residues: 692 loop : -1.74 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1019 TYR 0.051 0.003 TYR B 873 PHE 0.037 0.003 PHE B 338 TRP 0.029 0.003 TRP B 353 HIS 0.014 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00539 (25098) covalent geometry : angle 0.81853 (34129) SS BOND : bond 0.00760 ( 42) SS BOND : angle 2.06621 ( 84) hydrogen bonds : bond 0.09350 ( 1014) hydrogen bonds : angle 5.68895 ( 2748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.706 Fit side-chains REVERT: A 275 PHE cc_start: 0.3417 (OUTLIER) cc_final: 0.2774 (m-80) REVERT: A 585 LEU cc_start: 0.6244 (mt) cc_final: 0.5815 (mt) REVERT: A 960 ASN cc_start: 0.7674 (t0) cc_final: 0.7190 (m-40) REVERT: B 466 ARG cc_start: 0.4535 (OUTLIER) cc_final: 0.3699 (mtm180) REVERT: B 605 SER cc_start: 0.6729 (OUTLIER) cc_final: 0.6358 (m) REVERT: B 904 TYR cc_start: 0.6858 (m-10) cc_final: 0.6556 (m-80) REVERT: C 955 ASN cc_start: 0.7844 (t0) cc_final: 0.7479 (m-40) outliers start: 60 outliers final: 28 residues processed: 229 average time/residue: 0.1506 time to fit residues: 54.5560 Evaluate side-chains 140 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 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 150 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1125 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.261262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.211735 restraints weight = 38477.055| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.57 r_work: 0.3999 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25140 Z= 0.189 Angle : 0.657 12.572 34213 Z= 0.351 Chirality : 0.047 0.245 3873 Planarity : 0.006 0.067 4411 Dihedral : 4.629 22.697 3349 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 2.34 % Allowed : 12.61 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 3072 helix: 1.41 (0.20), residues: 697 sheet: 0.49 (0.19), residues: 703 loop : -1.61 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 498 TYR 0.024 0.002 TYR B 423 PHE 0.024 0.002 PHE B 497 TRP 0.026 0.002 TRP C 886 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00413 (25098) covalent geometry : angle 0.65069 (34129) SS BOND : bond 0.00634 ( 42) SS BOND : angle 1.93676 ( 84) hydrogen bonds : bond 0.08268 ( 1014) hydrogen bonds : angle 5.48633 ( 2748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.3978 (m-80) cc_final: 0.3622 (m-80) REVERT: A 291 CYS cc_start: -0.0583 (OUTLIER) cc_final: -0.1126 (p) REVERT: A 362 VAL cc_start: 0.3682 (OUTLIER) cc_final: 0.3414 (t) REVERT: A 368 LEU cc_start: 0.1196 (OUTLIER) cc_final: 0.0533 (pp) REVERT: A 585 LEU cc_start: 0.5892 (mt) cc_final: 0.5419 (mt) REVERT: A 590 CYS cc_start: 0.2509 (OUTLIER) cc_final: 0.1725 (m) REVERT: A 606 ASN cc_start: 0.6273 (t0) cc_final: 0.5567 (m-40) REVERT: A 646 ARG cc_start: 0.6891 (mmp80) cc_final: 0.6166 (mpp80) REVERT: A 960 ASN cc_start: 0.8019 (t0) cc_final: 0.7713 (m-40) REVERT: B 34 ARG cc_start: 0.5541 (mtp85) cc_final: 0.4913 (mmp80) REVERT: B 314 GLN cc_start: 0.7544 (tt0) cc_final: 0.7299 (tm-30) REVERT: B 759 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6805 (m-10) REVERT: B 904 TYR cc_start: 0.6890 (m-10) cc_final: 0.6572 (m-80) REVERT: C 525 CYS cc_start: 0.1654 (OUTLIER) cc_final: 0.1104 (t) REVERT: C 1139 ASP cc_start: 0.5056 (OUTLIER) cc_final: 0.4780 (p0) outliers start: 64 outliers final: 33 residues processed: 206 average time/residue: 0.1313 time to fit residues: 44.2202 Evaluate side-chains 147 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 297 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 213 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.259812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.211232 restraints weight = 38727.203| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 3.06 r_work: 0.3978 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25140 Z= 0.140 Angle : 0.585 8.551 34213 Z= 0.312 Chirality : 0.045 0.271 3873 Planarity : 0.005 0.061 4411 Dihedral : 4.373 34.003 3349 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 2.41 % Allowed : 13.85 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3072 helix: 1.72 (0.21), residues: 691 sheet: 0.51 (0.19), residues: 706 loop : -1.54 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.023 0.001 TYR B 741 PHE 0.015 0.001 PHE B 464 TRP 0.015 0.001 TRP C 886 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00292 (25098) covalent geometry : angle 0.57622 (34129) SS BOND : bond 0.00463 ( 42) SS BOND : angle 2.12732 ( 84) hydrogen bonds : bond 0.06955 ( 1014) hydrogen bonds : angle 5.27832 ( 2748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 122 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.1932 (OUTLIER) cc_final: 0.0919 (m-30) REVERT: A 362 VAL cc_start: 0.3677 (OUTLIER) cc_final: 0.3384 (t) REVERT: A 492 LEU cc_start: -0.0716 (OUTLIER) cc_final: -0.1090 (mp) REVERT: A 585 LEU cc_start: 0.6175 (mt) cc_final: 0.5699 (mt) REVERT: A 590 CYS cc_start: 0.2445 (OUTLIER) cc_final: 0.1747 (m) REVERT: A 606 ASN cc_start: 0.6556 (t0) cc_final: 0.5854 (m-40) REVERT: A 646 ARG cc_start: 0.6924 (mmp80) cc_final: 0.6032 (mtp180) REVERT: A 960 ASN cc_start: 0.8090 (t0) cc_final: 0.7688 (m-40) REVERT: B 34 ARG cc_start: 0.5879 (mtp85) cc_final: 0.5149 (mmp80) REVERT: B 605 SER cc_start: 0.7505 (OUTLIER) cc_final: 0.7164 (m) REVERT: B 749 CYS cc_start: 0.4792 (OUTLIER) cc_final: 0.4250 (t) REVERT: B 759 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6732 (m-10) REVERT: B 904 TYR cc_start: 0.7000 (m-10) cc_final: 0.6697 (m-80) REVERT: C 525 CYS cc_start: 0.1062 (OUTLIER) cc_final: 0.0740 (t) REVERT: C 644 GLN cc_start: 0.5686 (OUTLIER) cc_final: 0.5041 (tt0) REVERT: C 1139 ASP cc_start: 0.5185 (OUTLIER) cc_final: 0.4859 (p0) outliers start: 66 outliers final: 35 residues processed: 182 average time/residue: 0.1329 time to fit residues: 39.4967 Evaluate side-chains 151 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS 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 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 265 optimal weight: 0.4980 chunk 274 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN C 134 GLN C 422 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.252513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.207574 restraints weight = 37750.736| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 3.00 r_work: 0.3907 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25140 Z= 0.198 Angle : 0.673 8.697 34213 Z= 0.362 Chirality : 0.048 0.309 3873 Planarity : 0.006 0.062 4411 Dihedral : 4.776 32.584 3349 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 3.07 % Allowed : 14.80 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.15), residues: 3072 helix: 1.30 (0.20), residues: 693 sheet: 0.38 (0.19), residues: 702 loop : -1.70 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 190 TYR 0.023 0.002 TYR A1067 PHE 0.022 0.002 PHE C 194 TRP 0.021 0.002 TRP C 886 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00448 (25098) covalent geometry : angle 0.66187 (34129) SS BOND : bond 0.00666 ( 42) SS BOND : angle 2.49935 ( 84) hydrogen bonds : bond 0.09590 ( 1014) hydrogen bonds : angle 5.66509 ( 2748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 115 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.2887 (OUTLIER) cc_final: 0.2249 (m-30) REVERT: A 273 ARG cc_start: 0.2871 (OUTLIER) cc_final: 0.2649 (ptp-170) REVERT: A 276 LEU cc_start: 0.4254 (OUTLIER) cc_final: 0.3966 (mm) REVERT: A 291 CYS cc_start: 0.1688 (OUTLIER) cc_final: 0.1312 (p) REVERT: A 492 LEU cc_start: -0.0722 (OUTLIER) cc_final: -0.1056 (mp) REVERT: A 585 LEU cc_start: 0.6312 (mt) cc_final: 0.5691 (mt) REVERT: A 590 CYS cc_start: 0.2436 (OUTLIER) cc_final: 0.1803 (m) REVERT: A 606 ASN cc_start: 0.7076 (t0) cc_final: 0.6581 (m-40) REVERT: A 646 ARG cc_start: 0.6787 (mmp80) cc_final: 0.6350 (mtp180) REVERT: A 736 VAL cc_start: 0.8750 (p) cc_final: 0.8497 (t) REVERT: A 823 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7347 (t80) REVERT: A 904 TYR cc_start: 0.7631 (m-10) cc_final: 0.7386 (m-10) REVERT: A 960 ASN cc_start: 0.8303 (t0) cc_final: 0.8041 (m-40) REVERT: B 605 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7566 (m) REVERT: B 759 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7425 (m-10) REVERT: B 916 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8104 (tp) REVERT: C 202 LYS cc_start: 0.3632 (OUTLIER) cc_final: 0.3386 (tptt) REVERT: C 644 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.5835 (tt0) REVERT: C 1139 ASP cc_start: 0.5983 (OUTLIER) cc_final: 0.5632 (p0) outliers start: 84 outliers final: 49 residues processed: 191 average time/residue: 0.1366 time to fit residues: 42.5667 Evaluate side-chains 156 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 94 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 608 VAL 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 711 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 181 optimal weight: 0.2980 chunk 43 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.0170 chunk 210 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 120 optimal weight: 9.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 564 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.254210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.210901 restraints weight = 38327.110| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 3.00 r_work: 0.3973 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25140 Z= 0.139 Angle : 0.585 11.800 34213 Z= 0.310 Chirality : 0.045 0.253 3873 Planarity : 0.005 0.061 4411 Dihedral : 4.423 30.663 3349 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 2.45 % Allowed : 15.78 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.15), residues: 3072 helix: 1.62 (0.21), residues: 692 sheet: 0.43 (0.19), residues: 690 loop : -1.56 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 190 TYR 0.025 0.001 TYR B1138 PHE 0.021 0.001 PHE C 55 TRP 0.015 0.001 TRP C 886 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00291 (25098) covalent geometry : angle 0.57390 (34129) SS BOND : bond 0.00526 ( 42) SS BOND : angle 2.35053 ( 84) hydrogen bonds : bond 0.07369 ( 1014) hydrogen bonds : angle 5.36572 ( 2748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 110 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.2897 (OUTLIER) cc_final: 0.2416 (m-30) REVERT: A 291 CYS cc_start: 0.1690 (OUTLIER) cc_final: 0.1270 (p) REVERT: A 492 LEU cc_start: -0.0757 (OUTLIER) cc_final: -0.1178 (mp) REVERT: A 585 LEU cc_start: 0.6410 (mt) cc_final: 0.5809 (mt) REVERT: A 590 CYS cc_start: 0.2335 (OUTLIER) cc_final: 0.1588 (m) REVERT: A 606 ASN cc_start: 0.7076 (t0) cc_final: 0.6716 (m-40) REVERT: A 646 ARG cc_start: 0.6720 (mmp80) cc_final: 0.6316 (mtt180) REVERT: A 740 MET cc_start: 0.8350 (mtp) cc_final: 0.8096 (mtp) REVERT: A 960 ASN cc_start: 0.8214 (t0) cc_final: 0.7962 (m-40) REVERT: B 605 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7576 (m) REVERT: B 759 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7182 (m-10) REVERT: B 916 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7872 (tp) REVERT: B 1137 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8853 (t) outliers start: 67 outliers final: 39 residues processed: 174 average time/residue: 0.1454 time to fit residues: 41.5119 Evaluate side-chains 147 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1137 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 17 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 233 optimal weight: 0.5980 chunk 299 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 992 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.249471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.198326 restraints weight = 37760.324| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.90 r_work: 0.3875 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.7988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25140 Z= 0.166 Angle : 0.623 11.604 34213 Z= 0.332 Chirality : 0.046 0.303 3873 Planarity : 0.006 0.069 4411 Dihedral : 4.507 28.510 3349 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 2.67 % Allowed : 15.82 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 3072 helix: 1.50 (0.20), residues: 698 sheet: 0.35 (0.19), residues: 684 loop : -1.61 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1107 TYR 0.023 0.002 TYR A1138 PHE 0.020 0.002 PHE C 194 TRP 0.020 0.001 TRP C 353 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (25098) covalent geometry : angle 0.61398 (34129) SS BOND : bond 0.00596 ( 42) SS BOND : angle 2.17761 ( 84) hydrogen bonds : bond 0.08529 ( 1014) hydrogen bonds : angle 5.50328 ( 2748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 110 time to evaluate : 0.742 Fit side-chains REVERT: A 492 LEU cc_start: -0.0583 (OUTLIER) cc_final: -0.0887 (mp) REVERT: A 585 LEU cc_start: 0.6197 (mt) cc_final: 0.5668 (mt) REVERT: A 590 CYS cc_start: 0.2391 (OUTLIER) cc_final: 0.1507 (m) REVERT: A 606 ASN cc_start: 0.7512 (t0) cc_final: 0.7045 (m-40) REVERT: A 646 ARG cc_start: 0.6939 (mmp80) cc_final: 0.6610 (mtt180) REVERT: A 960 ASN cc_start: 0.8347 (t0) cc_final: 0.8031 (m-40) REVERT: B 759 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7436 (m-10) REVERT: B 916 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8075 (tp) REVERT: B 994 ASP cc_start: 0.5681 (m-30) cc_final: 0.5419 (m-30) REVERT: C 289 VAL cc_start: 0.4982 (OUTLIER) cc_final: 0.4743 (p) REVERT: C 644 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.5849 (tt0) outliers start: 73 outliers final: 52 residues processed: 176 average time/residue: 0.1387 time to fit residues: 40.7528 Evaluate side-chains 151 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL 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 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 115 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 222 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.246747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.195395 restraints weight = 37653.431| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 2.82 r_work: 0.3852 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.8470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25140 Z= 0.182 Angle : 0.637 12.509 34213 Z= 0.340 Chirality : 0.047 0.275 3873 Planarity : 0.005 0.063 4411 Dihedral : 4.633 29.312 3349 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.04 % Rotamer: Outliers : 2.56 % Allowed : 16.37 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 3072 helix: 1.44 (0.20), residues: 692 sheet: 0.32 (0.19), residues: 683 loop : -1.64 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 190 TYR 0.022 0.002 TYR A1067 PHE 0.027 0.002 PHE A 86 TRP 0.017 0.002 TRP C 353 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00412 (25098) covalent geometry : angle 0.62987 (34129) SS BOND : bond 0.00623 ( 42) SS BOND : angle 2.06833 ( 84) hydrogen bonds : bond 0.08894 ( 1014) hydrogen bonds : angle 5.61515 ( 2748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 110 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 277 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5718 (mp) REVERT: A 492 LEU cc_start: -0.0430 (OUTLIER) cc_final: -0.0721 (mp) REVERT: A 585 LEU cc_start: 0.6277 (mt) cc_final: 0.5776 (mt) REVERT: A 590 CYS cc_start: 0.2369 (OUTLIER) cc_final: 0.1534 (m) REVERT: A 606 ASN cc_start: 0.7561 (t0) cc_final: 0.7058 (m-40) REVERT: A 960 ASN cc_start: 0.8389 (t0) cc_final: 0.8090 (m-40) REVERT: B 605 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7606 (m) REVERT: B 759 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: B 916 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8022 (tp) REVERT: C 202 LYS cc_start: 0.3800 (OUTLIER) cc_final: 0.3276 (tptt) REVERT: C 289 VAL cc_start: 0.5121 (OUTLIER) cc_final: 0.4790 (p) REVERT: C 1139 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5207 (t0) outliers start: 70 outliers final: 49 residues processed: 173 average time/residue: 0.1405 time to fit residues: 40.6517 Evaluate side-chains 161 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 103 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 224 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 300 optimal weight: 0.5980 chunk 144 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.248051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.204299 restraints weight = 37921.950| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 2.89 r_work: 0.3898 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25140 Z= 0.141 Angle : 0.586 12.307 34213 Z= 0.311 Chirality : 0.045 0.204 3873 Planarity : 0.005 0.083 4411 Dihedral : 4.402 26.879 3349 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 2.30 % Allowed : 16.73 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 3072 helix: 1.70 (0.21), residues: 683 sheet: 0.26 (0.19), residues: 712 loop : -1.55 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.022 0.001 TYR A1138 PHE 0.024 0.001 PHE A 318 TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00299 (25098) covalent geometry : angle 0.57929 (34129) SS BOND : bond 0.00601 ( 42) SS BOND : angle 1.91021 ( 84) hydrogen bonds : bond 0.07534 ( 1014) hydrogen bonds : angle 5.39770 ( 2748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 110 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 277 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6181 (mp) REVERT: A 492 LEU cc_start: -0.0385 (OUTLIER) cc_final: -0.0673 (mp) REVERT: A 585 LEU cc_start: 0.6439 (mt) cc_final: 0.5955 (mt) REVERT: A 590 CYS cc_start: 0.2099 (OUTLIER) cc_final: 0.1217 (m) REVERT: A 606 ASN cc_start: 0.7533 (t0) cc_final: 0.7050 (m-40) REVERT: A 740 MET cc_start: 0.8519 (mtp) cc_final: 0.8286 (mtp) REVERT: A 960 ASN cc_start: 0.8330 (t0) cc_final: 0.8044 (m-40) REVERT: B 605 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7629 (m) REVERT: B 759 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: B 916 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7918 (tp) REVERT: C 202 LYS cc_start: 0.3846 (OUTLIER) cc_final: 0.3291 (tptt) REVERT: C 289 VAL cc_start: 0.4944 (OUTLIER) cc_final: 0.4584 (p) outliers start: 63 outliers final: 46 residues processed: 171 average time/residue: 0.1341 time to fit residues: 38.6988 Evaluate side-chains 155 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 101 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 180 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.245609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.191655 restraints weight = 36673.610| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 2.90 r_work: 0.3826 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.9204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 25140 Z= 0.219 Angle : 0.706 13.152 34213 Z= 0.378 Chirality : 0.049 0.262 3873 Planarity : 0.006 0.075 4411 Dihedral : 4.874 29.018 3349 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.26 % Favored : 92.71 % Rotamer: Outliers : 2.27 % Allowed : 16.70 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.15), residues: 3072 helix: 1.39 (0.20), residues: 671 sheet: 0.10 (0.19), residues: 705 loop : -1.74 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 273 TYR 0.024 0.002 TYR C 265 PHE 0.045 0.002 PHE B 377 TRP 0.026 0.002 TRP C 353 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00510 (25098) covalent geometry : angle 0.69692 (34129) SS BOND : bond 0.00616 ( 42) SS BOND : angle 2.36163 ( 84) hydrogen bonds : bond 0.10360 ( 1014) hydrogen bonds : angle 5.85339 ( 2748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 118 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: -0.0383 (OUTLIER) cc_final: -0.0729 (mp) REVERT: A 558 LYS cc_start: 0.5539 (mmpt) cc_final: 0.5277 (ptmm) REVERT: A 585 LEU cc_start: 0.6152 (mt) cc_final: 0.5548 (mt) REVERT: A 960 ASN cc_start: 0.8462 (t0) cc_final: 0.8146 (m-40) REVERT: B 276 LEU cc_start: 0.7461 (tp) cc_final: 0.6980 (tp) REVERT: B 466 ARG cc_start: 0.4461 (OUTLIER) cc_final: 0.4014 (mtm180) REVERT: B 605 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7627 (m) REVERT: B 759 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7701 (m-10) REVERT: B 916 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8156 (tp) outliers start: 62 outliers final: 50 residues processed: 175 average time/residue: 0.1223 time to fit residues: 36.0583 Evaluate side-chains 159 residues out of total 2737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 104 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 172 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 136 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 212 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS C 519 HIS C1106 GLN 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 = 0.248304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.196322 restraints weight = 38055.175| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.75 r_work: 0.3889 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.9193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25140 Z= 0.134 Angle : 0.581 12.283 34213 Z= 0.309 Chirality : 0.045 0.202 3873 Planarity : 0.005 0.069 4411 Dihedral : 4.419 25.963 3349 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 1.75 % Allowed : 17.35 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.15), residues: 3072 helix: 1.84 (0.21), residues: 670 sheet: 0.17 (0.19), residues: 711 loop : -1.61 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.023 0.001 TYR A1138 PHE 0.028 0.001 PHE A 318 TRP 0.015 0.001 TRP B 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00272 (25098) covalent geometry : angle 0.57498 (34129) SS BOND : bond 0.00502 ( 42) SS BOND : angle 1.75408 ( 84) hydrogen bonds : bond 0.07197 ( 1014) hydrogen bonds : angle 5.42762 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6121.94 seconds wall clock time: 105 minutes 13.52 seconds (6313.52 seconds total)