Starting phenix.real_space_refine on Thu Jun 26 07:57:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xea_38284/06_2025/8xea_38284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xea_38284/06_2025/8xea_38284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xea_38284/06_2025/8xea_38284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xea_38284/06_2025/8xea_38284.map" model { file = "/net/cci-nas-00/data/ceres_data/8xea_38284/06_2025/8xea_38284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xea_38284/06_2025/8xea_38284.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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 138 5.16 5 C 19265 2.51 5 N 5065 2.21 5 O 5745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.56s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30213 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8360 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "E" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8359 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "F" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8367 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 6 Chain: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "I" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "J" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 16.61, per 1000 atoms: 0.55 Number of scatterers: 30213 At special positions: 0 Unit cell: (154.96, 164.32, 209.04, 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 138 16.00 O 5745 8.00 N 5065 7.00 C 19265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.05 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 3.4 seconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7208 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 60 sheets defined 18.4% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.980A pdb=" N ASN A 32 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 406 through 410 removed outlier: 3.580A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 743 removed outlier: 4.227A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.640A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 783 removed outlier: 3.603A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 850 through 855 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 907 Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.716A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.960A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 964 removed outlier: 4.639A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS D 954 " --> pdb=" O ASP D 950 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN D 955 " --> pdb=" O VAL D 951 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 984 removed outlier: 3.619A pdb=" N LEU D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 993 removed outlier: 3.870A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1032 removed outlier: 3.658A pdb=" N GLU D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 406 through 410 removed outlier: 3.628A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.740A pdb=" N SER E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 783 removed outlier: 4.140A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E 780 " --> pdb=" O LYS E 776 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 851 through 855 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 890 removed outlier: 3.544A pdb=" N GLY E 889 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 907 Processing helix chain 'E' and resid 908 through 910 No H-bonds generated for 'chain 'E' and resid 908 through 910' Processing helix chain 'E' and resid 913 through 941 removed outlier: 3.657A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP E 936 " --> pdb=" O GLY E 932 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 941 " --> pdb=" O SER E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 964 removed outlier: 4.837A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS E 954 " --> pdb=" O ASP E 950 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN E 955 " --> pdb=" O VAL E 951 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 959 " --> pdb=" O ASN E 955 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN E 960 " --> pdb=" O ALA E 956 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 962 " --> pdb=" O ALA E 958 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 984 removed outlier: 3.562A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 988 Processing helix chain 'E' and resid 989 through 1032 removed outlier: 4.396A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E1017 " --> pdb=" O ILE E1013 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 364 through 370 removed outlier: 3.653A pdb=" N ILE F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 389 removed outlier: 4.147A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 removed outlier: 3.597A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 removed outlier: 4.438A pdb=" N TYR F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN F 422 " --> pdb=" O ILE F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 422' Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 757 removed outlier: 3.714A pdb=" N SER F 750 " --> pdb=" O SER F 746 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR F 756 " --> pdb=" O LEU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 783 removed outlier: 3.687A pdb=" N LEU F 763 " --> pdb=" O PHE F 759 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR F 778 " --> pdb=" O GLN F 774 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.523A pdb=" N VAL F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 855 Processing helix chain 'F' and resid 866 through 884 removed outlier: 3.530A pdb=" N ILE F 870 " --> pdb=" O THR F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 886 through 890 removed outlier: 3.513A pdb=" N GLY F 889 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 913 through 941 removed outlier: 3.606A pdb=" N TYR F 917 " --> pdb=" O GLN F 913 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS F 921 " --> pdb=" O TYR F 917 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU F 922 " --> pdb=" O GLU F 918 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 934 " --> pdb=" O ALA F 930 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR F 941 " --> pdb=" O SER F 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 965 removed outlier: 4.825A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS F 954 " --> pdb=" O ASP F 950 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 955 " --> pdb=" O VAL F 951 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 959 " --> pdb=" O ASN F 955 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN F 960 " --> pdb=" O ALA F 956 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 962 " --> pdb=" O ALA F 958 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 984 removed outlier: 3.715A pdb=" N LEU F 981 " --> pdb=" O LEU F 977 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 1033 removed outlier: 4.064A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU F 996 " --> pdb=" O GLN F 992 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F1033 " --> pdb=" O MET F1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.052A pdb=" N SER A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.722A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.454A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 31 removed outlier: 8.271A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR D 63 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER D 94 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG D 190 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 55 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 131 Processing sheet with id=AA9, first strand: chain 'D' and resid 277 through 279 removed outlier: 7.439A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 286 " --> pdb=" O LYS D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 311 through 314 removed outlier: 3.618A pdb=" N GLY D 311 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 597 " --> pdb=" O TYR D 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AB3, first strand: chain 'D' and resid 394 through 402 Processing sheet with id=AB4, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'D' and resid 654 through 660 removed outlier: 6.255A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL D 656 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 664 " --> pdb=" O ALA D 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 701 through 702 removed outlier: 6.320A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.971A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D1047 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 733 through 735 removed outlier: 4.611A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 861 " --> pdb=" O LYS D 733 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 787 through 788 removed outlier: 3.504A pdb=" N ILE D 788 " --> pdb=" O ALA F 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 3.685A pdb=" N SER D1123 " --> pdb=" O ALA D1087 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'E' and resid 28 through 31 removed outlier: 8.556A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 63 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL E 267 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 94 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 52 through 55 Processing sheet with id=AC6, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.778A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL E 126 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 172 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 277 through 279 removed outlier: 7.096A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 314 removed outlier: 3.544A pdb=" N TYR E 313 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 597 " --> pdb=" O TYR E 313 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AD1, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'E' and resid 394 through 402 removed outlier: 3.582A pdb=" N ILE E 434 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 513 " --> pdb=" O CYS E 432 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'E' and resid 654 through 660 removed outlier: 6.239A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 664 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.731A pdb=" N THR E1076 " --> pdb=" O SER E1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 718 through 728 removed outlier: 6.890A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 3.771A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 28 through 31 removed outlier: 8.275A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 267 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER F 94 " --> pdb=" O ARG F 190 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG F 190 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AE3, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.964A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 126 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 172 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 277 through 279 removed outlier: 7.059A pdb=" N LYS F 278 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 313 through 314 removed outlier: 3.542A pdb=" N TYR F 313 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 597 " --> pdb=" O TYR F 313 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 325 through 328 Processing sheet with id=AE7, first strand: chain 'F' and resid 394 through 403 removed outlier: 4.602A pdb=" N THR F 430 " --> pdb=" O PHE F 515 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'F' and resid 654 through 660 removed outlier: 6.273A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N VAL F 656 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 664 " --> pdb=" O ALA F 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.148A pdb=" N GLN F1071 " --> pdb=" O THR F 716 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE F 718 " --> pdb=" O PRO F1069 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE F 720 " --> pdb=" O TYR F1067 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR F1067 " --> pdb=" O ILE F 720 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL F 722 " --> pdb=" O VAL F1065 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL F1065 " --> pdb=" O VAL F 722 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR F 724 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F1063 " --> pdb=" O THR F 724 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 726 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL F1061 " --> pdb=" O ILE F 726 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY F1059 " --> pdb=" O PRO F 728 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER F1055 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F1061 " --> pdb=" O PRO F1053 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F1063 " --> pdb=" O SER F1051 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER F1051 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'F' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.878A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.538A pdb=" N SER G 106 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.700A pdb=" N SER I 22 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 45 through 49 removed outlier: 6.362A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.712A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AG5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.853A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2568 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: 12.21 Time building geometry restraints manager: 7.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9726 1.35 - 1.47: 7959 1.47 - 1.60: 13071 1.60 - 1.72: 0 1.72 - 1.84: 177 Bond restraints: 30933 Sorted by residual: bond pdb=" C PRO F 986 " pdb=" N PRO F 987 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.17e+01 bond pdb=" C THR F 250 " pdb=" N PRO F 251 " ideal model delta sigma weight residual 1.334 1.422 -0.088 2.34e-02 1.83e+03 1.43e+01 bond pdb=" C THR E 250 " pdb=" N PRO E 251 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.08e+01 bond pdb=" C THR D 250 " pdb=" N PRO D 251 " ideal model delta sigma weight residual 1.334 1.390 -0.057 2.34e-02 1.83e+03 5.84e+00 bond pdb=" C LEU F 560 " pdb=" N PRO F 561 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.44e-02 4.82e+03 4.24e+00 ... (remaining 30928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 41344 2.56 - 5.12: 602 5.12 - 7.68: 88 7.68 - 10.24: 27 10.24 - 12.80: 20 Bond angle restraints: 42081 Sorted by residual: angle pdb=" CB LYS E 786 " pdb=" CG LYS E 786 " pdb=" CD LYS E 786 " ideal model delta sigma weight residual 111.30 124.09 -12.79 2.30e+00 1.89e-01 3.09e+01 angle pdb=" C TYR E 489 " pdb=" N SER E 490 " pdb=" CA SER E 490 " ideal model delta sigma weight residual 120.68 128.29 -7.61 1.52e+00 4.33e-01 2.51e+01 angle pdb=" C LEU F 249 " pdb=" N THR F 250 " pdb=" CA THR F 250 " ideal model delta sigma weight residual 121.80 133.92 -12.12 2.44e+00 1.68e-01 2.47e+01 angle pdb=" N PRO D 986 " pdb=" CA PRO D 986 " pdb=" C PRO D 986 " ideal model delta sigma weight residual 110.70 116.45 -5.75 1.22e+00 6.72e-01 2.22e+01 angle pdb=" CA LYS E 786 " pdb=" CB LYS E 786 " pdb=" CG LYS E 786 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 ... (remaining 42076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 15889 17.69 - 35.39: 1881 35.39 - 53.08: 480 53.08 - 70.78: 133 70.78 - 88.47: 37 Dihedral angle restraints: 18420 sinusoidal: 7188 harmonic: 11232 Sorted by residual: dihedral pdb=" CB CYS F 15 " pdb=" SG CYS F 15 " pdb=" SG CYS F 136 " pdb=" CB CYS F 136 " ideal model delta sinusoidal sigma weight residual -86.00 -174.47 88.47 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS D 15 " pdb=" SG CYS D 15 " pdb=" SG CYS D 136 " pdb=" CB CYS D 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.83 85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.04 84.96 1 1.00e+01 1.00e-02 8.76e+01 ... (remaining 18417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4075 0.074 - 0.147: 614 0.147 - 0.221: 19 0.221 - 0.295: 4 0.295 - 0.368: 3 Chirality restraints: 4715 Sorted by residual: chirality pdb=" CG LEU G 80 " pdb=" CB LEU G 80 " pdb=" CD1 LEU G 80 " pdb=" CD2 LEU G 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB ILE E 101 " pdb=" CA ILE E 101 " pdb=" CG1 ILE E 101 " pdb=" CG2 ILE E 101 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE D 101 " pdb=" CA ILE D 101 " pdb=" CG1 ILE D 101 " pdb=" CG2 ILE D 101 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4712 not shown) Planarity restraints: 5443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 985 " 0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO D 986 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 986 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 986 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " -0.051 5.00e-02 4.00e+02 7.60e-02 9.23e+00 pdb=" N PRO D 987 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 152 " -0.025 2.00e-02 2.50e+03 1.92e-02 9.18e+00 pdb=" CG TRP D 152 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 152 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 152 " -0.009 2.00e-02 2.50e+03 ... (remaining 5440 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2625 2.74 - 3.28: 28846 3.28 - 3.82: 51578 3.82 - 4.36: 57037 4.36 - 4.90: 98576 Nonbonded interactions: 238662 Sorted by model distance: nonbonded pdb=" OG SER F 27 " pdb=" O TRP F 64 " model vdw 2.204 3.040 nonbonded pdb=" OG SER D 27 " pdb=" O TRP D 64 " model vdw 2.219 3.040 nonbonded pdb=" O ASN F 417 " pdb=" OH TYR F 453 " model vdw 2.224 3.040 nonbonded pdb=" OG SER E 27 " pdb=" O TRP E 64 " model vdw 2.238 3.040 nonbonded pdb=" O LEU D 966 " pdb=" OG SER D 975 " model vdw 2.265 3.040 ... (remaining 238657 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 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'D' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'E' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'F' and (resid 14 through 826 or resid 850 through 1140)) } 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: 2.020 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: 0.050 Extract box with map and model: 1.040 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 64.010 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 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 0.088 30981 Z= 0.170 Angle : 0.816 12.798 42177 Z= 0.429 Chirality : 0.049 0.368 4715 Planarity : 0.006 0.077 5443 Dihedral : 16.745 87.382 11068 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 0.45 % Allowed : 25.63 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3817 helix: -0.02 (0.21), residues: 613 sheet: -0.49 (0.17), residues: 886 loop : -1.94 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 152 HIS 0.004 0.001 HIS D 505 PHE 0.024 0.001 PHE E 79 TYR 0.036 0.001 TYR D 351 ARG 0.005 0.000 ARG F 454 Details of bonding type rmsd hydrogen bonds : bond 0.15409 ( 941) hydrogen bonds : angle 6.71112 ( 2568) SS BOND : bond 0.00335 ( 48) SS BOND : angle 1.19440 ( 96) covalent geometry : bond 0.00334 (30933) covalent geometry : angle 0.81542 (42081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 3.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.2754 (mmt) cc_final: 0.2262 (mmm) REVERT: A 82 MET cc_start: -0.0826 (ptt) cc_final: -0.1212 (mtm) REVERT: D 77 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5987 (ptpp) REVERT: D 177 MET cc_start: 0.4228 (ptt) cc_final: 0.4016 (ptm) REVERT: D 201 PHE cc_start: 0.8668 (t80) cc_final: 0.8174 (t80) REVERT: D 421 TYR cc_start: 0.5763 (m-80) cc_final: 0.5370 (m-10) REVERT: D 907 ASN cc_start: 0.8286 (t0) cc_final: 0.8028 (m110) REVERT: D 1031 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8274 (mt-10) REVERT: D 1088 HIS cc_start: 0.7309 (m90) cc_final: 0.7031 (m90) REVERT: D 1125 ASN cc_start: 0.6597 (p0) cc_final: 0.6299 (p0) REVERT: E 51 THR cc_start: 0.7656 (p) cc_final: 0.7404 (p) REVERT: E 420 ASP cc_start: 0.5116 (t0) cc_final: 0.4562 (t0) REVERT: E 716 THR cc_start: 0.7881 (p) cc_final: 0.7298 (p) REVERT: F 134 GLN cc_start: 0.9239 (mm110) cc_final: 0.8746 (pm20) REVERT: F 201 PHE cc_start: 0.8885 (t80) cc_final: 0.8397 (t80) REVERT: F 907 ASN cc_start: 0.8324 (t0) cc_final: 0.8049 (m110) REVERT: G 34 MET cc_start: 0.4082 (mmt) cc_final: 0.3829 (mmm) REVERT: I 103 THR cc_start: 0.3297 (p) cc_final: 0.3026 (p) outliers start: 15 outliers final: 2 residues processed: 266 average time/residue: 0.4164 time to fit residues: 179.0306 Evaluate side-chains 155 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain F residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 7.9990 chunk 288 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 181 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 345 optimal weight: 30.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN D 804 GLN D 901 GLN D 920 GLN D 935 GLN E 134 GLN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 751 ASN ** E 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 GLN F 563 GLN F 690 GLN F 804 GLN F 955 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.095576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.069206 restraints weight = 236320.665| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 11.72 r_work: 0.3602 rms_B_bonded: 11.49 restraints_weight: 2.0000 r_work: 0.3680 rms_B_bonded: 9.35 restraints_weight: 4.0000 r_work: 0.3794 rms_B_bonded: 6.16 restraints_weight: 8.0000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30981 Z= 0.110 Angle : 0.589 10.798 42177 Z= 0.303 Chirality : 0.044 0.184 4715 Planarity : 0.005 0.061 5443 Dihedral : 4.891 42.216 4179 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 2.62 % Allowed : 24.02 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3817 helix: 0.49 (0.21), residues: 643 sheet: -0.20 (0.18), residues: 842 loop : -1.81 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F1102 HIS 0.004 0.001 HIS F 505 PHE 0.023 0.001 PHE D1095 TYR 0.016 0.001 TYR D1110 ARG 0.008 0.000 ARG H 102 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 941) hydrogen bonds : angle 5.15610 ( 2568) SS BOND : bond 0.00290 ( 48) SS BOND : angle 0.76750 ( 96) covalent geometry : bond 0.00246 (30933) covalent geometry : angle 0.58882 (42081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 168 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: -0.0432 (m) cc_final: -0.0760 (t) REVERT: D 95 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8715 (m) REVERT: D 201 PHE cc_start: 0.8716 (t80) cc_final: 0.8286 (t80) REVERT: D 336 CYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6927 (m) REVERT: D 1050 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.6822 (ttp) REVERT: D 1125 ASN cc_start: 0.7157 (p0) cc_final: 0.6662 (p0) REVERT: E 95 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8148 (t) REVERT: E 1050 MET cc_start: 0.7730 (ptm) cc_final: 0.7459 (ptp) REVERT: F 201 PHE cc_start: 0.8760 (t80) cc_final: 0.8414 (t80) REVERT: F 1038 LYS cc_start: 0.8065 (mmpt) cc_final: 0.7855 (mmtt) REVERT: G 29 VAL cc_start: 0.0112 (m) cc_final: -0.0163 (t) REVERT: G 34 MET cc_start: 0.4328 (mmt) cc_final: 0.3486 (mmm) outliers start: 88 outliers final: 29 residues processed: 248 average time/residue: 0.5510 time to fit residues: 227.5396 Evaluate side-chains 166 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 4.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1067 TYR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 146 GLN Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1116 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 577 ARG Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain J residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 0 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 170 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 256 optimal weight: 40.0000 chunk 210 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 GLN D 804 GLN D 935 GLN D1011 GLN ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 314 GLN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN F 690 GLN F 920 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.087460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.058469 restraints weight = 225507.702| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 11.62 r_work: 0.3268 rms_B_bonded: 11.30 restraints_weight: 2.0000 r_work: 0.3346 rms_B_bonded: 9.23 restraints_weight: 4.0000 r_work: 0.3475 rms_B_bonded: 6.64 restraints_weight: 8.0000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 30981 Z= 0.238 Angle : 0.704 11.144 42177 Z= 0.374 Chirality : 0.046 0.274 4715 Planarity : 0.006 0.063 5443 Dihedral : 5.034 25.553 4171 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.96 % Favored : 91.88 % Rotamer: Outliers : 4.47 % Allowed : 23.01 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3817 helix: 0.35 (0.21), residues: 651 sheet: -0.43 (0.18), residues: 839 loop : -1.80 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 36 HIS 0.006 0.001 HIS E1088 PHE 0.021 0.002 PHE D 898 TYR 0.025 0.002 TYR D 904 ARG 0.012 0.001 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 941) hydrogen bonds : angle 5.40872 ( 2568) SS BOND : bond 0.00312 ( 48) SS BOND : angle 1.06942 ( 96) covalent geometry : bond 0.00512 (30933) covalent geometry : angle 0.70280 (42081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 122 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8603 (t) REVERT: D 153 MET cc_start: 0.6924 (mpp) cc_final: 0.6707 (mpp) REVERT: D 178 ASP cc_start: 0.7654 (p0) cc_final: 0.6694 (t0) REVERT: D 192 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: E 95 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8222 (t) REVERT: E 244 LEU cc_start: 0.1061 (OUTLIER) cc_final: 0.0825 (mm) REVERT: E 985 ASP cc_start: 0.8946 (t0) cc_final: 0.8616 (t0) REVERT: E 988 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8859 (pm20) REVERT: F 105 ILE cc_start: 0.7690 (mt) cc_final: 0.7299 (tp) outliers start: 150 outliers final: 64 residues processed: 262 average time/residue: 0.5333 time to fit residues: 247.7550 Evaluate side-chains 159 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 90 time to evaluate : 5.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 192 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 1109 PHE Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1136 THR Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 785 VAL Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1109 PHE Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1136 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 239 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 361 optimal weight: 50.0000 chunk 333 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 245 HIS ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 935 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E 935 GLN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS F 282 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN F 690 GLN F 955 ASN I 6 GLN I 89 GLN H 39 GLN J 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.082480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.057690 restraints weight = 227457.738| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 8.67 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 30981 Z= 0.291 Angle : 0.748 16.346 42177 Z= 0.393 Chirality : 0.047 0.207 4715 Planarity : 0.006 0.064 5443 Dihedral : 5.532 50.773 4171 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.38 % Favored : 91.43 % Rotamer: Outliers : 5.16 % Allowed : 22.44 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3817 helix: 0.35 (0.21), residues: 654 sheet: -0.68 (0.18), residues: 877 loop : -1.92 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 36 HIS 0.008 0.001 HIS F1083 PHE 0.033 0.002 PHE D1075 TYR 0.029 0.002 TYR F 380 ARG 0.008 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 941) hydrogen bonds : angle 5.60593 ( 2568) SS BOND : bond 0.01617 ( 48) SS BOND : angle 1.59707 ( 96) covalent geometry : bond 0.00622 (30933) covalent geometry : angle 0.74478 (42081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 105 time to evaluate : 5.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.7500 (mpp) cc_final: 0.7215 (mpp) REVERT: D 177 MET cc_start: 0.4112 (ptm) cc_final: 0.3744 (ppp) REVERT: D 178 ASP cc_start: 0.8489 (p0) cc_final: 0.8265 (t0) REVERT: D 796 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: D 983 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8576 (mtm110) REVERT: E 26 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: E 796 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: E 985 ASP cc_start: 0.9241 (t0) cc_final: 0.9020 (t0) REVERT: E 1018 ILE cc_start: 0.9754 (OUTLIER) cc_final: 0.9472 (tt) REVERT: F 105 ILE cc_start: 0.8533 (mt) cc_final: 0.8259 (tp) REVERT: F 896 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9281 (mm) REVERT: F 1113 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8492 (mp10) outliers start: 173 outliers final: 92 residues processed: 266 average time/residue: 0.5786 time to fit residues: 268.7918 Evaluate side-chains 185 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 86 time to evaluate : 6.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 334 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 860 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 983 ARG Chi-restraints excluded: chain D residue 985 ASP Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 722 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 1018 ILE Chi-restraints excluded: chain E residue 1120 THR Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 610 VAL Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 912 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 991 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1077 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain F residue 1133 VAL Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 26 optimal weight: 0.8980 chunk 332 optimal weight: 6.9990 chunk 380 optimal weight: 7.9990 chunk 248 optimal weight: 0.0060 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 237 optimal weight: 0.2980 chunk 124 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 644 GLN F 690 GLN ** F 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN F1036 GLN I 79 GLN I 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.084171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.067555 restraints weight = 239481.753| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 5.92 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30981 Z= 0.112 Angle : 0.603 12.870 42177 Z= 0.308 Chirality : 0.044 0.213 4715 Planarity : 0.004 0.057 5443 Dihedral : 4.912 34.544 4171 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.15 % Favored : 92.69 % Rotamer: Outliers : 2.21 % Allowed : 25.51 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3817 helix: 0.68 (0.21), residues: 652 sheet: -0.54 (0.18), residues: 865 loop : -1.80 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 35 HIS 0.012 0.001 HIS D1083 PHE 0.021 0.001 PHE E 79 TYR 0.021 0.001 TYR F 453 ARG 0.011 0.000 ARG F 905 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 941) hydrogen bonds : angle 5.08475 ( 2568) SS BOND : bond 0.00326 ( 48) SS BOND : angle 1.03377 ( 96) covalent geometry : bond 0.00250 (30933) covalent geometry : angle 0.60140 (42081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 93 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.7343 (mpp) cc_final: 0.6978 (mpp) REVERT: D 177 MET cc_start: 0.3509 (ptm) cc_final: 0.3006 (ppp) REVERT: D 178 ASP cc_start: 0.8218 (p0) cc_final: 0.7809 (t0) REVERT: D 745 ASP cc_start: 0.8900 (m-30) cc_final: 0.8085 (p0) REVERT: E 559 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7487 (t80) REVERT: E 985 ASP cc_start: 0.9274 (t0) cc_final: 0.8851 (t0) REVERT: E 988 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.9081 (pm20) REVERT: F 55 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7624 (m-10) REVERT: F 105 ILE cc_start: 0.8249 (mt) cc_final: 0.8023 (mm) REVERT: F 358 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7272 (mp) REVERT: F 725 GLU cc_start: 0.8728 (tt0) cc_final: 0.8460 (tt0) REVERT: F 1113 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8570 (mp-120) REVERT: I 89 GLN cc_start: 0.5003 (OUTLIER) cc_final: 0.4532 (tm-30) outliers start: 74 outliers final: 47 residues processed: 163 average time/residue: 0.3636 time to fit residues: 102.3481 Evaluate side-chains 136 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 83 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 194 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 644 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 991 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1076 THR Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 375 optimal weight: 0.7980 chunk 216 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 144 optimal weight: 0.0770 chunk 90 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 332 optimal weight: 7.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 ASN D 935 GLN D1036 GLN D1113 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS F 644 GLN F 690 GLN F 784 GLN F1036 GLN I 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.084123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.067210 restraints weight = 244695.476| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 6.01 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 30981 Z= 0.109 Angle : 0.573 12.314 42177 Z= 0.291 Chirality : 0.043 0.205 4715 Planarity : 0.004 0.056 5443 Dihedral : 4.723 33.331 4171 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.00 % Favored : 92.87 % Rotamer: Outliers : 2.12 % Allowed : 25.78 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3817 helix: 0.72 (0.21), residues: 657 sheet: -0.38 (0.18), residues: 858 loop : -1.78 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.011 0.001 HIS D1083 PHE 0.020 0.001 PHE E 79 TYR 0.019 0.001 TYR F 453 ARG 0.004 0.000 ARG E 158 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 941) hydrogen bonds : angle 4.97106 ( 2568) SS BOND : bond 0.00210 ( 48) SS BOND : angle 0.80628 ( 96) covalent geometry : bond 0.00245 (30933) covalent geometry : angle 0.57217 (42081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 91 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.7345 (mpp) cc_final: 0.6985 (mpp) REVERT: D 177 MET cc_start: 0.3682 (ptm) cc_final: 0.3134 (ppp) REVERT: D 178 ASP cc_start: 0.8239 (p0) cc_final: 0.7840 (t0) REVERT: D 358 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7841 (mp) REVERT: D 464 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5014 (m-10) REVERT: D 745 ASP cc_start: 0.8967 (m-30) cc_final: 0.8141 (p0) REVERT: E 95 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.8592 (t) REVERT: E 559 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7545 (t80) REVERT: E 985 ASP cc_start: 0.9285 (t0) cc_final: 0.8823 (t0) REVERT: E 988 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.8961 (pm20) REVERT: F 55 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7757 (m-10) REVERT: F 105 ILE cc_start: 0.8257 (mt) cc_final: 0.8045 (mm) REVERT: F 358 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7258 (mp) REVERT: F 725 GLU cc_start: 0.8747 (tt0) cc_final: 0.8469 (tt0) outliers start: 71 outliers final: 47 residues processed: 158 average time/residue: 0.3839 time to fit residues: 104.4495 Evaluate side-chains 138 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 84 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 194 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 644 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 991 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 340 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 288 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 350 optimal weight: 50.0000 chunk 312 optimal weight: 0.4980 chunk 360 optimal weight: 50.0000 chunk 221 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 207 HIS ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN E 360 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 856 ASN F1036 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.082884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.062181 restraints weight = 250396.817| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 5.89 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30981 Z= 0.150 Angle : 0.592 11.644 42177 Z= 0.303 Chirality : 0.043 0.247 4715 Planarity : 0.004 0.056 5443 Dihedral : 4.688 27.999 4171 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.91 % Favored : 91.93 % Rotamer: Outliers : 2.77 % Allowed : 25.45 % Favored : 71.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3817 helix: 0.90 (0.22), residues: 646 sheet: -0.48 (0.18), residues: 878 loop : -1.75 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP H 36 HIS 0.010 0.001 HIS D1083 PHE 0.020 0.001 PHE E 79 TYR 0.019 0.001 TYR F 453 ARG 0.009 0.000 ARG F 273 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 941) hydrogen bonds : angle 4.94646 ( 2568) SS BOND : bond 0.00230 ( 48) SS BOND : angle 0.80815 ( 96) covalent geometry : bond 0.00331 (30933) covalent geometry : angle 0.59127 (42081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 95 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 SER cc_start: 0.9160 (t) cc_final: 0.8912 (p) REVERT: D 177 MET cc_start: 0.4019 (ptm) cc_final: 0.3815 (ppp) REVERT: D 358 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8104 (mp) REVERT: D 464 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4686 (m-10) REVERT: D 697 MET cc_start: 0.8526 (mmm) cc_final: 0.8101 (tpt) REVERT: D 745 ASP cc_start: 0.8750 (m-30) cc_final: 0.7939 (p0) REVERT: D 796 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6713 (m-10) REVERT: E 559 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7965 (t80) REVERT: E 745 ASP cc_start: 0.8793 (m-30) cc_final: 0.7939 (p0) REVERT: E 985 ASP cc_start: 0.9322 (t0) cc_final: 0.9051 (t0) REVERT: F 201 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.9059 (t80) REVERT: F 358 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7575 (mp) REVERT: F 468 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.6761 (tp) REVERT: F 644 GLN cc_start: 0.9458 (OUTLIER) cc_final: 0.9221 (tp40) REVERT: F 725 GLU cc_start: 0.8717 (tt0) cc_final: 0.8442 (tt0) REVERT: F 902 MET cc_start: 0.9047 (mmt) cc_final: 0.8782 (mmt) REVERT: F 995 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8752 (ttm110) REVERT: F 1002 GLN cc_start: 0.9296 (mm-40) cc_final: 0.8963 (mm-40) REVERT: F 1018 ILE cc_start: 0.9773 (OUTLIER) cc_final: 0.9430 (tt) REVERT: F 1113 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8542 (mp-120) REVERT: I 29 PHE cc_start: 0.3926 (OUTLIER) cc_final: 0.3679 (p90) outliers start: 93 outliers final: 56 residues processed: 181 average time/residue: 0.3773 time to fit residues: 118.2599 Evaluate side-chains 151 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 83 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 644 GLN Chi-restraints excluded: chain F residue 720 ILE Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 991 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1018 ILE Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 131 optimal weight: 10.0000 chunk 192 optimal weight: 1.9990 chunk 150 optimal weight: 40.0000 chunk 245 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 319 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN D 317 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 751 ASN F 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.082000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.060497 restraints weight = 241078.055| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 5.82 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.7708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30981 Z= 0.170 Angle : 0.610 11.904 42177 Z= 0.313 Chirality : 0.044 0.187 4715 Planarity : 0.004 0.057 5443 Dihedral : 4.751 25.904 4171 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.52 % Favored : 92.32 % Rotamer: Outliers : 3.13 % Allowed : 24.74 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3817 helix: 0.88 (0.21), residues: 648 sheet: -0.62 (0.18), residues: 846 loop : -1.71 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP H 36 HIS 0.009 0.001 HIS D1083 PHE 0.017 0.001 PHE F 562 TYR 0.019 0.001 TYR F 453 ARG 0.004 0.000 ARG D1000 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 941) hydrogen bonds : angle 4.96592 ( 2568) SS BOND : bond 0.00437 ( 48) SS BOND : angle 0.96114 ( 96) covalent geometry : bond 0.00373 (30933) covalent geometry : angle 0.60919 (42081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 85 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8887 (t70) cc_final: 0.8545 (p0) REVERT: D 113 LYS cc_start: 0.8821 (tptp) cc_final: 0.8518 (tptp) REVERT: D 153 MET cc_start: 0.7726 (mpp) cc_final: 0.7182 (mpp) REVERT: D 177 MET cc_start: 0.4830 (ptm) cc_final: 0.4534 (ppp) REVERT: D 358 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8066 (mp) REVERT: D 796 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: D 1029 MET cc_start: 0.9658 (tpp) cc_final: 0.9357 (tpp) REVERT: E 111 ASP cc_start: 0.8754 (t70) cc_final: 0.8485 (p0) REVERT: E 559 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7991 (t80) REVERT: E 745 ASP cc_start: 0.8927 (m-30) cc_final: 0.8056 (p0) REVERT: E 985 ASP cc_start: 0.9400 (t0) cc_final: 0.9144 (t0) REVERT: F 358 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7535 (mp) REVERT: F 725 GLU cc_start: 0.8769 (tt0) cc_final: 0.8442 (tt0) REVERT: F 902 MET cc_start: 0.9007 (mmt) cc_final: 0.8760 (mmt) outliers start: 105 outliers final: 73 residues processed: 186 average time/residue: 0.3740 time to fit residues: 122.0928 Evaluate side-chains 152 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 75 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1101 HIS Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 55 PHE Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 991 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 255 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 chunk 265 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 GLN E 134 GLN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1106 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.082339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.060875 restraints weight = 238709.907| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 5.82 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30981 Z= 0.118 Angle : 0.591 12.105 42177 Z= 0.299 Chirality : 0.043 0.201 4715 Planarity : 0.004 0.057 5443 Dihedral : 4.655 26.094 4171 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.75 % Favored : 92.14 % Rotamer: Outliers : 2.44 % Allowed : 25.48 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3817 helix: 0.88 (0.21), residues: 649 sheet: -0.57 (0.18), residues: 853 loop : -1.67 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 36 HIS 0.008 0.001 HIS D1083 PHE 0.018 0.001 PHE E 79 TYR 0.018 0.001 TYR F 453 ARG 0.008 0.000 ARG D 319 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 941) hydrogen bonds : angle 4.86857 ( 2568) SS BOND : bond 0.00183 ( 48) SS BOND : angle 0.94775 ( 96) covalent geometry : bond 0.00268 (30933) covalent geometry : angle 0.58985 (42081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 81 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8944 (t70) cc_final: 0.8587 (p0) REVERT: D 153 MET cc_start: 0.7550 (mpp) cc_final: 0.7100 (mpp) REVERT: D 177 MET cc_start: 0.4747 (ptm) cc_final: 0.4500 (ppp) REVERT: D 358 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8134 (mp) REVERT: D 644 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (tp40) REVERT: D 796 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: E 111 ASP cc_start: 0.8785 (t70) cc_final: 0.8487 (p0) REVERT: E 559 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8007 (t80) REVERT: E 745 ASP cc_start: 0.8920 (m-30) cc_final: 0.8030 (p0) REVERT: E 985 ASP cc_start: 0.9362 (t0) cc_final: 0.9107 (t0) REVERT: F 111 ASP cc_start: 0.8889 (t70) cc_final: 0.8532 (p0) REVERT: F 358 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7505 (mp) REVERT: F 468 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.6932 (tp) REVERT: F 725 GLU cc_start: 0.8811 (tt0) cc_final: 0.8512 (tt0) REVERT: F 902 MET cc_start: 0.9043 (mmt) cc_final: 0.8794 (mmt) REVERT: F 1113 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8510 (mp-120) outliers start: 82 outliers final: 67 residues processed: 160 average time/residue: 0.4155 time to fit residues: 117.7598 Evaluate side-chains 152 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 78 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 991 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 147 optimal weight: 3.9990 chunk 365 optimal weight: 30.0000 chunk 127 optimal weight: 0.0670 chunk 218 optimal weight: 0.2980 chunk 358 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 ASN ** E1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.082075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.060905 restraints weight = 240276.879| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 5.81 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.8007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30981 Z= 0.133 Angle : 0.589 13.341 42177 Z= 0.298 Chirality : 0.043 0.268 4715 Planarity : 0.004 0.058 5443 Dihedral : 4.617 25.586 4171 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 2.41 % Allowed : 25.48 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3817 helix: 0.86 (0.21), residues: 655 sheet: -0.62 (0.18), residues: 864 loop : -1.64 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 36 HIS 0.009 0.001 HIS D1083 PHE 0.017 0.001 PHE E 79 TYR 0.018 0.001 TYR F 453 ARG 0.005 0.000 ARG E 319 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 941) hydrogen bonds : angle 4.85222 ( 2568) SS BOND : bond 0.00196 ( 48) SS BOND : angle 0.88270 ( 96) covalent geometry : bond 0.00300 (30933) covalent geometry : angle 0.58836 (42081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 81 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 ASP cc_start: 0.8962 (t70) cc_final: 0.8602 (p0) REVERT: D 153 MET cc_start: 0.7617 (mpp) cc_final: 0.7106 (mpp) REVERT: D 358 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8113 (mp) REVERT: D 644 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8354 (tp40) REVERT: D 697 MET cc_start: 0.8819 (mmm) cc_final: 0.8551 (tmm) REVERT: D 796 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6464 (m-10) REVERT: E 111 ASP cc_start: 0.8800 (t70) cc_final: 0.8488 (p0) REVERT: E 559 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8082 (t80) REVERT: E 745 ASP cc_start: 0.8931 (m-30) cc_final: 0.8075 (p0) REVERT: E 985 ASP cc_start: 0.9366 (t0) cc_final: 0.9107 (t0) REVERT: F 111 ASP cc_start: 0.8923 (t70) cc_final: 0.8569 (p0) REVERT: F 358 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7510 (mp) REVERT: F 468 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.6789 (tp) REVERT: F 725 GLU cc_start: 0.8785 (tt0) cc_final: 0.8489 (tt0) REVERT: F 902 MET cc_start: 0.9001 (mmt) cc_final: 0.8762 (mmt) REVERT: F 1113 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8582 (mp-120) outliers start: 81 outliers final: 69 residues processed: 158 average time/residue: 0.3566 time to fit residues: 99.4901 Evaluate side-chains 154 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 78 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 796 TYR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 906 PHE Chi-restraints excluded: chain D residue 941 THR Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1048 HIS Chi-restraints excluded: chain D residue 1101 HIS Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 559 PHE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 587 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 796 TYR Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 941 THR Chi-restraints excluded: chain E residue 976 VAL Chi-restraints excluded: chain E residue 991 VAL Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 66 HIS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 194 PHE Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 690 GLN Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 941 THR Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 991 VAL Chi-restraints excluded: chain F residue 995 ARG Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1101 HIS Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1120 THR Chi-restraints excluded: chain F residue 1128 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain J residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 344 optimal weight: 20.0000 chunk 357 optimal weight: 9.9990 chunk 366 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 349 optimal weight: 40.0000 chunk 239 optimal weight: 9.9990 chunk 94 optimal weight: 0.0670 chunk 275 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 GLN F 751 ASN F 856 ASN F1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.079375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.049350 restraints weight = 220616.867| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 10.15 r_work: 0.2990 rms_B_bonded: 9.55 restraints_weight: 2.0000 r_work: 0.3043 rms_B_bonded: 6.97 restraints_weight: 4.0000 r_work: 0.3176 rms_B_bonded: 5.30 restraints_weight: 8.0000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.8800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 30981 Z= 0.337 Angle : 0.762 13.427 42177 Z= 0.394 Chirality : 0.046 0.261 4715 Planarity : 0.005 0.068 5443 Dihedral : 5.151 25.414 4171 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.14 % Favored : 89.68 % Rotamer: Outliers : 2.86 % Allowed : 25.07 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3817 helix: 0.80 (0.21), residues: 632 sheet: -0.86 (0.18), residues: 829 loop : -1.79 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 36 HIS 0.012 0.002 HIS D1083 PHE 0.021 0.002 PHE F 157 TYR 0.025 0.002 TYR F 453 ARG 0.010 0.001 ARG E 319 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 941) hydrogen bonds : angle 5.36034 ( 2568) SS BOND : bond 0.00416 ( 48) SS BOND : angle 1.31154 ( 96) covalent geometry : bond 0.00718 (30933) covalent geometry : angle 0.76050 (42081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30283.53 seconds wall clock time: 531 minutes 46.83 seconds (31906.83 seconds total)