Starting phenix.real_space_refine on Wed May 28 02:06:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrm_37781/05_2025/8wrm_37781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrm_37781/05_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_37781/05_2025/8wrm_37781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrm_37781/05_2025/8wrm_37781.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrm_37781/05_2025/8wrm_37781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrm_37781/05_2025/8wrm_37781.cif" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.08, per 1000 atoms: 0.57 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: 7.36 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.81 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: 12.10 Time building geometry restraints manager: 8.68 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: 2.430 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: 0.040 Extract box with map and model: 1.100 Check model and map are aligned: 0.240 Set scattering table: 0.250 Process input model: 65.890 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.063 0.002 TRP C 436 HIS 0.007 0.001 HIS G 245 PHE 0.040 0.002 PHE F1052 TYR 0.038 0.002 TYR D 199 ARG 0.011 0.001 ARG G1019 Details of bonding type rmsd hydrogen bonds : bond 0.14709 ( 1033) hydrogen bonds : angle 6.82433 ( 2883) SS BOND : bond 0.00335 ( 40) SS BOND : angle 1.03792 ( 80) covalent geometry : bond 0.00370 (30670) covalent geometry : angle 0.89410 (41720) *********************** 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 : 3.005 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: 0.7888 (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: 0.8165 (mtp) REVERT: G 773 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8840 (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: 0.5958 (mmm) REVERT: D 82 MET cc_start: 0.4953 (ppp) cc_final: 0.4603 (ppp) REVERT: D 152 MET cc_start: 0.2421 (mtt) cc_final: 0.1949 (mtt) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.3943 time to fit residues: 179.5735 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 : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 192 optimal weight: 0.0050 chunk 152 optimal weight: 30.0000 chunk 295 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 342 optimal weight: 1.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 245 HIS ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN F1048 HIS ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 774 GLN G 895 GLN G 920 GLN G 954 HIS G1010 GLN C 52 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.100162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.069658 restraints weight = 190221.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.070769 restraints weight = 109172.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.071465 restraints weight = 74033.648| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30710 Z= 0.145 Angle : 0.595 9.050 41800 Z= 0.313 Chirality : 0.043 0.186 4642 Planarity : 0.005 0.063 5401 Dihedral : 5.046 24.114 4071 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.06 % Favored : 91.86 % Rotamer: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.13), residues: 3749 helix: 0.07 (0.16), residues: 995 sheet: -0.16 (0.22), residues: 531 loop : -2.32 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 459 HIS 0.014 0.001 HIS G 954 PHE 0.029 0.001 PHE F 592 TYR 0.025 0.001 TYR G 904 ARG 0.006 0.000 ARG F 319 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 1033) hydrogen bonds : angle 5.20749 ( 2883) SS BOND : bond 0.00248 ( 40) SS BOND : angle 0.76429 ( 80) covalent geometry : bond 0.00310 (30670) covalent geometry : angle 0.59428 (41720) *********************** 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 256 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 3.091 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: 0.8490 (tmm) cc_final: 0.8238 (tmm) REVERT: F 759 PHE cc_start: 0.7845 (m-80) cc_final: 0.7624 (m-80) REVERT: F 1017 GLU cc_start: 0.9084 (tt0) cc_final: 0.8829 (tt0) REVERT: G 740 MET cc_start: 0.8651 (mtp) cc_final: 0.8235 (mtt) REVERT: G 869 MET cc_start: 0.9068 (pmm) cc_final: 0.8846 (pmm) REVERT: G 1019 ARG cc_start: 0.8918 (ttp-110) cc_final: 0.8643 (ttp80) REVERT: G 1050 MET cc_start: 0.8543 (tmm) cc_final: 0.8294 (tmm) REVERT: C 248 TYR cc_start: 0.5600 (p90) cc_final: 0.5396 (p90) REVERT: C 731 MET cc_start: 0.8924 (ppp) cc_final: 0.8611 (ppp) REVERT: D 62 MET cc_start: 0.7800 (mmp) cc_final: 0.7491 (mmp) REVERT: D 82 MET cc_start: 0.5410 (ppp) cc_final: 0.5160 (ppp) REVERT: D 152 MET cc_start: -0.2539 (mtt) cc_final: -0.2767 (mtt) REVERT: D 190 MET cc_start: 0.1692 (ptt) cc_final: 0.1491 (ptm) outliers start: 2 outliers final: 0 residues processed: 255 average time/residue: 0.3787 time to fit residues: 159.8037 Evaluate side-chains 174 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 372 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 330 optimal weight: 0.4980 chunk 160 optimal weight: 7.9990 chunk 259 optimal weight: 0.0670 chunk 276 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 GLN F 506 GLN ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G1010 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN D 265 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.100798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.071455 restraints weight = 192109.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.071716 restraints weight = 109548.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.072425 restraints weight = 73706.582| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30710 Z= 0.107 Angle : 0.568 9.272 41800 Z= 0.294 Chirality : 0.043 0.173 4642 Planarity : 0.004 0.058 5401 Dihedral : 4.841 31.089 4071 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.66 % Favored : 92.26 % Rotamer: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.13), residues: 3749 helix: 0.34 (0.17), residues: 994 sheet: -0.22 (0.21), residues: 601 loop : -2.23 (0.12), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 152 HIS 0.015 0.001 HIS C 954 PHE 0.018 0.001 PHE D 369 TYR 0.019 0.001 TYR D 183 ARG 0.006 0.000 ARG F 78 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 1033) hydrogen bonds : angle 4.95095 ( 2883) SS BOND : bond 0.00179 ( 40) SS BOND : angle 0.71684 ( 80) covalent geometry : bond 0.00232 (30670) covalent geometry : angle 0.56755 (41720) *********************** 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 265 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 2.973 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 740 MET cc_start: 0.8518 (tmm) cc_final: 0.8207 (tmm) REVERT: F 759 PHE cc_start: 0.7777 (m-80) cc_final: 0.7492 (m-80) REVERT: F 1038 LYS cc_start: 0.8954 (ptpp) cc_final: 0.8729 (ptmm) REVERT: G 104 TRP cc_start: 0.6804 (m-90) cc_final: 0.6542 (m-90) REVERT: G 731 MET cc_start: 0.9339 (pmm) cc_final: 0.9051 (pmm) REVERT: G 869 MET cc_start: 0.9153 (pmm) cc_final: 0.8920 (pmm) REVERT: G 1019 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8643 (ttp80) REVERT: G 1050 MET cc_start: 0.8559 (tmm) cc_final: 0.7448 (tmm) REVERT: G 1052 PHE cc_start: 0.8745 (m-10) cc_final: 0.8242 (m-10) REVERT: C 90 VAL cc_start: 0.8065 (t) cc_final: 0.7859 (p) REVERT: C 731 MET cc_start: 0.8941 (ppp) cc_final: 0.8602 (ppp) REVERT: C 759 PHE cc_start: 0.8115 (p90) cc_final: 0.7832 (p90) REVERT: C 855 PHE cc_start: 0.6900 (m-80) cc_final: 0.6664 (m-80) REVERT: D 62 MET cc_start: 0.6931 (mmp) cc_final: 0.6609 (mmp) REVERT: D 82 MET cc_start: 0.5440 (ppp) cc_final: 0.5172 (ppp) REVERT: D 152 MET cc_start: 0.0482 (mtt) cc_final: 0.0247 (mtt) REVERT: D 190 MET cc_start: 0.1776 (ptt) cc_final: 0.1516 (ptm) outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.3855 time to fit residues: 169.0796 Evaluate side-chains 167 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 343 optimal weight: 0.9990 chunk 362 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 33 optimal weight: 0.0060 chunk 91 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G1010 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN C1106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.107107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.085706 restraints weight = 222626.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.086140 restraints weight = 133866.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086697 restraints weight = 84529.228| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30710 Z= 0.117 Angle : 0.568 9.140 41800 Z= 0.292 Chirality : 0.044 0.238 4642 Planarity : 0.004 0.075 5401 Dihedral : 4.724 29.555 4071 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.00 % Favored : 91.92 % Rotamer: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3749 helix: 0.43 (0.17), residues: 1020 sheet: -0.03 (0.23), residues: 536 loop : -2.17 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 152 HIS 0.007 0.001 HIS F 245 PHE 0.028 0.001 PHE G 800 TYR 0.029 0.001 TYR D 183 ARG 0.007 0.000 ARG F1019 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 1033) hydrogen bonds : angle 4.81260 ( 2883) SS BOND : bond 0.00203 ( 40) SS BOND : angle 0.78011 ( 80) covalent geometry : bond 0.00253 (30670) covalent geometry : angle 0.56787 (41720) *********************** 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 251 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 3.271 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 697 MET cc_start: 0.8681 (mmp) cc_final: 0.8362 (tpp) REVERT: F 731 MET cc_start: 0.8921 (ppp) cc_final: 0.8357 (ppp) REVERT: F 740 MET cc_start: 0.8574 (tmm) cc_final: 0.8226 (tmm) REVERT: G 104 TRP cc_start: 0.7022 (m-90) cc_final: 0.6781 (m-90) REVERT: G 740 MET cc_start: 0.8517 (mtp) cc_final: 0.8009 (mtt) REVERT: G 869 MET cc_start: 0.9176 (pmm) cc_final: 0.8859 (pmm) REVERT: G 1019 ARG cc_start: 0.9186 (ttp-110) cc_final: 0.8934 (ttp80) REVERT: G 1050 MET cc_start: 0.8546 (tmm) cc_final: 0.7394 (tmm) REVERT: G 1052 PHE cc_start: 0.8942 (m-10) cc_final: 0.8387 (m-10) REVERT: C 90 VAL cc_start: 0.8341 (t) cc_final: 0.8100 (p) REVERT: C 239 GLN cc_start: 0.6427 (mm-40) cc_final: 0.6093 (mp10) REVERT: C 731 MET cc_start: 0.9043 (ppp) cc_final: 0.8694 (ppp) REVERT: D 82 MET cc_start: 0.5182 (ppp) cc_final: 0.4821 (ppp) REVERT: D 152 MET cc_start: 0.3274 (mtt) cc_final: 0.2865 (mtt) REVERT: D 270 MET cc_start: 0.4288 (tpt) cc_final: 0.3531 (tpp) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.3825 time to fit residues: 158.2596 Evaluate side-chains 163 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 93 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 352 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 165 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN G 920 GLN G1010 GLN G1036 GLN C 69 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 207 HIS C 394 ASN C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1106 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.096572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.065778 restraints weight = 187435.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066715 restraints weight = 106188.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067567 restraints weight = 74694.899| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30710 Z= 0.167 Angle : 0.621 8.084 41800 Z= 0.323 Chirality : 0.045 0.251 4642 Planarity : 0.005 0.056 5401 Dihedral : 4.882 29.195 4071 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.64 % Favored : 91.28 % Rotamer: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3749 helix: 0.45 (0.17), residues: 1018 sheet: -0.37 (0.22), residues: 583 loop : -2.19 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 152 HIS 0.004 0.001 HIS C 505 PHE 0.022 0.002 PHE C 855 TYR 0.032 0.002 TYR D 217 ARG 0.011 0.001 ARG G1091 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 1033) hydrogen bonds : angle 4.90717 ( 2883) SS BOND : bond 0.00234 ( 40) SS BOND : angle 0.95135 ( 80) covalent geometry : bond 0.00361 (30670) covalent geometry : angle 0.62011 (41720) *********************** 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 232 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 3.142 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 203 ILE cc_start: 0.8671 (mm) cc_final: 0.8382 (mp) REVERT: F 731 MET cc_start: 0.8951 (ppp) cc_final: 0.8505 (ppp) REVERT: F 740 MET cc_start: 0.8703 (tmm) cc_final: 0.8343 (tmm) REVERT: F 774 GLN cc_start: 0.8807 (tt0) cc_final: 0.8548 (tt0) REVERT: G 731 MET cc_start: 0.9164 (pmm) cc_final: 0.8799 (pmm) REVERT: G 869 MET cc_start: 0.9356 (pmm) cc_final: 0.8901 (pmm) REVERT: G 988 GLU cc_start: 0.9190 (mp0) cc_final: 0.8990 (mp0) REVERT: G 1050 MET cc_start: 0.8677 (tmm) cc_final: 0.7851 (tmm) REVERT: G 1052 PHE cc_start: 0.8795 (m-10) cc_final: 0.8315 (m-10) REVERT: C 239 GLN cc_start: 0.6531 (mm-40) cc_final: 0.6245 (mp10) REVERT: C 248 TYR cc_start: 0.4208 (p90) cc_final: 0.3823 (p90) REVERT: C 360 ASN cc_start: 0.8848 (t0) cc_final: 0.8595 (m-40) REVERT: C 731 MET cc_start: 0.8963 (ppp) cc_final: 0.8508 (ppp) REVERT: C 770 ILE cc_start: 0.9554 (mm) cc_final: 0.9347 (mm) REVERT: D 62 MET cc_start: 0.7925 (mmp) cc_final: 0.7706 (mmt) REVERT: D 190 MET cc_start: 0.4143 (ptp) cc_final: 0.3593 (ptp) REVERT: D 566 TRP cc_start: 0.5708 (p-90) cc_final: 0.5476 (p-90) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.3793 time to fit residues: 146.4739 Evaluate side-chains 156 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 257 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 360 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 345 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 69 HIS F 134 GLN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN F1119 ASN ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 239 GLN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 536 ASN G 895 GLN G 920 GLN G 935 GLN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 607 GLN C 804 GLN C 935 GLN C1058 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 535 HIS D 552 GLN D 601 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.098572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077944 restraints weight = 222836.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.076941 restraints weight = 132431.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077159 restraints weight = 101572.836| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 30710 Z= 0.273 Angle : 0.747 13.657 41800 Z= 0.393 Chirality : 0.047 0.234 4642 Planarity : 0.005 0.060 5401 Dihedral : 5.500 28.863 4071 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.51 % Favored : 89.41 % Rotamer: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3749 helix: 0.18 (0.16), residues: 1019 sheet: -0.42 (0.23), residues: 508 loop : -2.30 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP D 478 HIS 0.007 0.002 HIS C1064 PHE 0.033 0.003 PHE F 201 TYR 0.028 0.002 TYR F 873 ARG 0.012 0.001 ARG G1091 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 1033) hydrogen bonds : angle 5.30548 ( 2883) SS BOND : bond 0.00555 ( 40) SS BOND : angle 1.29817 ( 80) covalent geometry : bond 0.00583 (30670) covalent geometry : angle 0.74514 (41720) *********************** 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 217 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 3.103 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: F 731 MET cc_start: 0.8917 (ppp) cc_final: 0.8389 (ppp) REVERT: F 740 MET cc_start: 0.8984 (tmm) cc_final: 0.8522 (tmm) REVERT: F 779 GLN cc_start: 0.9109 (mp10) cc_final: 0.8833 (mp10) REVERT: F 869 MET cc_start: 0.9297 (mpp) cc_final: 0.8975 (mtt) REVERT: G 740 MET cc_start: 0.8463 (mtp) cc_final: 0.7983 (mtt) REVERT: G 869 MET cc_start: 0.9402 (pmm) cc_final: 0.9184 (pmm) REVERT: G 1050 MET cc_start: 0.8731 (tmm) cc_final: 0.8431 (tmm) REVERT: C 360 ASN cc_start: 0.8998 (t0) cc_final: 0.8747 (m-40) REVERT: C 731 MET cc_start: 0.8926 (ppp) cc_final: 0.8383 (ppp) REVERT: C 855 PHE cc_start: 0.7741 (m-10) cc_final: 0.7483 (m-80) REVERT: C 858 LEU cc_start: 0.9142 (mt) cc_final: 0.8915 (mt) REVERT: C 882 ILE cc_start: 0.9554 (tt) cc_final: 0.9333 (mt) REVERT: D 82 MET cc_start: 0.5230 (ppp) cc_final: 0.4882 (ppp) REVERT: D 152 MET cc_start: 0.3337 (mtt) cc_final: 0.2873 (mtt) REVERT: D 297 MET cc_start: 0.2159 (mtm) cc_final: 0.0776 (tpp) REVERT: D 499 ASP cc_start: 0.4183 (m-30) cc_final: 0.3507 (m-30) outliers start: 2 outliers final: 0 residues processed: 217 average time/residue: 0.3918 time to fit residues: 141.3735 Evaluate side-chains 134 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 360 optimal weight: 8.9990 chunk 328 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 342 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 344 optimal weight: 8.9990 chunk 293 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 536 ASN ** 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 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN ** G 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 920 GLN ** G1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 69 HIS ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 63 ASN 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 = 0.3935 r_free = 0.3935 target = 0.096672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075628 restraints weight = 221977.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.075368 restraints weight = 124798.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.075630 restraints weight = 84403.597| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30710 Z= 0.280 Angle : 0.746 8.199 41800 Z= 0.393 Chirality : 0.048 0.309 4642 Planarity : 0.005 0.081 5401 Dihedral : 5.758 28.540 4071 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.51 % Favored : 89.41 % Rotamer: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3749 helix: -0.07 (0.16), residues: 1018 sheet: -0.63 (0.24), residues: 504 loop : -2.41 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 152 HIS 0.008 0.002 HIS D 493 PHE 0.033 0.002 PHE D 400 TYR 0.027 0.002 TYR C 248 ARG 0.010 0.001 ARG G1091 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 1033) hydrogen bonds : angle 5.45800 ( 2883) SS BOND : bond 0.01155 ( 40) SS BOND : angle 1.35260 ( 80) covalent geometry : bond 0.00589 (30670) covalent geometry : angle 0.74387 (41720) *********************** 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 185 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 3.458 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 731 MET cc_start: 0.9041 (ppp) cc_final: 0.8616 (ppp) REVERT: F 740 MET cc_start: 0.8976 (tmm) cc_final: 0.8524 (tmm) REVERT: F 773 GLU cc_start: 0.8621 (pp20) cc_final: 0.8396 (pp20) REVERT: F 779 GLN cc_start: 0.9011 (mp10) cc_final: 0.8709 (mp10) REVERT: F 1017 GLU cc_start: 0.9358 (tt0) cc_final: 0.9125 (tt0) REVERT: G 740 MET cc_start: 0.8294 (mtp) cc_final: 0.7925 (mtt) REVERT: G 869 MET cc_start: 0.9416 (pmm) cc_final: 0.9181 (pmm) REVERT: G 1050 MET cc_start: 0.8682 (tmm) cc_final: 0.8397 (tmm) REVERT: C 177 MET cc_start: 0.4317 (ttp) cc_final: 0.3563 (tmm) REVERT: C 248 TYR cc_start: 0.4397 (p90) cc_final: 0.4197 (p90) REVERT: C 351 TYR cc_start: 0.8454 (p90) cc_final: 0.8244 (p90) REVERT: C 360 ASN cc_start: 0.9012 (t0) cc_final: 0.8793 (m-40) REVERT: C 731 MET cc_start: 0.8870 (ppp) cc_final: 0.8364 (ppp) REVERT: C 858 LEU cc_start: 0.9146 (mt) cc_final: 0.8915 (mt) REVERT: C 902 MET cc_start: 0.9305 (mmp) cc_final: 0.9051 (mmp) REVERT: D 82 MET cc_start: 0.5352 (ppp) cc_final: 0.5075 (ppp) REVERT: D 152 MET cc_start: 0.2380 (mtt) cc_final: 0.1922 (mtt) REVERT: D 297 MET cc_start: 0.2273 (mtm) cc_final: 0.1170 (tpp) REVERT: D 499 ASP cc_start: 0.2910 (m-30) cc_final: 0.2644 (m-30) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.3999 time to fit residues: 123.6754 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 : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 82 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 252 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 287 optimal weight: 0.0470 chunk 23 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN F1011 GLN G 52 GLN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 ASN G 895 GLN G 920 GLN G1010 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN D 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.100878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080290 restraints weight = 219831.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080086 restraints weight = 128085.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.080202 restraints weight = 89245.681| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30710 Z= 0.124 Angle : 0.631 9.382 41800 Z= 0.326 Chirality : 0.045 0.175 4642 Planarity : 0.004 0.061 5401 Dihedral : 5.246 26.709 4071 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.91 % Favored : 91.01 % Rotamer: Outliers : 0.09 % Allowed : 1.59 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3749 helix: 0.32 (0.16), residues: 1018 sheet: -0.59 (0.21), residues: 595 loop : -2.31 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 152 HIS 0.006 0.001 HIS C1083 PHE 0.024 0.002 PHE F 201 TYR 0.026 0.001 TYR G 904 ARG 0.008 0.001 ARG F 158 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 1033) hydrogen bonds : angle 5.04230 ( 2883) SS BOND : bond 0.00274 ( 40) SS BOND : angle 0.96147 ( 80) covalent geometry : bond 0.00268 (30670) covalent geometry : angle 0.63015 (41720) *********************** 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 213 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 3.140 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: 0.9101 (ppp) cc_final: 0.8744 (ppp) REVERT: F 740 MET cc_start: 0.8950 (tmm) cc_final: 0.8525 (tmm) REVERT: F 774 GLN cc_start: 0.8914 (tt0) cc_final: 0.8703 (tt0) REVERT: F 779 GLN cc_start: 0.9068 (mp10) cc_final: 0.8656 (mp10) REVERT: F 869 MET cc_start: 0.9290 (mpp) cc_final: 0.9024 (mtt) REVERT: G 513 LEU cc_start: 0.8725 (mm) cc_final: 0.8474 (mm) REVERT: G 697 MET cc_start: 0.8640 (tpp) cc_final: 0.7898 (mmm) REVERT: G 731 MET cc_start: 0.9394 (pmm) cc_final: 0.9138 (pmm) REVERT: G 740 MET cc_start: 0.8388 (mtp) cc_final: 0.8044 (mtt) REVERT: G 869 MET cc_start: 0.9387 (pmm) cc_final: 0.9138 (pmm) REVERT: G 1029 MET cc_start: 0.9469 (tpp) cc_final: 0.9233 (tpp) REVERT: G 1050 MET cc_start: 0.8564 (tmm) cc_final: 0.8334 (tmm) REVERT: C 248 TYR cc_start: 0.4398 (p90) cc_final: 0.4177 (p90) REVERT: C 731 MET cc_start: 0.9092 (ppp) cc_final: 0.8586 (ppp) REVERT: C 979 ASP cc_start: 0.8989 (p0) cc_final: 0.8701 (p0) REVERT: D 82 MET cc_start: 0.5608 (ppp) cc_final: 0.5258 (ppp) REVERT: D 152 MET cc_start: 0.3050 (mtt) cc_final: 0.2684 (mtt) REVERT: D 297 MET cc_start: 0.2079 (mtm) cc_final: 0.1195 (ttm) REVERT: D 474 MET cc_start: -0.4248 (mmt) cc_final: -0.4453 (mmt) outliers start: 3 outliers final: 0 residues processed: 213 average time/residue: 0.4132 time to fit residues: 142.8200 Evaluate side-chains 136 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 355 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 163 optimal weight: 0.3980 chunk 373 optimal weight: 8.9990 chunk 306 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 75 optimal weight: 0.1980 chunk 348 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN ** G 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.099127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078719 restraints weight = 218744.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.078200 restraints weight = 126905.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.078553 restraints weight = 83581.409| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30710 Z= 0.159 Angle : 0.641 8.800 41800 Z= 0.331 Chirality : 0.045 0.190 4642 Planarity : 0.004 0.054 5401 Dihedral : 5.187 26.760 4071 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.55 % Favored : 90.37 % Rotamer: Outliers : 0.03 % Allowed : 0.72 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 3749 helix: 0.37 (0.16), residues: 1024 sheet: -0.49 (0.23), residues: 508 loop : -2.28 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 152 HIS 0.005 0.001 HIS D 401 PHE 0.024 0.002 PHE F 201 TYR 0.024 0.001 TYR F1067 ARG 0.005 0.001 ARG F 246 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 1033) hydrogen bonds : angle 5.04124 ( 2883) SS BOND : bond 0.00262 ( 40) SS BOND : angle 1.09999 ( 80) covalent geometry : bond 0.00347 (30670) covalent geometry : angle 0.63991 (41720) *********************** 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 191 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 3.219 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: F 201 PHE cc_start: 0.9663 (t80) cc_final: 0.9455 (t80) REVERT: F 697 MET cc_start: 0.9050 (tpt) cc_final: 0.8281 (tpp) REVERT: F 731 MET cc_start: 0.9092 (ppp) cc_final: 0.8579 (ppp) REVERT: F 740 MET cc_start: 0.9003 (tmm) cc_final: 0.8627 (tmm) REVERT: F 774 GLN cc_start: 0.8900 (tt0) cc_final: 0.8647 (tt0) REVERT: F 1002 GLN cc_start: 0.9058 (mp10) cc_final: 0.8650 (mp10) REVERT: F 1107 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8008 (tpp80) REVERT: G 513 LEU cc_start: 0.8733 (mm) cc_final: 0.8502 (mm) REVERT: G 697 MET cc_start: 0.8678 (tpp) cc_final: 0.8344 (mmm) REVERT: G 740 MET cc_start: 0.8413 (mtp) cc_final: 0.8037 (mtt) REVERT: G 773 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8275 (tm-30) REVERT: G 904 TYR cc_start: 0.8736 (m-10) cc_final: 0.8294 (m-10) REVERT: G 1050 MET cc_start: 0.8692 (tmm) cc_final: 0.8427 (tmm) REVERT: C 90 VAL cc_start: 0.9131 (t) cc_final: 0.8898 (p) REVERT: C 360 ASN cc_start: 0.9058 (t0) cc_final: 0.8839 (m-40) REVERT: C 731 MET cc_start: 0.8920 (ppp) cc_final: 0.8428 (ppp) REVERT: C 1109 PHE cc_start: 0.8221 (t80) cc_final: 0.7865 (t80) REVERT: D 82 MET cc_start: 0.5585 (ppp) cc_final: 0.5286 (ppp) REVERT: D 152 MET cc_start: 0.3564 (mtt) cc_final: 0.3083 (mtt) REVERT: D 297 MET cc_start: 0.2231 (mtm) cc_final: 0.1417 (ttt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.4000 time to fit residues: 125.4007 Evaluate side-chains 132 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 ASN ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.099122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078630 restraints weight = 220050.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078741 restraints weight = 123399.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078594 restraints weight = 73982.267| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30710 Z= 0.156 Angle : 0.639 10.599 41800 Z= 0.329 Chirality : 0.045 0.211 4642 Planarity : 0.004 0.053 5401 Dihedral : 5.190 25.338 4071 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.18 % Favored : 90.74 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3749 helix: 0.41 (0.16), residues: 1015 sheet: -0.50 (0.23), residues: 522 loop : -2.24 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 152 HIS 0.005 0.001 HIS C1064 PHE 0.030 0.002 PHE G 65 TYR 0.022 0.001 TYR C 248 ARG 0.005 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 1033) hydrogen bonds : angle 5.05638 ( 2883) SS BOND : bond 0.00237 ( 40) SS BOND : angle 1.03846 ( 80) covalent geometry : bond 0.00341 (30670) covalent geometry : angle 0.63837 (41720) ********************** 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 188 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 697 MET cc_start: 0.9092 (tpt) cc_final: 0.8741 (tpp) REVERT: F 731 MET cc_start: 0.9047 (ppp) cc_final: 0.8495 (ppp) REVERT: F 740 MET cc_start: 0.9004 (tmm) cc_final: 0.8659 (tmm) REVERT: F 774 GLN cc_start: 0.8920 (tt0) cc_final: 0.8550 (tt0) REVERT: F 1002 GLN cc_start: 0.9014 (mp10) cc_final: 0.8555 (mp10) REVERT: F 1107 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7650 (tpp80) REVERT: G 177 MET cc_start: 0.1924 (ttp) cc_final: 0.1622 (ttp) REVERT: G 513 LEU cc_start: 0.8746 (mm) cc_final: 0.8508 (mm) REVERT: G 697 MET cc_start: 0.8665 (tpp) cc_final: 0.7988 (mmm) REVERT: G 740 MET cc_start: 0.8376 (mtp) cc_final: 0.8031 (mtt) REVERT: G 904 TYR cc_start: 0.8843 (m-10) cc_final: 0.8366 (m-10) REVERT: G 1050 MET cc_start: 0.8690 (tmm) cc_final: 0.8369 (tmm) REVERT: C 40 ASP cc_start: 0.9164 (p0) cc_final: 0.8896 (p0) REVERT: C 90 VAL cc_start: 0.9128 (t) cc_final: 0.8906 (p) REVERT: C 481 ASN cc_start: 0.7466 (m-40) cc_final: 0.7107 (t0) REVERT: C 518 LEU cc_start: 0.8786 (mp) cc_final: 0.8511 (tp) REVERT: C 731 MET cc_start: 0.8936 (ppp) cc_final: 0.8456 (ppp) REVERT: C 1109 PHE cc_start: 0.8396 (t80) cc_final: 0.8036 (t80) REVERT: D 82 MET cc_start: 0.5675 (ppp) cc_final: 0.5388 (ppp) REVERT: D 152 MET cc_start: 0.3744 (mtt) cc_final: 0.3279 (mtt) REVERT: D 297 MET cc_start: 0.2097 (mtm) cc_final: 0.1386 (ttm) REVERT: D 447 VAL cc_start: 0.6837 (t) cc_final: 0.6436 (t) REVERT: D 579 MET cc_start: 0.4898 (tpt) cc_final: 0.4618 (tpt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.4068 time to fit residues: 126.0915 Evaluate side-chains 138 residues out of total 3328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 121 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 306 optimal weight: 0.9980 chunk 348 optimal weight: 0.0870 chunk 361 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.3362 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 955 ASN ** G 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 ASN G 895 GLN ** G 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 920 GLN G1010 GLN ** 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 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.098466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.078145 restraints weight = 220764.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.077551 restraints weight = 124182.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.077865 restraints weight = 85908.057| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30710 Z= 0.164 Angle : 0.645 9.357 41800 Z= 0.334 Chirality : 0.045 0.184 4642 Planarity : 0.004 0.052 5401 Dihedral : 5.201 25.999 4071 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.68 % Favored : 90.24 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 3749 helix: 0.51 (0.17), residues: 1003 sheet: -0.58 (0.23), residues: 526 loop : -2.24 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 275 HIS 0.005 0.001 HIS C1064 PHE 0.023 0.002 PHE F 201 TYR 0.024 0.002 TYR G 904 ARG 0.005 0.000 ARG F 246 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 1033) hydrogen bonds : angle 5.05067 ( 2883) SS BOND : bond 0.00261 ( 40) SS BOND : angle 1.03532 ( 80) covalent geometry : bond 0.00357 (30670) covalent geometry : angle 0.64386 (41720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9689.13 seconds wall clock time: 171 minutes 7.53 seconds (10267.53 seconds total)