Starting phenix.real_space_refine on Thu Mar 5 13:44:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x27_32960/03_2026/7x27_32960_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x27_32960/03_2026/7x27_32960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x27_32960/03_2026/7x27_32960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x27_32960/03_2026/7x27_32960.map" model { file = "/net/cci-nas-00/data/ceres_data/7x27_32960/03_2026/7x27_32960_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x27_32960/03_2026/7x27_32960_neut.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 120 5.16 5 C 14427 2.51 5 N 3816 2.21 5 O 4407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22770 Number of models: 1 Model: "" Number of chains: 3 Chain: "G" Number of atoms: 7590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7590 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 45, 'TRANS': 937} Chain breaks: 3 Chain: "I" Number of atoms: 7590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7590 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 45, 'TRANS': 937} Chain breaks: 3 Chain: "J" Number of atoms: 7590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7590 Classifications: {'peptide': 983} Link IDs: {'PTRANS': 45, 'TRANS': 937} Chain breaks: 3 Time building chain proxies: 5.28, per 1000 atoms: 0.23 Number of scatterers: 22770 At special positions: 0 Unit cell: (153.715, 143.972, 163.457, 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 120 16.00 O 4407 8.00 N 3816 7.00 C 14427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 30 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 176 " - pdb=" SG CYS G 214 " distance=2.04 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 237 " distance=2.04 Simple disulfide: pdb=" SG CYS G 339 " - pdb=" SG CYS G 349 " distance=2.03 Simple disulfide: pdb=" SG CYS G 603 " - pdb=" SG CYS G 654 " distance=2.03 Simple disulfide: pdb=" SG CYS G 620 " - pdb=" SG CYS G 650 " distance=2.03 Simple disulfide: pdb=" SG CYS G 727 " - pdb=" SG CYS G 736 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.03 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.03 Simple disulfide: pdb=" SG CYS I 30 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 185 " - pdb=" SG CYS I 237 " distance=2.04 Simple disulfide: pdb=" SG CYS I 339 " - pdb=" SG CYS I 349 " distance=2.03 Simple disulfide: pdb=" SG CYS I 603 " - pdb=" SG CYS I 654 " distance=2.03 Simple disulfide: pdb=" SG CYS I 620 " - pdb=" SG CYS I 650 " distance=2.04 Simple disulfide: pdb=" SG CYS I 727 " - pdb=" SG CYS I 736 " distance=2.03 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.03 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=2.03 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.03 Simple disulfide: pdb=" SG CYS I1106 " - pdb=" SG CYS I1117 " distance=2.03 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.03 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.03 Simple disulfide: pdb=" SG CYS J 806 " - pdb=" SG CYS J 828 " distance=2.03 Simple disulfide: pdb=" SG CYS J 811 " - pdb=" SG CYS J 817 " distance=2.03 Simple disulfide: pdb=" SG CYS J 912 " - pdb=" SG CYS J 925 " distance=2.03 Simple disulfide: pdb=" SG CYS J1106 " - pdb=" SG CYS J1117 " distance=2.03 Simple disulfide: pdb=" SG CYS J1156 " - pdb=" SG CYS J1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 965.2 milliseconds 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5460 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 25.4% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'G' and resid 36 through 41 removed outlier: 4.095A pdb=" N PHE G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 103 through 108 removed outlier: 4.687A pdb=" N SER G 106 " --> pdb=" O ALA G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 232 removed outlier: 4.007A pdb=" N TYR G 231 " --> pdb=" O SER G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 805 through 812 Processing helix chain 'G' and resid 814 through 823 removed outlier: 3.616A pdb=" N GLN G 819 " --> pdb=" O GLN G 815 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 820 " --> pdb=" O LYS G 816 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 823 " --> pdb=" O GLN G 819 " (cutoff:3.500A) Processing helix chain 'G' and resid 826 through 854 removed outlier: 3.600A pdb=" N LYS G 830 " --> pdb=" O GLN G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 915 removed outlier: 3.711A pdb=" N CYS G 912 " --> pdb=" O GLY G 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET G 913 " --> pdb=" O TYR G 909 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN G 914 " --> pdb=" O ASP G 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 926 through 931 Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1012 removed outlier: 4.473A pdb=" N PHE G1012 " --> pdb=" O GLN G1009 " (cutoff:3.500A) Processing helix chain 'G' and resid 1016 through 1039 removed outlier: 3.601A pdb=" N LEU G1036 " --> pdb=" O ALA G1032 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1056 removed outlier: 3.722A pdb=" N GLN G1056 " --> pdb=" O GLY G1052 " (cutoff:3.500A) Processing helix chain 'G' and resid 1059 through 1107 removed outlier: 3.991A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G1094 " --> pdb=" O GLU G1090 " (cutoff:3.500A) Processing helix chain 'G' and resid 1219 through 1223 Processing helix chain 'I' and resid 36 through 41 removed outlier: 4.101A pdb=" N PHE I 40 " --> pdb=" O GLN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 222 through 232 removed outlier: 4.065A pdb=" N TYR I 231 " --> pdb=" O SER I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 351 Processing helix chain 'I' and resid 805 through 812 Processing helix chain 'I' and resid 814 through 823 removed outlier: 3.792A pdb=" N GLU I 823 " --> pdb=" O GLN I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 826 through 854 removed outlier: 3.564A pdb=" N LYS I 830 " --> pdb=" O GLN I 826 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 915 removed outlier: 3.604A pdb=" N CYS I 912 " --> pdb=" O GLY I 908 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN I 914 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 931 Processing helix chain 'I' and resid 940 through 954 removed outlier: 3.626A pdb=" N SER I 954 " --> pdb=" O SER I 950 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1007 Processing helix chain 'I' and resid 1008 through 1012 removed outlier: 4.414A pdb=" N PHE I1012 " --> pdb=" O GLN I1009 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1039 removed outlier: 3.597A pdb=" N LEU I1036 " --> pdb=" O ALA I1032 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1056 removed outlier: 3.820A pdb=" N GLN I1056 " --> pdb=" O GLY I1052 " (cutoff:3.500A) Processing helix chain 'I' and resid 1059 through 1107 removed outlier: 3.982A pdb=" N ALA I1065 " --> pdb=" O PRO I1061 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU I1094 " --> pdb=" O GLU I1090 " (cutoff:3.500A) Processing helix chain 'I' and resid 1219 through 1223 Processing helix chain 'J' and resid 36 through 41 removed outlier: 4.067A pdb=" N PHE J 40 " --> pdb=" O GLN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 222 through 232 removed outlier: 4.028A pdb=" N TYR J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 805 through 812 Processing helix chain 'J' and resid 814 through 823 removed outlier: 3.822A pdb=" N GLU J 823 " --> pdb=" O GLN J 819 " (cutoff:3.500A) Processing helix chain 'J' and resid 826 through 854 removed outlier: 3.654A pdb=" N LYS J 830 " --> pdb=" O GLN J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 888 through 898 Processing helix chain 'J' and resid 907 through 915 removed outlier: 3.936A pdb=" N GLN J 914 " --> pdb=" O ASP J 910 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 931 Processing helix chain 'J' and resid 940 through 953 Processing helix chain 'J' and resid 971 through 982 Processing helix chain 'J' and resid 986 through 993 Processing helix chain 'J' and resid 993 through 1007 Processing helix chain 'J' and resid 1008 through 1012 removed outlier: 4.467A pdb=" N PHE J1012 " --> pdb=" O GLN J1009 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1039 removed outlier: 3.630A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1050 through 1056 removed outlier: 3.670A pdb=" N GLN J1056 " --> pdb=" O GLY J1052 " (cutoff:3.500A) Processing helix chain 'J' and resid 1059 through 1107 removed outlier: 3.938A pdb=" N ALA J1065 " --> pdb=" O PRO J1061 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU J1094 " --> pdb=" O GLU J1090 " (cutoff:3.500A) Processing helix chain 'J' and resid 1219 through 1223 Processing sheet with id=AA1, first strand: chain 'G' and resid 33 through 35 removed outlier: 6.432A pdb=" N HIS G 91 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 67 through 75 removed outlier: 4.301A pdb=" N ARG G 335 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.532A pdb=" N TYR G 314 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL G 263 " --> pdb=" O THR G 283 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR G 283 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU G 265 " --> pdb=" O PHE G 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 88 through 89 removed outlier: 7.322A pdb=" N SER G 88 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 206 " --> pdb=" O SER G 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 110 through 111 Processing sheet with id=AA6, first strand: chain 'G' and resid 127 through 129 removed outlier: 3.879A pdb=" N ALA G 309 " --> pdb=" O THR G 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'G' and resid 689 through 690 removed outlier: 5.499A pdb=" N VAL G 360 " --> pdb=" O TYR G 663 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR G 663 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER G 362 " --> pdb=" O VAL G 661 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL G 661 " --> pdb=" O SER G 362 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER G 364 " --> pdb=" O VAL G 659 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL G 659 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS G 713 " --> pdb=" O PHE G 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 373 through 376 removed outlier: 4.615A pdb=" N VAL G 639 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 631 " --> pdb=" O VAL G 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 717 through 724 removed outlier: 6.739A pdb=" N VAL G 718 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N SER G 761 " --> pdb=" O VAL G 718 " (cutoff:3.500A) removed outlier: 9.927A pdb=" N SER G 720 " --> pdb=" O SER G 761 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU G 735 " --> pdb=" O LEU G 731 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 768 through 769 removed outlier: 5.799A pdb=" N ILE G 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.072A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY G1188 " --> pdb=" O ALA G1193 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA G1193 " --> pdb=" O GLY G1188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.072A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS G 779 " --> pdb=" O ALA I 969 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AB6, first strand: chain 'G' and resid 857 through 858 Processing sheet with id=AB7, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.304A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL J1124 " --> pdb=" O VAL J1139 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR J1141 " --> pdb=" O HIS J1122 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N HIS J1122 " --> pdb=" O TYR J1141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.304A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL J1150 " --> pdb=" O LYS J1174 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE J1172 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY J1188 " --> pdb=" O ALA J1193 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA J1193 " --> pdb=" O GLY J1188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.413A pdb=" N HIS I 91 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 67 through 75 removed outlier: 4.233A pdb=" N ARG I 335 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 83 through 85 removed outlier: 6.312A pdb=" N VAL I 263 " --> pdb=" O THR I 283 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR I 283 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU I 265 " --> pdb=" O PHE I 281 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AC5, first strand: chain 'I' and resid 127 through 129 removed outlier: 3.718A pdb=" N ALA I 309 " --> pdb=" O THR I 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 153 through 155 Processing sheet with id=AC7, first strand: chain 'I' and resid 206 through 208 removed outlier: 6.400A pdb=" N THR I 206 " --> pdb=" O SER I 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 689 through 690 removed outlier: 4.544A pdb=" N VAL I 659 " --> pdb=" O VAL I 363 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER I 365 " --> pdb=" O VAL I 657 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL I 657 " --> pdb=" O SER I 365 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS I 713 " --> pdb=" O PHE I 674 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 372 through 376 removed outlier: 6.765A pdb=" N GLY I 372 " --> pdb=" O GLU I 605 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N SER I 607 " --> pdb=" O GLY I 372 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL I 374 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL I 639 " --> pdb=" O LEU I 651 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL I 631 " --> pdb=" O VAL I 639 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 717 through 724 removed outlier: 6.707A pdb=" N VAL I 718 " --> pdb=" O LEU I 759 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N SER I 761 " --> pdb=" O VAL I 718 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N SER I 720 " --> pdb=" O SER I 761 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU I 735 " --> pdb=" O LEU I 731 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 768 through 769 removed outlier: 5.811A pdb=" N ILE I 768 " --> pdb=" O SER J 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA I1152 " --> pdb=" O TYR I 777 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR I 777 " --> pdb=" O ALA I1152 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS I 779 " --> pdb=" O ALA J 969 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AD6, first strand: chain 'I' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS I1164 " --> pdb=" O VAL I1205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'J' and resid 67 through 75 removed outlier: 4.297A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.528A pdb=" N TYR J 314 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL J 263 " --> pdb=" O THR J 283 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR J 283 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU J 265 " --> pdb=" O PHE J 281 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.291A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR J 206 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 110 through 111 Processing sheet with id=AE3, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.828A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AE5, first strand: chain 'J' and resid 689 through 690 removed outlier: 4.596A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 372 through 376 removed outlier: 3.907A pdb=" N GLY J 372 " --> pdb=" O CYS J 603 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 717 through 724 removed outlier: 6.729A pdb=" N VAL J 718 " --> pdb=" O LEU J 759 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N SER J 761 " --> pdb=" O VAL J 718 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N SER J 720 " --> pdb=" O SER J 761 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU J 735 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 802 through 804 Processing sheet with id=AE9, first strand: chain 'J' and resid 1202 through 1205 removed outlier: 4.167A pdb=" N CYS J1164 " --> pdb=" O VAL J1205 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2517 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7446 1.34 - 1.47: 5822 1.47 - 1.59: 9859 1.59 - 1.71: 0 1.71 - 1.84: 162 Bond restraints: 23289 Sorted by residual: bond pdb=" N GLN G 377 " pdb=" CA GLN G 377 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" N GLU G 376 " pdb=" CA GLU G 376 " ideal model delta sigma weight residual 1.455 1.502 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N ASN J 592 " pdb=" CA ASN J 592 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.18e+00 bond pdb=" N LYS G 595 " pdb=" CA LYS G 595 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.16e+00 bond pdb=" N ASP J 593 " pdb=" CA ASP J 593 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.79e+00 ... (remaining 23284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 31196 2.60 - 5.19: 424 5.19 - 7.79: 34 7.79 - 10.39: 11 10.39 - 12.99: 3 Bond angle restraints: 31668 Sorted by residual: angle pdb=" N ASN G 592 " pdb=" CA ASN G 592 " pdb=" C ASN G 592 " ideal model delta sigma weight residual 114.75 106.92 7.83 1.26e+00 6.30e-01 3.86e+01 angle pdb=" CA GLU G 376 " pdb=" C GLU G 376 " pdb=" O GLU G 376 " ideal model delta sigma weight residual 120.99 115.81 5.18 1.12e+00 7.97e-01 2.14e+01 angle pdb=" CB MET J 161 " pdb=" CG MET J 161 " pdb=" SD MET J 161 " ideal model delta sigma weight residual 112.70 125.69 -12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CB LYS J 698 " pdb=" CG LYS J 698 " pdb=" CD LYS J 698 " ideal model delta sigma weight residual 111.30 121.17 -9.87 2.30e+00 1.89e-01 1.84e+01 angle pdb=" CA CYS I 650 " pdb=" CB CYS I 650 " pdb=" SG CYS I 650 " ideal model delta sigma weight residual 114.40 124.25 -9.85 2.30e+00 1.89e-01 1.83e+01 ... (remaining 31663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11854 17.97 - 35.94: 1376 35.94 - 53.92: 466 53.92 - 71.89: 125 71.89 - 89.86: 57 Dihedral angle restraints: 13878 sinusoidal: 5316 harmonic: 8562 Sorted by residual: dihedral pdb=" CB CYS I 176 " pdb=" SG CYS I 176 " pdb=" SG CYS I 214 " pdb=" CB CYS I 214 " ideal model delta sinusoidal sigma weight residual -86.00 -160.84 74.84 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS I 30 " pdb=" SG CYS I 30 " pdb=" SG CYS I 195 " pdb=" CB CYS I 195 " ideal model delta sinusoidal sigma weight residual -86.00 -154.46 68.46 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS G 30 " pdb=" SG CYS G 30 " pdb=" SG CYS G 195 " pdb=" CB CYS G 195 " ideal model delta sinusoidal sigma weight residual -86.00 -154.19 68.19 1 1.00e+01 1.00e-02 6.03e+01 ... (remaining 13875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2410 0.038 - 0.077: 782 0.077 - 0.115: 289 0.115 - 0.153: 38 0.153 - 0.192: 6 Chirality restraints: 3525 Sorted by residual: chirality pdb=" CA GLN G 377 " pdb=" N GLN G 377 " pdb=" C GLN G 377 " pdb=" CB GLN G 377 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ASP G 593 " pdb=" N ASP G 593 " pdb=" C ASP G 593 " pdb=" CB ASP G 593 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA PRO J1131 " pdb=" N PRO J1131 " pdb=" C PRO J1131 " pdb=" CB PRO J1131 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 3522 not shown) Planarity restraints: 4140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 377 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLN I 377 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN I 377 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA I 378 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 284 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO I 285 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 285 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 285 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 284 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO J 285 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO J 285 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 285 " 0.031 5.00e-02 4.00e+02 ... (remaining 4137 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 1 1.82 - 2.59: 222 2.59 - 3.36: 28051 3.36 - 4.13: 55344 4.13 - 4.90: 101433 Nonbonded interactions: 185051 Sorted by model distance: nonbonded pdb=" OE2 GLU I 376 " pdb=" NZ LYS I 595 " model vdw 1.052 3.120 nonbonded pdb=" OG1 THR G 667 " pdb=" OG1 THR G 669 " model vdw 2.135 3.040 nonbonded pdb=" O THR I 594 " pdb=" OG1 THR I 594 " model vdw 2.160 3.040 nonbonded pdb=" NH2 ARG J 181 " pdb=" O ARG J 221 " model vdw 2.164 3.120 nonbonded pdb=" N ASP J 216 " pdb=" OD1 ASP J 216 " model vdw 2.171 3.120 ... (remaining 185046 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: 0.04 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.004 0.050 23325 Z= 0.195 Angle : 0.753 12.987 31740 Z= 0.447 Chirality : 0.044 0.192 3525 Planarity : 0.005 0.058 4140 Dihedral : 18.743 89.861 8310 Min Nonbonded Distance : 1.052 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 9.19 % Allowed : 23.94 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 2925 helix: 1.45 (0.21), residues: 639 sheet: -0.85 (0.20), residues: 543 loop : -1.73 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 235 TYR 0.023 0.001 TYR J 635 PHE 0.022 0.002 PHE J 156 TRP 0.008 0.001 TRP J 310 HIS 0.007 0.001 HIS G 194 Details of bonding type rmsd covalent geometry : bond 0.00370 (23289) covalent geometry : angle 0.75196 (31668) SS BOND : bond 0.00346 ( 36) SS BOND : angle 1.00925 ( 72) hydrogen bonds : bond 0.16703 ( 896) hydrogen bonds : angle 7.15314 ( 2517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 180 time to evaluate : 0.837 Fit side-chains REVERT: I 592 ASN cc_start: 0.6283 (OUTLIER) cc_final: 0.5628 (t0) REVERT: I 1090 GLU cc_start: 0.8000 (tp30) cc_final: 0.7688 (tp30) REVERT: I 1137 MET cc_start: 0.8645 (mtm) cc_final: 0.8401 (mtm) REVERT: J 666 GLU cc_start: 0.8068 (tp30) cc_final: 0.7856 (mm-30) REVERT: J 1008 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8098 (tpp) REVERT: J 1090 GLU cc_start: 0.7928 (tp30) cc_final: 0.7684 (tp30) outliers start: 230 outliers final: 179 residues processed: 394 average time/residue: 0.4384 time to fit residues: 208.3892 Evaluate side-chains 329 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 148 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 110 LYS Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 604 VAL Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 677 VAL Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 694 ARG Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 717 LEU Chi-restraints excluded: chain G residue 720 SER Chi-restraints excluded: chain G residue 729 LEU Chi-restraints excluded: chain G residue 781 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 804 VAL Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 856 SER Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 873 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 924 ILE Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1010 THR Chi-restraints excluded: chain G residue 1034 SER Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1095 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain G residue 1226 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLN Chi-restraints excluded: chain I residue 592 ASN Chi-restraints excluded: chain I residue 596 ILE Chi-restraints excluded: chain I residue 604 VAL Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 669 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 720 SER Chi-restraints excluded: chain I residue 729 LEU Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 804 VAL Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 856 SER Chi-restraints excluded: chain I residue 858 SER Chi-restraints excluded: chain I residue 859 SER Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 910 ASP Chi-restraints excluded: chain I residue 924 ILE Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 965 SER Chi-restraints excluded: chain I residue 975 SER Chi-restraints excluded: chain I residue 994 GLN Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1015 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1082 VAL Chi-restraints excluded: chain I residue 1089 SER Chi-restraints excluded: chain I residue 1091 SER Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1175 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1209 VAL Chi-restraints excluded: chain I residue 1216 THR Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 294 SER Chi-restraints excluded: chain J residue 302 SER Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 353 SER Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 604 VAL Chi-restraints excluded: chain J residue 620 CYS Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 669 THR Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 704 TYR Chi-restraints excluded: chain J residue 720 SER Chi-restraints excluded: chain J residue 729 LEU Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 829 SER Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 858 SER Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 THR Chi-restraints excluded: chain J residue 873 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 910 ASP Chi-restraints excluded: chain J residue 924 ILE Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 1008 MET Chi-restraints excluded: chain J residue 1010 THR Chi-restraints excluded: chain J residue 1034 SER Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1055 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1095 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1112 LYS Chi-restraints excluded: chain J residue 1131 PRO Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1226 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 819 GLN I 37 GLN I 194 HIS I 377 GLN I 681 HIS J 628 GLN J1129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068365 restraints weight = 36436.778| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.60 r_work: 0.2722 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 23325 Z= 0.255 Angle : 0.665 7.937 31740 Z= 0.355 Chirality : 0.047 0.221 3525 Planarity : 0.005 0.055 4140 Dihedral : 10.228 69.682 3484 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.22 % Favored : 93.68 % Rotamer: Outliers : 7.31 % Allowed : 22.14 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 2925 helix: 1.29 (0.20), residues: 666 sheet: -0.67 (0.19), residues: 618 loop : -1.60 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 652 TYR 0.022 0.002 TYR G 184 PHE 0.016 0.002 PHE I 865 TRP 0.008 0.001 TRP J 310 HIS 0.008 0.001 HIS G 194 Details of bonding type rmsd covalent geometry : bond 0.00599 (23289) covalent geometry : angle 0.66322 (31668) SS BOND : bond 0.00382 ( 36) SS BOND : angle 1.12094 ( 72) hydrogen bonds : bond 0.06285 ( 896) hydrogen bonds : angle 5.97479 ( 2517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 159 time to evaluate : 0.930 Fit side-chains REVERT: G 110 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7640 (mttp) REVERT: G 235 ARG cc_start: 0.7274 (tpp-160) cc_final: 0.6985 (mmp80) REVERT: G 628 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6363 (mt0) REVERT: G 830 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8759 (mmmt) REVERT: G 907 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6501 (pp30) REVERT: G 960 TRP cc_start: 0.7109 (OUTLIER) cc_final: 0.6296 (m-90) REVERT: I 110 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7485 (mtpt) REVERT: I 377 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6605 (mt0) REVERT: I 592 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6628 (t0) REVERT: I 1090 GLU cc_start: 0.9050 (tp30) cc_final: 0.8603 (tp30) REVERT: J 110 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7729 (mtpt) REVERT: J 240 MET cc_start: 0.8628 (tmt) cc_final: 0.8316 (tmt) REVERT: J 292 TYR cc_start: 0.8853 (m-80) cc_final: 0.8428 (m-80) REVERT: J 666 GLU cc_start: 0.8899 (tp30) cc_final: 0.8580 (mm-30) REVERT: J 808 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8829 (tt0) REVERT: J 820 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8786 (mm) outliers start: 183 outliers final: 112 residues processed: 325 average time/residue: 0.5533 time to fit residues: 210.1107 Evaluate side-chains 265 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 143 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 110 LYS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 185 CYS Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 677 VAL Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 804 VAL Chi-restraints excluded: chain G residue 812 ASN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 907 GLN Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 994 GLN Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1094 LEU Chi-restraints excluded: chain G residue 1095 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 156 PHE Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 377 GLN Chi-restraints excluded: chain I residue 592 ASN Chi-restraints excluded: chain I residue 596 ILE Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 694 ARG Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 779 LYS Chi-restraints excluded: chain I residue 804 VAL Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 859 SER Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1094 LEU Chi-restraints excluded: chain I residue 1095 SER Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1209 VAL Chi-restraints excluded: chain I residue 1216 THR Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 294 SER Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 704 TYR Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 820 LEU Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 858 SER Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 THR Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1095 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1131 PRO Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 23 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 265 optimal weight: 0.3980 chunk 276 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 194 HIS G1129 ASN I 194 HIS I1072 ASN J 628 GLN J1217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.070615 restraints weight = 36243.457| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.61 r_work: 0.2769 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23325 Z= 0.147 Angle : 0.581 7.404 31740 Z= 0.311 Chirality : 0.043 0.165 3525 Planarity : 0.004 0.053 4140 Dihedral : 8.436 69.229 3347 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.40 % Allowed : 22.86 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 2925 helix: 1.54 (0.21), residues: 666 sheet: -0.49 (0.20), residues: 567 loop : -1.44 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 652 TYR 0.017 0.001 TYR J 635 PHE 0.016 0.001 PHE I 112 TRP 0.006 0.001 TRP J 310 HIS 0.003 0.001 HIS G 208 Details of bonding type rmsd covalent geometry : bond 0.00334 (23289) covalent geometry : angle 0.58092 (31668) SS BOND : bond 0.00407 ( 36) SS BOND : angle 0.79392 ( 72) hydrogen bonds : bond 0.05082 ( 896) hydrogen bonds : angle 5.59824 ( 2517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 164 time to evaluate : 0.695 Fit side-chains REVERT: G 628 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6172 (mt0) REVERT: G 728 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8713 (mmmt) REVERT: G 830 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8740 (mmmt) REVERT: G 872 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8894 (p) REVERT: G 960 TRP cc_start: 0.7072 (OUTLIER) cc_final: 0.6178 (m-90) REVERT: I 110 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7530 (mtpt) REVERT: I 377 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6712 (mt0) REVERT: I 1090 GLU cc_start: 0.9053 (tp30) cc_final: 0.8638 (tp30) REVERT: J 292 TYR cc_start: 0.8830 (m-80) cc_final: 0.8407 (m-80) REVERT: J 608 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8296 (mt) REVERT: J 628 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6131 (mt0) REVERT: J 666 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8605 (mm-30) REVERT: J 862 ILE cc_start: 0.8918 (pt) cc_final: 0.8686 (pp) outliers start: 135 outliers final: 77 residues processed: 287 average time/residue: 0.5266 time to fit residues: 176.0899 Evaluate side-chains 239 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 153 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 812 ASN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 214 CYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 377 GLN Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 734 SER Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 628 GLN Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 194 HIS G1042 ASN G1132 ASN I 194 HIS J 194 HIS J 628 GLN J1160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.066814 restraints weight = 36761.683| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.60 r_work: 0.2688 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 23325 Z= 0.396 Angle : 0.735 9.753 31740 Z= 0.390 Chirality : 0.050 0.250 3525 Planarity : 0.005 0.054 4140 Dihedral : 8.363 74.295 3301 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 6.95 % Allowed : 21.42 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 2925 helix: 1.22 (0.20), residues: 663 sheet: -0.58 (0.20), residues: 570 loop : -1.47 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 652 TYR 0.026 0.002 TYR G 184 PHE 0.026 0.003 PHE G 156 TRP 0.013 0.002 TRP G 960 HIS 0.011 0.002 HIS I1138 Details of bonding type rmsd covalent geometry : bond 0.00946 (23289) covalent geometry : angle 0.73246 (31668) SS BOND : bond 0.00550 ( 36) SS BOND : angle 1.41192 ( 72) hydrogen bonds : bond 0.06920 ( 896) hydrogen bonds : angle 5.96641 ( 2517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 152 time to evaluate : 0.908 Fit side-chains REVERT: G 184 TYR cc_start: 0.6413 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: G 284 LEU cc_start: 0.8386 (mt) cc_final: 0.8178 (mp) REVERT: G 628 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.6417 (mt0) REVERT: G 728 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8740 (mmmt) REVERT: G 830 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8845 (mmmt) REVERT: G 907 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6301 (pp30) REVERT: G 960 TRP cc_start: 0.7013 (OUTLIER) cc_final: 0.6439 (m-90) REVERT: I 110 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7448 (mtpt) REVERT: I 184 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: I 377 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7117 (mt0) REVERT: I 628 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6161 (mt0) REVERT: I 960 TRP cc_start: 0.7071 (OUTLIER) cc_final: 0.5577 (m-90) REVERT: I 1090 GLU cc_start: 0.9088 (tp30) cc_final: 0.8669 (tp30) REVERT: J 184 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5521 (m-80) REVERT: J 289 THR cc_start: 0.9151 (m) cc_final: 0.8803 (t) REVERT: J 292 TYR cc_start: 0.8887 (m-80) cc_final: 0.8464 (m-80) REVERT: J 608 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8410 (mt) REVERT: J 666 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8592 (mm-30) REVERT: J 700 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7230 (pmt-80) REVERT: J 808 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8338 (tp40) REVERT: J 862 ILE cc_start: 0.8852 (pt) cc_final: 0.8598 (pp) REVERT: J 960 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.5858 (m-90) outliers start: 174 outliers final: 113 residues processed: 302 average time/residue: 0.4808 time to fit residues: 171.9924 Evaluate side-chains 273 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 144 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 812 ASN Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 859 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 907 GLN Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1015 THR Chi-restraints excluded: chain G residue 1031 GLN Chi-restraints excluded: chain G residue 1038 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 156 PHE Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 377 GLN Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 628 GLN Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 829 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 872 THR Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1008 MET Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1055 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 203 SER Chi-restraints excluded: chain J residue 305 SER Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 365 SER Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 700 ARG Chi-restraints excluded: chain J residue 704 TYR Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1131 PRO Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 290 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 HIS J 194 HIS J 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.107255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.070836 restraints weight = 36187.525| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.57 r_work: 0.2774 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23325 Z= 0.142 Angle : 0.588 9.059 31740 Z= 0.313 Chirality : 0.043 0.160 3525 Planarity : 0.004 0.052 4140 Dihedral : 7.504 77.504 3296 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.15 % Rotamer: Outliers : 4.80 % Allowed : 23.46 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2925 helix: 1.56 (0.21), residues: 666 sheet: -0.42 (0.20), residues: 597 loop : -1.34 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 652 TYR 0.015 0.001 TYR J 635 PHE 0.017 0.001 PHE I 112 TRP 0.006 0.001 TRP J 310 HIS 0.005 0.001 HIS G 194 Details of bonding type rmsd covalent geometry : bond 0.00322 (23289) covalent geometry : angle 0.58731 (31668) SS BOND : bond 0.00248 ( 36) SS BOND : angle 0.93719 ( 72) hydrogen bonds : bond 0.04989 ( 896) hydrogen bonds : angle 5.52137 ( 2517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 157 time to evaluate : 0.786 Fit side-chains REVERT: G 628 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6047 (mt0) REVERT: G 629 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8097 (ptm160) REVERT: G 728 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8676 (mmmt) REVERT: G 771 ASP cc_start: 0.8933 (m-30) cc_final: 0.8593 (m-30) REVERT: G 830 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8787 (mmmt) REVERT: G 960 TRP cc_start: 0.7103 (OUTLIER) cc_final: 0.6241 (m-90) REVERT: I 110 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7499 (mtpt) REVERT: I 1090 GLU cc_start: 0.9067 (tp30) cc_final: 0.8659 (tp30) REVERT: J 289 THR cc_start: 0.9150 (m) cc_final: 0.8820 (t) REVERT: J 608 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8297 (mt) REVERT: J 666 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8631 (mm-30) REVERT: J 862 ILE cc_start: 0.8917 (pt) cc_final: 0.8676 (pp) REVERT: J 960 TRP cc_start: 0.7176 (OUTLIER) cc_final: 0.5662 (m-90) REVERT: J 1090 GLU cc_start: 0.8931 (tp30) cc_final: 0.8671 (tp30) outliers start: 120 outliers final: 76 residues processed: 263 average time/residue: 0.5422 time to fit residues: 165.6835 Evaluate side-chains 230 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 146 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 373 SER Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 877 VAL Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 LYS Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 844 ASP Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 628 GLN Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1038 SER Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 133 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 95 optimal weight: 0.0170 chunk 242 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 186 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 194 HIS G 261 GLN I 194 HIS J 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.071164 restraints weight = 36415.537| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.59 r_work: 0.2785 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23325 Z= 0.137 Angle : 0.583 9.882 31740 Z= 0.307 Chirality : 0.043 0.167 3525 Planarity : 0.004 0.059 4140 Dihedral : 7.039 78.054 3284 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.36 % Allowed : 23.74 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2925 helix: 1.70 (0.21), residues: 666 sheet: -0.37 (0.20), residues: 597 loop : -1.27 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 141 TYR 0.013 0.001 TYR J 184 PHE 0.016 0.001 PHE I 112 TRP 0.006 0.001 TRP J 310 HIS 0.003 0.001 HIS G1138 Details of bonding type rmsd covalent geometry : bond 0.00312 (23289) covalent geometry : angle 0.58154 (31668) SS BOND : bond 0.00231 ( 36) SS BOND : angle 0.93747 ( 72) hydrogen bonds : bond 0.04795 ( 896) hydrogen bonds : angle 5.39462 ( 2517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 169 time to evaluate : 0.819 Fit side-chains REVERT: G 261 GLN cc_start: 0.8489 (mt0) cc_final: 0.8110 (mp10) REVERT: G 628 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.5976 (mt0) REVERT: G 629 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8129 (ptm160) REVERT: G 728 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8636 (mmmt) REVERT: G 771 ASP cc_start: 0.8950 (m-30) cc_final: 0.8627 (m-30) REVERT: G 830 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8738 (mmmt) REVERT: G 960 TRP cc_start: 0.7064 (OUTLIER) cc_final: 0.6208 (m-90) REVERT: I 259 THR cc_start: 0.8260 (p) cc_final: 0.8000 (p) REVERT: I 261 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: I 960 TRP cc_start: 0.6965 (OUTLIER) cc_final: 0.5448 (m-90) REVERT: I 1090 GLU cc_start: 0.9052 (tp30) cc_final: 0.8676 (tp30) REVERT: J 289 THR cc_start: 0.9182 (m) cc_final: 0.8862 (t) REVERT: J 608 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8319 (mt) REVERT: J 666 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: J 694 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7411 (mtp85) REVERT: J 808 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8260 (tp40) REVERT: J 862 ILE cc_start: 0.8957 (pt) cc_final: 0.8737 (pp) REVERT: J 960 TRP cc_start: 0.7235 (OUTLIER) cc_final: 0.5720 (m-90) REVERT: J 1008 MET cc_start: 0.8716 (mtm) cc_final: 0.8488 (ttp) REVERT: J 1090 GLU cc_start: 0.8948 (tp30) cc_final: 0.8660 (tp30) outliers start: 109 outliers final: 68 residues processed: 263 average time/residue: 0.5118 time to fit residues: 157.8744 Evaluate side-chains 229 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 150 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 261 GLN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 69 optimal weight: 0.0870 chunk 109 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 194 HIS G 993 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 HIS J 194 HIS J 628 GLN J1097 GLN J1160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.106246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.069609 restraints weight = 36421.030| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.57 r_work: 0.2751 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23325 Z= 0.211 Angle : 0.627 10.938 31740 Z= 0.329 Chirality : 0.044 0.196 3525 Planarity : 0.005 0.059 4140 Dihedral : 6.934 80.366 3267 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.88 % Rotamer: Outliers : 4.88 % Allowed : 23.42 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2925 helix: 1.63 (0.21), residues: 666 sheet: -0.39 (0.20), residues: 597 loop : -1.23 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 141 TYR 0.016 0.001 TYR J 184 PHE 0.015 0.002 PHE I 112 TRP 0.007 0.001 TRP J 310 HIS 0.004 0.001 HIS I1138 Details of bonding type rmsd covalent geometry : bond 0.00501 (23289) covalent geometry : angle 0.62526 (31668) SS BOND : bond 0.00314 ( 36) SS BOND : angle 1.06607 ( 72) hydrogen bonds : bond 0.05457 ( 896) hydrogen bonds : angle 5.50931 ( 2517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 154 time to evaluate : 0.833 Fit side-chains REVERT: G 235 ARG cc_start: 0.7425 (mmt-90) cc_final: 0.7175 (mmt-90) REVERT: G 261 GLN cc_start: 0.8460 (mt0) cc_final: 0.8145 (mp10) REVERT: G 628 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.6204 (mt0) REVERT: G 629 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8184 (ptm160) REVERT: G 728 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8674 (mmmt) REVERT: G 830 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8773 (mmmt) REVERT: G 960 TRP cc_start: 0.6955 (OUTLIER) cc_final: 0.6187 (m-90) REVERT: I 184 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5439 (m-80) REVERT: I 259 THR cc_start: 0.8245 (p) cc_final: 0.7985 (p) REVERT: I 261 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: I 960 TRP cc_start: 0.7016 (OUTLIER) cc_final: 0.5490 (m-90) REVERT: I 1090 GLU cc_start: 0.9071 (tp30) cc_final: 0.8686 (tp30) REVERT: J 184 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.5551 (m-80) REVERT: J 289 THR cc_start: 0.9175 (m) cc_final: 0.8852 (t) REVERT: J 608 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8316 (mt) REVERT: J 666 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8644 (mm-30) REVERT: J 862 ILE cc_start: 0.8936 (pt) cc_final: 0.8700 (pp) REVERT: J 960 TRP cc_start: 0.7260 (OUTLIER) cc_final: 0.5807 (m-90) REVERT: J 1090 GLU cc_start: 0.8960 (tp30) cc_final: 0.8697 (tp30) outliers start: 122 outliers final: 82 residues processed: 262 average time/residue: 0.5462 time to fit residues: 167.0470 Evaluate side-chains 239 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 146 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1031 GLN Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 261 GLN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 679 CYS Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1175 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 628 GLN Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 812 ASN Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1175 THR Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 12 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 293 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 194 HIS I1129 ASN J 194 HIS J 628 GLN J1145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.071904 restraints weight = 35950.946| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.57 r_work: 0.2798 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23325 Z= 0.128 Angle : 0.589 11.624 31740 Z= 0.309 Chirality : 0.043 0.157 3525 Planarity : 0.004 0.058 4140 Dihedral : 6.586 81.217 3265 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.60 % Allowed : 24.66 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2925 helix: 1.92 (0.21), residues: 669 sheet: -0.33 (0.20), residues: 606 loop : -1.27 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 652 TYR 0.013 0.001 TYR J1141 PHE 0.016 0.001 PHE I 112 TRP 0.006 0.001 TRP J 310 HIS 0.005 0.001 HIS G 194 Details of bonding type rmsd covalent geometry : bond 0.00291 (23289) covalent geometry : angle 0.58811 (31668) SS BOND : bond 0.00229 ( 36) SS BOND : angle 0.88682 ( 72) hydrogen bonds : bond 0.04589 ( 896) hydrogen bonds : angle 5.29256 ( 2517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 170 time to evaluate : 0.844 Fit side-chains REVERT: G 235 ARG cc_start: 0.7477 (mmt-90) cc_final: 0.7154 (mmt-90) REVERT: G 259 THR cc_start: 0.7989 (p) cc_final: 0.7777 (t) REVERT: G 261 GLN cc_start: 0.8476 (mt0) cc_final: 0.8040 (mp10) REVERT: G 629 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8102 (ptm160) REVERT: G 728 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8666 (mmmt) REVERT: G 771 ASP cc_start: 0.8972 (m-30) cc_final: 0.8657 (m-30) REVERT: G 830 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8730 (mmmt) REVERT: G 960 TRP cc_start: 0.6926 (OUTLIER) cc_final: 0.6050 (m-90) REVERT: I 259 THR cc_start: 0.8300 (p) cc_final: 0.8060 (p) REVERT: I 261 GLN cc_start: 0.8723 (mt0) cc_final: 0.8311 (mp10) REVERT: I 960 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.5355 (m-90) REVERT: I 1090 GLU cc_start: 0.9051 (tp30) cc_final: 0.8675 (tp30) REVERT: J 261 GLN cc_start: 0.8574 (mt0) cc_final: 0.8162 (mp10) REVERT: J 289 THR cc_start: 0.9190 (m) cc_final: 0.8884 (t) REVERT: J 608 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8302 (mt) REVERT: J 666 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8685 (mm-30) REVERT: J 862 ILE cc_start: 0.8965 (pt) cc_final: 0.8748 (pp) REVERT: J 960 TRP cc_start: 0.7238 (OUTLIER) cc_final: 0.5816 (m-90) REVERT: J 1090 GLU cc_start: 0.8990 (tp30) cc_final: 0.8700 (tp30) outliers start: 90 outliers final: 62 residues processed: 250 average time/residue: 0.5268 time to fit residues: 154.2799 Evaluate side-chains 221 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 152 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 995 LYS Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1054 ILE Chi-restraints excluded: chain I residue 1175 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 100 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 277 optimal weight: 2.9990 chunk 191 optimal weight: 0.5980 chunk 245 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 194 HIS G 681 HIS G 819 GLN I 194 HIS I 819 GLN J 194 HIS J 628 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.071973 restraints weight = 36289.022| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.59 r_work: 0.2794 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23325 Z= 0.137 Angle : 0.596 12.673 31740 Z= 0.311 Chirality : 0.043 0.168 3525 Planarity : 0.004 0.059 4140 Dihedral : 6.314 81.907 3257 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.40 % Allowed : 25.30 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2925 helix: 1.98 (0.21), residues: 669 sheet: -0.25 (0.20), residues: 612 loop : -1.17 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 652 TYR 0.013 0.001 TYR J1141 PHE 0.015 0.001 PHE G 112 TRP 0.007 0.001 TRP J 310 HIS 0.009 0.001 HIS G 681 Details of bonding type rmsd covalent geometry : bond 0.00317 (23289) covalent geometry : angle 0.59463 (31668) SS BOND : bond 0.00260 ( 36) SS BOND : angle 1.03784 ( 72) hydrogen bonds : bond 0.04623 ( 896) hydrogen bonds : angle 5.25372 ( 2517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 170 time to evaluate : 0.908 Fit side-chains REVERT: G 164 PHE cc_start: 0.8037 (m-80) cc_final: 0.7731 (m-80) REVERT: G 235 ARG cc_start: 0.7448 (mmt-90) cc_final: 0.7194 (mmt-90) REVERT: G 259 THR cc_start: 0.7988 (p) cc_final: 0.7788 (t) REVERT: G 261 GLN cc_start: 0.8452 (mt0) cc_final: 0.8006 (mp10) REVERT: G 629 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8103 (ptm160) REVERT: G 728 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8649 (mmmt) REVERT: G 771 ASP cc_start: 0.8965 (m-30) cc_final: 0.8641 (m-30) REVERT: G 830 LYS cc_start: 0.8937 (mmtm) cc_final: 0.8686 (mmmt) REVERT: G 960 TRP cc_start: 0.7056 (OUTLIER) cc_final: 0.6207 (m-90) REVERT: I 259 THR cc_start: 0.8239 (p) cc_final: 0.7999 (p) REVERT: I 261 GLN cc_start: 0.8692 (mt0) cc_final: 0.8288 (mp10) REVERT: I 960 TRP cc_start: 0.6982 (OUTLIER) cc_final: 0.5362 (m-90) REVERT: I 1090 GLU cc_start: 0.9053 (tp30) cc_final: 0.8693 (tp30) REVERT: J 169 LEU cc_start: 0.8617 (tt) cc_final: 0.8327 (tp) REVERT: J 184 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: J 261 GLN cc_start: 0.8561 (mt0) cc_final: 0.8129 (mp10) REVERT: J 289 THR cc_start: 0.9188 (m) cc_final: 0.8894 (t) REVERT: J 608 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8301 (mt) REVERT: J 652 ARG cc_start: 0.7811 (mtt90) cc_final: 0.7275 (mtt-85) REVERT: J 666 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8708 (mm-30) REVERT: J 862 ILE cc_start: 0.8957 (pt) cc_final: 0.8741 (pp) REVERT: J 960 TRP cc_start: 0.7221 (OUTLIER) cc_final: 0.5685 (m-90) REVERT: J 1090 GLU cc_start: 0.8994 (tp30) cc_final: 0.8707 (tp30) outliers start: 85 outliers final: 66 residues processed: 247 average time/residue: 0.5565 time to fit residues: 160.1005 Evaluate side-chains 232 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 158 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 156 PHE Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1175 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 194 HIS I 194 HIS J 194 HIS J 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.070261 restraints weight = 36223.948| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.59 r_work: 0.2763 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23325 Z= 0.192 Angle : 0.621 12.812 31740 Z= 0.326 Chirality : 0.044 0.190 3525 Planarity : 0.005 0.058 4140 Dihedral : 6.351 82.486 3253 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.28 % Allowed : 25.18 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2925 helix: 1.81 (0.21), residues: 666 sheet: -0.26 (0.20), residues: 612 loop : -1.17 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 652 TYR 0.013 0.001 TYR J 635 PHE 0.015 0.002 PHE I 156 TRP 0.008 0.001 TRP J 310 HIS 0.004 0.001 HIS G1138 Details of bonding type rmsd covalent geometry : bond 0.00455 (23289) covalent geometry : angle 0.61983 (31668) SS BOND : bond 0.00284 ( 36) SS BOND : angle 1.10068 ( 72) hydrogen bonds : bond 0.05193 ( 896) hydrogen bonds : angle 5.38363 ( 2517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5850 Ramachandran restraints generated. 2925 Oldfield, 0 Emsley, 2925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 0.845 Fit side-chains REVERT: G 235 ARG cc_start: 0.7466 (mmt-90) cc_final: 0.6910 (mmt-90) REVERT: G 259 THR cc_start: 0.7958 (p) cc_final: 0.7756 (t) REVERT: G 261 GLN cc_start: 0.8437 (mt0) cc_final: 0.8004 (mp10) REVERT: G 628 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6187 (mm-40) REVERT: G 629 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8193 (ptm160) REVERT: G 728 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8684 (mmmt) REVERT: G 830 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8747 (mmmt) REVERT: G 960 TRP cc_start: 0.6869 (OUTLIER) cc_final: 0.6108 (m-90) REVERT: I 259 THR cc_start: 0.8232 (p) cc_final: 0.7981 (p) REVERT: I 261 GLN cc_start: 0.8686 (mt0) cc_final: 0.8269 (mp10) REVERT: I 700 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7084 (pmt-80) REVERT: I 960 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.5513 (m-90) REVERT: I 1008 MET cc_start: 0.8844 (ttp) cc_final: 0.8620 (ttp) REVERT: I 1090 GLU cc_start: 0.9053 (tp30) cc_final: 0.8680 (tp30) REVERT: J 169 LEU cc_start: 0.8608 (tt) cc_final: 0.8294 (tp) REVERT: J 184 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5719 (m-80) REVERT: J 261 GLN cc_start: 0.8554 (mt0) cc_final: 0.8111 (mp10) REVERT: J 289 THR cc_start: 0.9178 (m) cc_final: 0.8865 (t) REVERT: J 608 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8335 (mt) REVERT: J 652 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7487 (mtt-85) REVERT: J 666 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8688 (mm-30) REVERT: J 862 ILE cc_start: 0.8942 (pt) cc_final: 0.8711 (pp) REVERT: J 960 TRP cc_start: 0.7254 (OUTLIER) cc_final: 0.5818 (m-90) REVERT: J 1090 GLU cc_start: 0.8995 (tp30) cc_final: 0.8704 (tp30) outliers start: 82 outliers final: 67 residues processed: 232 average time/residue: 0.5508 time to fit residues: 149.1105 Evaluate side-chains 229 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 152 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 367 GLU Chi-restraints excluded: chain G residue 596 ILE Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 679 CYS Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain G residue 728 LYS Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 802 VAL Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 960 TRP Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1180 ILE Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 688 GLN Chi-restraints excluded: chain I residue 700 ARG Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 874 LEU Chi-restraints excluded: chain I residue 893 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 960 TRP Chi-restraints excluded: chain I residue 1112 LYS Chi-restraints excluded: chain I residue 1175 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain I residue 1218 LEU Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 184 TYR Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 376 GLU Chi-restraints excluded: chain J residue 608 LEU Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 679 CYS Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 874 LEU Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 948 THR Chi-restraints excluded: chain J residue 960 TRP Chi-restraints excluded: chain J residue 1054 ILE Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1111 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 192 optimal weight: 0.7980 chunk 172 optimal weight: 0.0470 chunk 100 optimal weight: 0.0670 chunk 263 optimal weight: 0.0170 chunk 188 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 284 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1217 ASN I 194 HIS J 194 HIS J 628 GLN J1217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.110674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.075199 restraints weight = 37089.211| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.58 r_work: 0.2896 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23325 Z= 0.111 Angle : 0.579 12.605 31740 Z= 0.302 Chirality : 0.042 0.146 3525 Planarity : 0.004 0.058 4140 Dihedral : 5.918 80.362 3253 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.56 % Allowed : 25.98 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2925 helix: 2.13 (0.21), residues: 669 sheet: -0.14 (0.21), residues: 594 loop : -1.25 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 652 TYR 0.015 0.001 TYR J1141 PHE 0.018 0.001 PHE G 112 TRP 0.008 0.001 TRP J 253 HIS 0.005 0.001 HIS G 194 Details of bonding type rmsd covalent geometry : bond 0.00249 (23289) covalent geometry : angle 0.57796 (31668) SS BOND : bond 0.00210 ( 36) SS BOND : angle 0.86702 ( 72) hydrogen bonds : bond 0.03991 ( 896) hydrogen bonds : angle 5.04682 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10457.53 seconds wall clock time: 178 minutes 1.88 seconds (10681.88 seconds total)