Starting phenix.real_space_refine on Mon Aug 25 19:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrm_37781/08_2025/8wrm_37781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrm_37781/08_2025/8wrm_37781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrm_37781/08_2025/8wrm_37781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrm_37781/08_2025/8wrm_37781.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrm_37781/08_2025/8wrm_37781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrm_37781/08_2025/8wrm_37781.cif" } resolution = 4.34 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= 0.043 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 146 5.16 5 C 19139 2.51 5 N 4992 2.21 5 O 5654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29931 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8360 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "G" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8359 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 57, 'TRANS': 1008} Chain breaks: 6 Chain: "C" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8367 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 57, 'TRANS': 1009} Chain breaks: 6 Chain: "D" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Time building chain proxies: 5.97, per 1000 atoms: 0.20 Number of scatterers: 29931 At special positions: 0 Unit cell: (150.8, 157.04, 237.12, 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 146 16.00 O 5654 8.00 N 4992 7.00 C 19139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.04 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 136 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.04 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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: 2.35 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7126 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 45 sheets defined 29.2% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'F' and resid 96 through 99 removed outlier: 4.157A pdb=" N ASN F 99 " --> pdb=" O GLU F 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 96 through 99' Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 364 through 369 removed outlier: 4.433A pdb=" N ILE F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 removed outlier: 4.069A pdb=" N LEU F 387 " --> pdb=" O PRO F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 411 removed outlier: 3.678A pdb=" N ALA F 411 " --> pdb=" O SER F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 757 removed outlier: 3.637A pdb=" N SER F 750 " --> pdb=" O SER F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 783 removed outlier: 4.047A pdb=" N THR F 778 " --> pdb=" O GLN F 774 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU F 780 " --> pdb=" O LYS F 776 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL F 781 " --> pdb=" O ASN F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 removed outlier: 3.782A pdb=" N VAL F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 855 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 886 through 890 removed outlier: 3.596A pdb=" N GLY F 889 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 Processing helix chain 'F' and resid 912 through 919 removed outlier: 4.478A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 removed outlier: 3.639A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR F 941 " --> pdb=" O SER F 937 " (cutoff:3.500A) Processing helix chain 'F' and resid 942 through 944 No H-bonds generated for 'chain 'F' and resid 942 through 944' Processing helix chain 'F' and resid 945 through 964 removed outlier: 3.679A pdb=" N ASP F 950 " --> pdb=" O GLY F 946 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 954 " --> pdb=" O ASP F 950 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN F 955 " --> pdb=" O VAL F 951 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA F 958 " --> pdb=" O HIS F 954 " (cutoff:3.500A) Processing helix chain 'F' and resid 976 through 982 removed outlier: 4.134A pdb=" N ILE F 980 " --> pdb=" O VAL F 976 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 981 " --> pdb=" O LEU F 977 " (cutoff:3.500A) Processing helix chain 'F' and resid 985 through 993 removed outlier: 3.941A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 994 through 1033 removed outlier: 3.902A pdb=" N THR F 998 " --> pdb=" O ASP F 994 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F1033 " --> pdb=" O MET F1029 " (cutoff:3.500A) Processing helix chain 'F' and resid 1116 through 1118 No H-bonds generated for 'chain 'F' and resid 1116 through 1118' Processing helix chain 'G' and resid 96 through 99 removed outlier: 3.714A pdb=" N ASN G 99 " --> pdb=" O GLU G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 96 through 99' Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 366 through 370 removed outlier: 3.530A pdb=" N TYR G 369 " --> pdb=" O SER G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 removed outlier: 3.929A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 removed outlier: 3.712A pdb=" N TYR G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 755 removed outlier: 3.587A pdb=" N SER G 750 " --> pdb=" O SER G 746 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN G 755 " --> pdb=" O ASN G 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 759 through 776 Processing helix chain 'G' and resid 776 through 783 removed outlier: 4.559A pdb=" N GLU G 780 " --> pdb=" O LYS G 776 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL G 781 " --> pdb=" O ASN G 777 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 825 Processing helix chain 'G' and resid 851 through 855 Processing helix chain 'G' and resid 866 through 884 removed outlier: 3.592A pdb=" N ILE G 870 " --> pdb=" O THR G 866 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 890 removed outlier: 3.613A pdb=" N GLY G 889 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 removed outlier: 3.588A pdb=" N TYR G 904 " --> pdb=" O MET G 900 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 941 removed outlier: 6.779A pdb=" N LYS G 921 " --> pdb=" O TYR G 917 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU G 922 " --> pdb=" O GLU G 918 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR G 941 " --> pdb=" O SER G 937 " (cutoff:3.500A) Processing helix chain 'G' and resid 945 through 964 removed outlier: 3.596A pdb=" N GLN G 949 " --> pdb=" O LEU G 945 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP G 950 " --> pdb=" O GLY G 946 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 977 through 982 Processing helix chain 'G' and resid 989 through 1033 removed outlier: 4.141A pdb=" N ARG G 995 " --> pdb=" O VAL G 991 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G1003 " --> pdb=" O GLY G 999 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G1016 " --> pdb=" O LEU G1012 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G1033 " --> pdb=" O MET G1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 1116 through 1118 No H-bonds generated for 'chain 'G' and resid 1116 through 1118' Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.869A pdb=" N ASN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 100' Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.588A pdb=" N GLU C 154 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.668A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 removed outlier: 4.004A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.297A pdb=" N ILE C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.958A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 removed outlier: 4.386A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.789A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.809A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.765A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 777 removed outlier: 4.026A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.698A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 940 removed outlier: 4.413A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.551A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.573A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.332A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.501A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.715A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.556A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 247 removed outlier: 3.944A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.796A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.840A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.893A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.638A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 414 removed outlier: 3.608A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 445 through 466 removed outlier: 4.220A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix removed outlier: 3.525A pdb=" N GLY D 466 " --> pdb=" O MET D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.610A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.157A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.554A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.723A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 571 removed outlier: 4.555A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'F' and resid 28 through 30 removed outlier: 7.912A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 63 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 227 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 55 Processing sheet with id=AA3, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.798A pdb=" N LEU F 84 " --> pdb=" O PHE F 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 277 through 278 removed outlier: 4.084A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 325 through 328 removed outlier: 6.467A pdb=" N ILE F 326 " --> pdb=" O ASN F 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 356 through 357 removed outlier: 6.544A pdb=" N ALA F 435 " --> pdb=" O PHE F 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 595 through 598 Processing sheet with id=AA8, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.194A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 701 through 702 removed outlier: 6.667A pdb=" N ALA F 701 " --> pdb=" O ILE G 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.663A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN F 717 " --> pdb=" O ALA F1070 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR F1067 " --> pdb=" O HIS F1048 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS F1048 " --> pdb=" O TYR F1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 733 through 735 removed outlier: 4.207A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 787 through 788 removed outlier: 3.584A pdb=" N ILE F 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 3.538A pdb=" N SER F1123 " --> pdb=" O ALA F1087 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.625A pdb=" N SER G 31 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER G 60 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR G 63 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL G 267 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 48 through 49 removed outlier: 3.758A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 52 through 55 Processing sheet with id=AB9, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.972A pdb=" N LEU G 84 " --> pdb=" O PHE G 238 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG G 237 " --> pdb=" O PHE G 106 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE G 106 " --> pdb=" O ARG G 237 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN G 239 " --> pdb=" O TRP G 104 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP G 104 " --> pdb=" O GLN G 239 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU G 241 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 311 through 314 removed outlier: 4.108A pdb=" N THR G 599 " --> pdb=" O GLY G 311 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR G 313 " --> pdb=" O VAL G 597 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 324 through 328 removed outlier: 6.447A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE G 326 " --> pdb=" O ASN G 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.670A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 374 through 378 removed outlier: 7.236A pdb=" N PHE G 374 " --> pdb=" O ASN G 437 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN G 437 " --> pdb=" O PHE G 374 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'G' and resid 654 through 660 removed outlier: 3.523A pdb=" N GLU G 654 " --> pdb=" O ILE G 692 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR G 696 " --> pdb=" O VAL G 656 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN G 658 " --> pdb=" O THR G 696 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 664 " --> pdb=" O ALA G 672 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 711 through 715 Processing sheet with id=AC8, first strand: chain 'G' and resid 718 through 728 removed outlier: 6.386A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.273A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'G' and resid 1094 through 1097 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.809A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 49 removed outlier: 4.083A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 52 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.215A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.631A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.314A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.509A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.969A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.405A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.334A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 1035 hydrogen bonds defined for protein. 2883 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: 5.70 Time building geometry restraints manager: 3.14 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: 9592 1.34 - 1.47: 7554 1.47 - 1.59: 13327 1.59 - 1.71: 0 1.71 - 1.84: 197 Bond restraints: 30670 Sorted by residual: bond pdb=" CA PRO C 792 " pdb=" C PRO C 792 " ideal model delta sigma weight residual 1.517 1.499 0.018 6.70e-03 2.23e+04 7.47e+00 bond pdb=" C GLU D 145 " pdb=" N PRO D 146 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.39e+00 bond pdb=" C THR G 250 " pdb=" N PRO G 251 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.90e+00 bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.46e+00 bond pdb=" C GLY F 485 " pdb=" N PRO F 486 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.30e-02 5.92e+03 4.34e+00 ... (remaining 30665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 40953 2.85 - 5.71: 642 5.71 - 8.56: 104 8.56 - 11.41: 19 11.41 - 14.27: 2 Bond angle restraints: 41720 Sorted by residual: angle pdb=" C PHE F 559 " pdb=" CA PHE F 559 " pdb=" CB PHE F 559 " ideal model delta sigma weight residual 115.79 108.12 7.67 1.19e+00 7.06e-01 4.15e+01 angle pdb=" N ILE C 909 " pdb=" CA ILE C 909 " pdb=" C ILE C 909 " ideal model delta sigma weight residual 112.29 106.41 5.88 9.40e-01 1.13e+00 3.92e+01 angle pdb=" N GLU C 773 " pdb=" CA GLU C 773 " pdb=" CB GLU C 773 " ideal model delta sigma weight residual 110.40 119.32 -8.92 1.63e+00 3.76e-01 2.99e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.21 -6.51 1.22e+00 6.72e-01 2.85e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 123.84 -5.91 1.20e+00 6.94e-01 2.42e+01 ... (remaining 41715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16417 17.99 - 35.99: 1538 35.99 - 53.98: 218 53.98 - 71.98: 58 71.98 - 89.97: 41 Dihedral angle restraints: 18272 sinusoidal: 7201 harmonic: 11071 Sorted by residual: dihedral pdb=" CB CYS F 738 " pdb=" SG CYS F 738 " pdb=" SG CYS F 760 " pdb=" CB CYS F 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.37 88.63 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS G 15 " pdb=" SG CYS G 15 " pdb=" SG CYS G 136 " pdb=" CB CYS G 136 " ideal model delta sinusoidal sigma weight residual -86.00 -171.46 85.46 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS G 738 " pdb=" SG CYS G 738 " pdb=" SG CYS G 760 " pdb=" CB CYS G 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.93 84.07 1 1.00e+01 1.00e-02 8.61e+01 ... (remaining 18269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4070 0.083 - 0.166: 533 0.166 - 0.249: 35 0.249 - 0.332: 2 0.332 - 0.415: 2 Chirality restraints: 4642 Sorted by residual: chirality pdb=" CB ILE G 410 " pdb=" CA ILE G 410 " pdb=" CG1 ILE G 410 " pdb=" CG2 ILE G 410 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CB ILE C 714 " pdb=" CA ILE C 714 " pdb=" CG1 ILE C 714 " pdb=" CG2 ILE C 714 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB VAL D 293 " pdb=" CA VAL D 293 " pdb=" CG1 VAL D 293 " pdb=" CG2 VAL D 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 4639 not shown) Planarity restraints: 5401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 436 " -0.017 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP C 436 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP C 436 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP C 436 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 436 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TRP C 436 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 436 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 436 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 436 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 436 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 560 " 0.065 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO F 561 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 561 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 561 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 769 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C GLY C 769 " 0.059 2.00e-02 2.50e+03 pdb=" O GLY C 769 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE C 770 " -0.020 2.00e-02 2.50e+03 ... (remaining 5398 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2140 2.74 - 3.28: 29909 3.28 - 3.82: 49789 3.82 - 4.36: 57172 4.36 - 4.90: 95588 Nonbonded interactions: 234598 Sorted by model distance: nonbonded pdb=" OG SER F 27 " pdb=" O TRP F 64 " model vdw 2.196 3.040 nonbonded pdb=" OG SER C 27 " pdb=" O TRP C 64 " model vdw 2.204 3.040 nonbonded pdb=" OG SER G 27 " pdb=" O TRP G 64 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR G 396 " pdb=" OE1 GLU G 516 " model vdw 2.244 3.040 nonbonded pdb=" O LEU C 966 " pdb=" OG SER C 975 " model vdw 2.248 3.040 ... (remaining 234593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'F' and (resid 14 through 826 or resid 850 through 1140)) selection = (chain 'G' and (resid 14 through 826 or resid 850 through 1140)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.060 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 0.067 30710 Z= 0.187 Angle : 0.894 14.267 41800 Z= 0.477 Chirality : 0.054 0.415 4642 Planarity : 0.007 0.105 5401 Dihedral : 14.465 89.974 11026 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.40 % Favored : 91.52 % Rotamer: Outliers : 0.03 % Allowed : 0.54 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.12), residues: 3749 helix: -0.93 (0.15), residues: 967 sheet: -0.20 (0.22), residues: 551 loop : -2.52 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G1019 TYR 0.038 0.002 TYR D 199 PHE 0.040 0.002 PHE F1052 TRP 0.063 0.002 TRP C 436 HIS 0.007 0.001 HIS G 245 Details of bonding type rmsd covalent geometry : bond 0.00370 (30670) covalent geometry : angle 0.89410 (41720) SS BOND : bond 0.00335 ( 40) SS BOND : angle 1.03792 ( 80) hydrogen bonds : bond 0.14709 ( 1033) hydrogen bonds : angle 6.82433 ( 2883) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 740 MET cc_start: 0.8592 (tmm) cc_final: 0.8317 (tmm) REVERT: F 759 PHE cc_start: 0.8114 (m-80) cc_final: 0.7887 (m-80) REVERT: F 773 GLU cc_start: 0.8824 (tt0) cc_final: 0.8602 (tm-30) REVERT: F 979 ASP cc_start: 0.8894 (p0) cc_final: 0.8684 (p0) REVERT: F 1017 GLU cc_start: 0.9227 (tt0) cc_final: 0.8898 (tt0) REVERT: G 740 MET cc_start: 0.8550 (mtp) cc_final: 0.8254 (mtt) REVERT: G 773 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8839 (tm-30) REVERT: G 1019 ARG cc_start: 0.9142 (ttp-110) cc_final: 0.8808 (ttp80) REVERT: C 855 PHE cc_start: 0.6922 (m-80) cc_final: 0.6511 (m-80) REVERT: C 936 ASP cc_start: 0.9139 (t0) cc_final: 0.8891 (t0) REVERT: D 62 MET cc_start: 0.6213 (mmp) cc_final: 0.5957 (mmm) REVERT: D 82 MET cc_start: 0.4953 (ppp) cc_final: 0.4602 (ppp) REVERT: D 152 MET cc_start: 0.2421 (mtt) cc_final: 0.1949 (mtt) REVERT: D 566 TRP cc_start: 0.5750 (p-90) cc_final: 0.4633 (p-90) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.1649 time to fit residues: 75.9979 Evaluate side-chains 188 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN F 965 GLN F1048 HIS G 52 GLN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 774 GLN G 895 GLN G 920 GLN G 954 HIS G1010 GLN G1036 GLN C 52 GLN C 69 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 448 ASN C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.097164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.066576 restraints weight = 188449.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066648 restraints weight = 115369.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067275 restraints weight = 79843.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067676 restraints weight = 62455.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067918 restraints weight = 53570.369| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30710 Z= 0.226 Angle : 0.702 9.393 41800 Z= 0.372 Chirality : 0.046 0.207 4642 Planarity : 0.006 0.068 5401 Dihedral : 5.291 25.473 4071 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.02 % Favored : 90.90 % Rotamer: Outliers : 0.18 % Allowed : 8.05 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.13), residues: 3749 helix: -0.05 (0.16), residues: 1003 sheet: -0.52 (0.22), residues: 559 loop : -2.38 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 765 TYR 0.027 0.002 TYR G 204 PHE 0.037 0.002 PHE F 592 TRP 0.014 0.002 TRP D 459 HIS 0.010 0.002 HIS G 954 Details of bonding type rmsd covalent geometry : bond 0.00484 (30670) covalent geometry : angle 0.70143 (41720) SS BOND : bond 0.00359 ( 40) SS BOND : angle 1.03927 ( 80) hydrogen bonds : bond 0.04002 ( 1033) hydrogen bonds : angle 5.33807 ( 2883) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 239 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 740 MET cc_start: 0.8669 (tmm) cc_final: 0.8397 (tmm) REVERT: F 759 PHE cc_start: 0.7896 (m-80) cc_final: 0.7651 (m-80) REVERT: F 779 GLN cc_start: 0.8978 (mp10) cc_final: 0.8668 (mp10) REVERT: G 1050 MET cc_start: 0.8644 (tmm) cc_final: 0.8322 (tmm) REVERT: C 239 GLN cc_start: 0.6759 (mm-40) cc_final: 0.6440 (mp10) REVERT: C 248 TYR cc_start: 0.5582 (p90) cc_final: 0.4980 (p90) REVERT: C 731 MET cc_start: 0.8898 (ppp) cc_final: 0.8377 (ppp) REVERT: C 855 PHE cc_start: 0.7063 (m-80) cc_final: 0.6821 (m-80) REVERT: C 869 MET cc_start: 0.9386 (pmm) cc_final: 0.9144 (pmm) REVERT: C 936 ASP cc_start: 0.8917 (t0) cc_final: 0.8705 (p0) REVERT: C 1050 MET cc_start: 0.8360 (tmm) cc_final: 0.8077 (tmm) REVERT: D 152 MET cc_start: -0.2786 (mtt) cc_final: -0.3214 (mtt) REVERT: D 190 MET cc_start: 0.2361 (ptt) cc_final: 0.2124 (ptm) REVERT: D 455 MET cc_start: -0.2055 (ttt) cc_final: -0.2439 (ttt) REVERT: D 462 MET cc_start: 0.1918 (ptm) cc_final: 0.1681 (ptm) REVERT: D 566 TRP cc_start: 0.4724 (p-90) cc_final: 0.4122 (p-90) outliers start: 6 outliers final: 3 residues processed: 244 average time/residue: 0.1638 time to fit residues: 66.6595 Evaluate side-chains 157 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 334 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 331 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 309 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 GLN ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN G 895 GLN G 920 GLN C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 265 HIS D 601 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.103390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.082390 restraints weight = 223142.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.082372 restraints weight = 128754.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082387 restraints weight = 82836.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.082470 restraints weight = 71853.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082591 restraints weight = 63792.192| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30710 Z= 0.160 Angle : 0.621 8.785 41800 Z= 0.325 Chirality : 0.044 0.179 4642 Planarity : 0.005 0.061 5401 Dihedral : 5.190 39.107 4071 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.14 % Favored : 91.78 % Rotamer: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.13), residues: 3749 helix: 0.23 (0.17), residues: 992 sheet: -0.30 (0.22), residues: 568 loop : -2.30 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 78 TYR 0.020 0.001 TYR D 183 PHE 0.027 0.001 PHE C 133 TRP 0.020 0.001 TRP D 459 HIS 0.016 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00336 (30670) covalent geometry : angle 0.62034 (41720) SS BOND : bond 0.00228 ( 40) SS BOND : angle 0.92557 ( 80) hydrogen bonds : bond 0.03604 ( 1033) hydrogen bonds : angle 5.13220 ( 2883) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 661 GLU cc_start: 0.8505 (tp30) cc_final: 0.8229 (tm-30) REVERT: F 699 LEU cc_start: 0.8790 (mt) cc_final: 0.8564 (mt) REVERT: F 731 MET cc_start: 0.8749 (ppp) cc_final: 0.8537 (ppp) REVERT: F 740 MET cc_start: 0.8708 (tmm) cc_final: 0.8369 (tmm) REVERT: F 759 PHE cc_start: 0.7931 (m-80) cc_final: 0.7617 (m-80) REVERT: G 104 TRP cc_start: 0.7393 (m-90) cc_final: 0.7189 (m-90) REVERT: G 869 MET cc_start: 0.9150 (pmm) cc_final: 0.8906 (pmm) REVERT: G 1050 MET cc_start: 0.8734 (tmm) cc_final: 0.7882 (tmm) REVERT: G 1052 PHE cc_start: 0.9019 (m-10) cc_final: 0.8611 (m-10) REVERT: C 239 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6688 (mp10) REVERT: C 731 MET cc_start: 0.9114 (ppp) cc_final: 0.8696 (ppp) REVERT: C 855 PHE cc_start: 0.7440 (m-80) cc_final: 0.7215 (m-80) REVERT: C 858 LEU cc_start: 0.9430 (mt) cc_final: 0.9185 (mt) REVERT: C 869 MET cc_start: 0.9457 (pmm) cc_final: 0.9043 (pmm) REVERT: C 882 ILE cc_start: 0.9521 (tt) cc_final: 0.9280 (mt) REVERT: D 82 MET cc_start: 0.5112 (ppp) cc_final: 0.4720 (ppp) REVERT: D 152 MET cc_start: 0.3129 (mtt) cc_final: 0.2794 (mtt) REVERT: D 190 MET cc_start: 0.1020 (ptt) cc_final: 0.0787 (ptm) REVERT: D 455 MET cc_start: -0.1335 (ttt) cc_final: -0.2202 (ttt) REVERT: D 566 TRP cc_start: 0.5427 (p-90) cc_final: 0.5199 (p-90) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.1569 time to fit residues: 65.7865 Evaluate side-chains 159 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 130 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 245 HIS ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN G 52 GLN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS D 330 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.101574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.080475 restraints weight = 220588.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.079751 restraints weight = 137324.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080087 restraints weight = 102138.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.080376 restraints weight = 68617.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.080121 restraints weight = 56939.820| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30710 Z= 0.176 Angle : 0.629 10.456 41800 Z= 0.328 Chirality : 0.045 0.247 4642 Planarity : 0.005 0.073 5401 Dihedral : 5.126 30.733 4071 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.36 % Favored : 90.56 % Rotamer: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.13), residues: 3749 helix: 0.33 (0.16), residues: 1010 sheet: -0.48 (0.22), residues: 571 loop : -2.26 (0.12), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1091 TYR 0.027 0.002 TYR C 248 PHE 0.015 0.002 PHE F1052 TRP 0.027 0.002 TRP D 478 HIS 0.004 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00378 (30670) covalent geometry : angle 0.62793 (41720) SS BOND : bond 0.00529 ( 40) SS BOND : angle 0.91147 ( 80) hydrogen bonds : bond 0.03544 ( 1033) hydrogen bonds : angle 5.05517 ( 2883) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 203 ILE cc_start: 0.8718 (mp) cc_final: 0.8398 (mp) REVERT: F 697 MET cc_start: 0.8690 (mmp) cc_final: 0.8348 (tpp) REVERT: F 731 MET cc_start: 0.8948 (ppp) cc_final: 0.8297 (ppp) REVERT: F 740 MET cc_start: 0.8833 (tmm) cc_final: 0.8451 (tmm) REVERT: F 759 PHE cc_start: 0.7939 (m-80) cc_final: 0.7697 (m-80) REVERT: F 779 GLN cc_start: 0.9150 (mp10) cc_final: 0.8838 (mp10) REVERT: F 976 VAL cc_start: 0.8815 (t) cc_final: 0.8611 (t) REVERT: G 740 MET cc_start: 0.8482 (mtp) cc_final: 0.8205 (mtp) REVERT: G 1050 MET cc_start: 0.8725 (tmm) cc_final: 0.8470 (tmm) REVERT: C 731 MET cc_start: 0.8961 (ppp) cc_final: 0.8518 (ppp) REVERT: C 759 PHE cc_start: 0.8316 (p90) cc_final: 0.7884 (p90) REVERT: C 869 MET cc_start: 0.9571 (pmm) cc_final: 0.9092 (pmm) REVERT: D 62 MET cc_start: 0.6109 (mmp) cc_final: 0.5897 (mmp) REVERT: D 82 MET cc_start: 0.5416 (ppp) cc_final: 0.5168 (ppp) REVERT: D 152 MET cc_start: 0.3229 (mtt) cc_final: 0.2742 (mtt) REVERT: D 190 MET cc_start: 0.1702 (ptt) cc_final: 0.1220 (ptt) REVERT: D 270 MET cc_start: 0.3724 (tpt) cc_final: 0.3467 (tpp) REVERT: D 320 LEU cc_start: 0.4528 (mt) cc_final: 0.4313 (mt) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.1579 time to fit residues: 59.4720 Evaluate side-chains 147 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 353 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 348 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 314 optimal weight: 0.6980 chunk 273 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 327 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 134 GLN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 ASN ** F 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 GLN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G 935 GLN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.099315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078485 restraints weight = 221087.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078041 restraints weight = 129050.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.077994 restraints weight = 82475.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078031 restraints weight = 71638.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078102 restraints weight = 67109.087| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30710 Z= 0.213 Angle : 0.665 7.885 41800 Z= 0.351 Chirality : 0.046 0.192 4642 Planarity : 0.005 0.069 5401 Dihedral : 5.317 33.054 4071 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.55 % Favored : 90.37 % Rotamer: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.13), residues: 3749 helix: 0.20 (0.16), residues: 1014 sheet: -0.43 (0.23), residues: 508 loop : -2.28 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 498 TYR 0.023 0.002 TYR D 183 PHE 0.021 0.002 PHE G1075 TRP 0.025 0.002 TRP C 152 HIS 0.008 0.001 HIS G 245 Details of bonding type rmsd covalent geometry : bond 0.00456 (30670) covalent geometry : angle 0.66440 (41720) SS BOND : bond 0.00300 ( 40) SS BOND : angle 1.02092 ( 80) hydrogen bonds : bond 0.03709 ( 1033) hydrogen bonds : angle 5.18952 ( 2883) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 731 MET cc_start: 0.9181 (ppp) cc_final: 0.8490 (ppp) REVERT: F 740 MET cc_start: 0.8957 (tmm) cc_final: 0.8504 (tmm) REVERT: F 759 PHE cc_start: 0.7939 (m-80) cc_final: 0.7692 (m-80) REVERT: F 774 GLN cc_start: 0.9105 (tt0) cc_final: 0.8686 (tt0) REVERT: G 104 TRP cc_start: 0.8276 (m-90) cc_final: 0.7954 (m-90) REVERT: G 513 LEU cc_start: 0.8738 (mm) cc_final: 0.8174 (tp) REVERT: G 697 MET cc_start: 0.9010 (tpt) cc_final: 0.8704 (tpp) REVERT: G 1050 MET cc_start: 0.8731 (tmm) cc_final: 0.8387 (tmm) REVERT: C 90 VAL cc_start: 0.8934 (t) cc_final: 0.8705 (p) REVERT: C 731 MET cc_start: 0.8912 (ppp) cc_final: 0.8492 (ppp) REVERT: C 759 PHE cc_start: 0.8211 (p90) cc_final: 0.7894 (p90) REVERT: C 858 LEU cc_start: 0.9169 (mt) cc_final: 0.8966 (mt) REVERT: C 869 MET cc_start: 0.9596 (pmm) cc_final: 0.9304 (pmm) REVERT: D 62 MET cc_start: 0.5883 (mmp) cc_final: 0.5667 (mmp) REVERT: D 82 MET cc_start: 0.5383 (ppp) cc_final: 0.5106 (ppp) REVERT: D 152 MET cc_start: 0.3090 (mtt) cc_final: 0.2757 (mtt) REVERT: D 190 MET cc_start: 0.1831 (ptt) cc_final: 0.1144 (ptp) REVERT: D 297 MET cc_start: 0.2083 (mtm) cc_final: 0.0698 (tpp) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1448 time to fit residues: 53.3721 Evaluate side-chains 140 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 294 optimal weight: 6.9990 chunk 59 optimal weight: 0.0870 chunk 301 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 118 optimal weight: 0.1980 chunk 264 optimal weight: 5.9990 chunk 355 optimal weight: 9.9990 chunk 29 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN F 955 ASN F1011 GLN F1048 HIS ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G1010 GLN C 239 GLN C 607 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.094958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.065396 restraints weight = 183172.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.066002 restraints weight = 105580.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.066692 restraints weight = 72435.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.067116 restraints weight = 56304.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.067311 restraints weight = 47455.834| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30710 Z= 0.115 Angle : 0.599 8.560 41800 Z= 0.310 Chirality : 0.045 0.229 4642 Planarity : 0.004 0.055 5401 Dihedral : 5.023 31.333 4071 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.51 % Favored : 91.41 % Rotamer: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.13), residues: 3749 helix: 0.39 (0.17), residues: 1025 sheet: -0.45 (0.22), residues: 563 loop : -2.23 (0.12), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G1091 TYR 0.026 0.001 TYR C 248 PHE 0.021 0.001 PHE C1052 TRP 0.029 0.001 TRP C 152 HIS 0.008 0.001 HIS F1048 Details of bonding type rmsd covalent geometry : bond 0.00254 (30670) covalent geometry : angle 0.59859 (41720) SS BOND : bond 0.00251 ( 40) SS BOND : angle 0.94595 ( 80) hydrogen bonds : bond 0.03290 ( 1033) hydrogen bonds : angle 4.94907 ( 2883) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 699 LEU cc_start: 0.8817 (mt) cc_final: 0.8574 (mt) REVERT: F 731 MET cc_start: 0.9064 (ppp) cc_final: 0.8397 (ppp) REVERT: F 740 MET cc_start: 0.8763 (tmm) cc_final: 0.8304 (tmm) REVERT: F 759 PHE cc_start: 0.7915 (m-80) cc_final: 0.7593 (m-80) REVERT: F 774 GLN cc_start: 0.8843 (tt0) cc_final: 0.8577 (tt0) REVERT: G 869 MET cc_start: 0.9134 (pmm) cc_final: 0.8922 (pmm) REVERT: G 1050 MET cc_start: 0.8534 (tmm) cc_final: 0.8257 (tmm) REVERT: C 248 TYR cc_start: 0.5017 (p90) cc_final: 0.4746 (p90) REVERT: C 731 MET cc_start: 0.8989 (ppp) cc_final: 0.8547 (ppp) REVERT: C 855 PHE cc_start: 0.7696 (m-80) cc_final: 0.7487 (m-80) REVERT: C 869 MET cc_start: 0.9455 (pmm) cc_final: 0.9196 (pmm) REVERT: C 985 ASP cc_start: 0.9445 (m-30) cc_final: 0.9130 (t0) REVERT: C 1089 PHE cc_start: 0.8995 (m-10) cc_final: 0.8648 (m-10) REVERT: D 190 MET cc_start: 0.3066 (ptt) cc_final: 0.2338 (ptp) REVERT: D 297 MET cc_start: 0.0707 (mtm) cc_final: -0.0586 (tpp) outliers start: 2 outliers final: 0 residues processed: 230 average time/residue: 0.1537 time to fit residues: 59.6758 Evaluate side-chains 153 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 5 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 369 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 69 HIS ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G1010 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 51 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.095538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075305 restraints weight = 222349.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.074452 restraints weight = 134052.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.074605 restraints weight = 94028.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074584 restraints weight = 77217.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074697 restraints weight = 67949.440| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 30710 Z= 0.337 Angle : 0.789 8.788 41800 Z= 0.420 Chirality : 0.048 0.199 4642 Planarity : 0.006 0.112 5401 Dihedral : 5.737 34.276 4071 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.82 % Favored : 88.10 % Rotamer: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.13), residues: 3749 helix: -0.02 (0.16), residues: 1019 sheet: -0.71 (0.23), residues: 517 loop : -2.36 (0.12), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 78 TYR 0.029 0.002 TYR C 248 PHE 0.029 0.003 PHE C 55 TRP 0.031 0.003 TRP C 152 HIS 0.007 0.002 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00706 (30670) covalent geometry : angle 0.78633 (41720) SS BOND : bond 0.01002 ( 40) SS BOND : angle 1.58819 ( 80) hydrogen bonds : bond 0.04320 ( 1033) hydrogen bonds : angle 5.51099 ( 2883) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 731 MET cc_start: 0.9176 (ppp) cc_final: 0.8521 (ppp) REVERT: F 740 MET cc_start: 0.9118 (tmm) cc_final: 0.8618 (tmm) REVERT: F 759 PHE cc_start: 0.8097 (m-80) cc_final: 0.7722 (m-80) REVERT: G 1050 MET cc_start: 0.8792 (tmm) cc_final: 0.8474 (tmm) REVERT: C 351 TYR cc_start: 0.8443 (p90) cc_final: 0.8229 (p90) REVERT: C 731 MET cc_start: 0.8901 (ppp) cc_final: 0.8390 (ppp) REVERT: C 858 LEU cc_start: 0.9216 (mt) cc_final: 0.9011 (mt) REVERT: C 936 ASP cc_start: 0.8962 (m-30) cc_final: 0.8741 (p0) REVERT: D 59 VAL cc_start: 0.7497 (t) cc_final: 0.7282 (t) REVERT: D 82 MET cc_start: 0.5240 (ppp) cc_final: 0.4892 (ppp) REVERT: D 190 MET cc_start: 0.1995 (ptt) cc_final: 0.1538 (ptt) REVERT: D 297 MET cc_start: 0.2474 (mtm) cc_final: 0.1393 (tpp) REVERT: D 447 VAL cc_start: 0.6910 (t) cc_final: 0.6709 (t) outliers start: 2 outliers final: 0 residues processed: 186 average time/residue: 0.1598 time to fit residues: 49.2669 Evaluate side-chains 128 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 133 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 358 optimal weight: 0.0470 chunk 327 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 293 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 268 optimal weight: 8.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN F 955 ASN ** F1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 87 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G1010 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.100608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.080213 restraints weight = 220366.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.080125 restraints weight = 125457.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081002 restraints weight = 74135.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080703 restraints weight = 59016.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080530 restraints weight = 55743.444| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30710 Z= 0.122 Angle : 0.646 8.803 41800 Z= 0.330 Chirality : 0.046 0.219 4642 Planarity : 0.004 0.056 5401 Dihedral : 5.258 29.907 4071 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.54 % Favored : 91.38 % Rotamer: Outliers : 0.09 % Allowed : 1.35 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.13), residues: 3749 helix: 0.35 (0.17), residues: 1013 sheet: -0.55 (0.22), residues: 567 loop : -2.27 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1091 TYR 0.028 0.001 TYR C 248 PHE 0.030 0.002 PHE C 55 TRP 0.029 0.001 TRP C 152 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00270 (30670) covalent geometry : angle 0.64428 (41720) SS BOND : bond 0.00252 ( 40) SS BOND : angle 1.16030 ( 80) hydrogen bonds : bond 0.03426 ( 1033) hydrogen bonds : angle 5.04287 ( 2883) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 177 MET cc_start: 0.5295 (ttp) cc_final: 0.4965 (tmm) REVERT: F 731 MET cc_start: 0.8827 (ppp) cc_final: 0.8218 (ppp) REVERT: F 740 MET cc_start: 0.8932 (tmm) cc_final: 0.8522 (tmm) REVERT: F 759 PHE cc_start: 0.8129 (m-80) cc_final: 0.7645 (m-80) REVERT: F 779 GLN cc_start: 0.8930 (mp10) cc_final: 0.8718 (mp10) REVERT: G 265 TYR cc_start: 0.8859 (p90) cc_final: 0.8543 (p90) REVERT: G 513 LEU cc_start: 0.8719 (mm) cc_final: 0.8507 (mm) REVERT: G 731 MET cc_start: 0.9398 (pmm) cc_final: 0.9021 (pmm) REVERT: G 1050 MET cc_start: 0.8581 (tmm) cc_final: 0.8286 (tmm) REVERT: C 90 VAL cc_start: 0.9015 (t) cc_final: 0.8782 (p) REVERT: C 248 TYR cc_start: 0.4851 (p90) cc_final: 0.4604 (p90) REVERT: C 731 MET cc_start: 0.9074 (ppp) cc_final: 0.8521 (ppp) REVERT: C 869 MET cc_start: 0.9579 (pmm) cc_final: 0.9296 (pmm) REVERT: C 985 ASP cc_start: 0.9468 (m-30) cc_final: 0.9199 (t0) REVERT: D 59 VAL cc_start: 0.7402 (t) cc_final: 0.7195 (t) REVERT: D 82 MET cc_start: 0.5320 (ppp) cc_final: 0.4962 (ppp) REVERT: D 152 MET cc_start: 0.3306 (mtt) cc_final: 0.2926 (mtt) REVERT: D 190 MET cc_start: 0.1647 (ptt) cc_final: 0.1008 (ptp) REVERT: D 297 MET cc_start: 0.2107 (mtm) cc_final: 0.1335 (ttp) outliers start: 3 outliers final: 0 residues processed: 211 average time/residue: 0.1564 time to fit residues: 55.3727 Evaluate side-chains 147 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 367 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 224 optimal weight: 0.0970 chunk 344 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 154 optimal weight: 40.0000 chunk 112 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN G 87 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 ASN G 895 GLN G 920 GLN G1010 GLN C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.079005 restraints weight = 220077.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078173 restraints weight = 139200.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.078623 restraints weight = 88344.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078462 restraints weight = 70024.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078634 restraints weight = 64442.498| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30710 Z= 0.152 Angle : 0.633 8.056 41800 Z= 0.327 Chirality : 0.045 0.186 4642 Planarity : 0.004 0.053 5401 Dihedral : 5.146 30.648 4071 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.82 % Favored : 90.10 % Rotamer: Outliers : 0.06 % Allowed : 1.20 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.13), residues: 3749 helix: 0.44 (0.17), residues: 1007 sheet: -0.59 (0.22), residues: 535 loop : -2.22 (0.12), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 498 TYR 0.026 0.001 TYR C 248 PHE 0.035 0.001 PHE C 759 TRP 0.042 0.002 TRP C 152 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00336 (30670) covalent geometry : angle 0.63156 (41720) SS BOND : bond 0.00258 ( 40) SS BOND : angle 1.09710 ( 80) hydrogen bonds : bond 0.03446 ( 1033) hydrogen bonds : angle 5.05546 ( 2883) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 177 MET cc_start: 0.5381 (ttp) cc_final: 0.5056 (tmm) REVERT: F 697 MET cc_start: 0.8938 (tpt) cc_final: 0.8149 (tpp) REVERT: F 731 MET cc_start: 0.8829 (ppp) cc_final: 0.8326 (ppp) REVERT: F 740 MET cc_start: 0.9015 (tmm) cc_final: 0.8625 (tmm) REVERT: F 773 GLU cc_start: 0.8685 (pp20) cc_final: 0.8421 (pp20) REVERT: F 774 GLN cc_start: 0.8896 (tt0) cc_final: 0.8602 (tt0) REVERT: G 265 TYR cc_start: 0.8808 (p90) cc_final: 0.8444 (p90) REVERT: G 513 LEU cc_start: 0.8727 (mm) cc_final: 0.8497 (mm) REVERT: G 740 MET cc_start: 0.8459 (mtp) cc_final: 0.8245 (mtp) REVERT: G 1050 MET cc_start: 0.8671 (tmm) cc_final: 0.8395 (tmm) REVERT: C 248 TYR cc_start: 0.4630 (p90) cc_final: 0.4418 (p90) REVERT: C 360 ASN cc_start: 0.9030 (t0) cc_final: 0.8816 (m-40) REVERT: C 731 MET cc_start: 0.9055 (ppp) cc_final: 0.8480 (ppp) REVERT: C 869 MET cc_start: 0.9563 (pmm) cc_final: 0.9269 (pmm) REVERT: D 59 VAL cc_start: 0.7350 (t) cc_final: 0.7133 (t) REVERT: D 62 MET cc_start: 0.5287 (mmp) cc_final: 0.5031 (mmp) REVERT: D 82 MET cc_start: 0.5399 (ppp) cc_final: 0.5089 (ppp) REVERT: D 152 MET cc_start: 0.3458 (mtt) cc_final: 0.3102 (mtt) REVERT: D 190 MET cc_start: 0.1746 (ptt) cc_final: 0.1079 (ptp) REVERT: D 297 MET cc_start: 0.2224 (mtm) cc_final: 0.1360 (ttm) REVERT: D 447 VAL cc_start: 0.6641 (t) cc_final: 0.6058 (t) REVERT: D 499 ASP cc_start: 0.4665 (m-30) cc_final: 0.4383 (m-30) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.1676 time to fit residues: 55.3087 Evaluate side-chains 140 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 348 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 211 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN G 87 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G1010 GLN C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 330 ASN D 442 GLN ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.096583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074771 restraints weight = 220281.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075061 restraints weight = 121451.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.075157 restraints weight = 83058.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.075273 restraints weight = 69907.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.075677 restraints weight = 48407.511| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30710 Z= 0.233 Angle : 0.708 9.644 41800 Z= 0.369 Chirality : 0.047 0.194 4642 Planarity : 0.005 0.100 5401 Dihedral : 5.492 30.999 4071 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.04 % Favored : 88.88 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.13), residues: 3749 helix: 0.21 (0.16), residues: 1013 sheet: -0.72 (0.23), residues: 527 loop : -2.32 (0.12), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G1091 TYR 0.029 0.002 TYR C 248 PHE 0.026 0.002 PHE C 55 TRP 0.045 0.002 TRP C 152 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00497 (30670) covalent geometry : angle 0.70669 (41720) SS BOND : bond 0.00324 ( 40) SS BOND : angle 1.30074 ( 80) hydrogen bonds : bond 0.03768 ( 1033) hydrogen bonds : angle 5.28568 ( 2883) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 697 MET cc_start: 0.8885 (tpt) cc_final: 0.8470 (tpp) REVERT: F 731 MET cc_start: 0.8814 (ppp) cc_final: 0.8302 (ppp) REVERT: F 740 MET cc_start: 0.9023 (tmm) cc_final: 0.8666 (tmm) REVERT: F 759 PHE cc_start: 0.8017 (m-80) cc_final: 0.7676 (m-80) REVERT: F 1002 GLN cc_start: 0.8964 (mp10) cc_final: 0.8652 (mp10) REVERT: G 513 LEU cc_start: 0.8667 (mm) cc_final: 0.8409 (mm) REVERT: G 697 MET cc_start: 0.8639 (mmp) cc_final: 0.8260 (mmp) REVERT: G 740 MET cc_start: 0.8301 (mtp) cc_final: 0.8090 (mtt) REVERT: G 1050 MET cc_start: 0.8715 (tmm) cc_final: 0.8439 (tmm) REVERT: G 1067 TYR cc_start: 0.8047 (t80) cc_final: 0.7795 (t80) REVERT: C 351 TYR cc_start: 0.8397 (p90) cc_final: 0.8137 (p90) REVERT: C 481 ASN cc_start: 0.7526 (m-40) cc_final: 0.7224 (t0) REVERT: C 518 LEU cc_start: 0.8805 (mp) cc_final: 0.8474 (tp) REVERT: C 731 MET cc_start: 0.8925 (ppp) cc_final: 0.8388 (ppp) REVERT: C 869 MET cc_start: 0.9572 (pmm) cc_final: 0.9326 (pmm) REVERT: D 62 MET cc_start: 0.5588 (mmp) cc_final: 0.5372 (mmp) REVERT: D 82 MET cc_start: 0.5544 (ppp) cc_final: 0.5254 (ppp) REVERT: D 152 MET cc_start: 0.2585 (mtt) cc_final: 0.2379 (mtt) REVERT: D 190 MET cc_start: 0.2221 (ptt) cc_final: 0.1720 (ptt) REVERT: D 297 MET cc_start: 0.2034 (mtm) cc_final: 0.1384 (tpp) REVERT: D 499 ASP cc_start: 0.3652 (m-30) cc_final: 0.3413 (m-30) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.1498 time to fit residues: 48.5843 Evaluate side-chains 135 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 152 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 351 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 350 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN G 87 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 ASN G 895 GLN G 920 GLN G1010 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.098876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078283 restraints weight = 220900.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078379 restraints weight = 125180.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078244 restraints weight = 77226.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.078257 restraints weight = 72256.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.078974 restraints weight = 63755.725| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30710 Z= 0.134 Angle : 0.641 8.885 41800 Z= 0.330 Chirality : 0.046 0.200 4642 Planarity : 0.004 0.055 5401 Dihedral : 5.262 29.637 4071 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.42 % Favored : 90.50 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.13), residues: 3749 helix: 0.31 (0.16), residues: 1024 sheet: -0.64 (0.22), residues: 555 loop : -2.26 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G1091 TYR 0.026 0.001 TYR C 248 PHE 0.028 0.002 PHE C 759 TRP 0.046 0.002 TRP C 152 HIS 0.015 0.001 HIS G 69 Details of bonding type rmsd covalent geometry : bond 0.00296 (30670) covalent geometry : angle 0.63964 (41720) SS BOND : bond 0.00267 ( 40) SS BOND : angle 1.02053 ( 80) hydrogen bonds : bond 0.03386 ( 1033) hydrogen bonds : angle 5.06405 ( 2883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4834.96 seconds wall clock time: 84 minutes 41.40 seconds (5081.40 seconds total)