Starting phenix.real_space_refine on Sun Jul 5 04:29:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgm_37226/07_2026/8kgm_37226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgm_37226/07_2026/8kgm_37226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kgm_37226/07_2026/8kgm_37226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgm_37226/07_2026/8kgm_37226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kgm_37226/07_2026/8kgm_37226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgm_37226/07_2026/8kgm_37226.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6198 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 96 5.16 5 C 12879 2.51 5 N 3519 2.21 5 O 3924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20494 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9447 Classifications: {'peptide': 1181} Link IDs: {'PCIS': 3, 'PTRANS': 44, 'TRANS': 1133} Chain breaks: 1 Chain: "B" Number of atoms: 9490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9490 Classifications: {'peptide': 1186} Link IDs: {'PCIS': 3, 'PTRANS': 44, 'TRANS': 1138} Chain breaks: 1 Chain: "C" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 781 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 776 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Time building chain proxies: 4.63, per 1000 atoms: 0.23 Number of scatterers: 20494 At special positions: 0 Unit cell: (132.84, 127.1, 184.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 76 15.00 O 3924 8.00 N 3519 7.00 C 12879 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 761.4 milliseconds 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4462 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 30 sheets defined 46.9% alpha, 14.2% beta 18 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 51 through 73 removed outlier: 3.706A pdb=" N PHE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 211 through 233 Processing helix chain 'A' and resid 250 through 260 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 312 through 334 removed outlier: 3.744A pdb=" N THR A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 385 through 403 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 546 through 560 Processing helix chain 'A' and resid 560 through 567 removed outlier: 4.058A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.721A pdb=" N LYS A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.759A pdb=" N ALA A 619 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 removed outlier: 4.413A pdb=" N SER A 627 " --> pdb=" O HIS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.948A pdb=" N VAL A 636 " --> pdb=" O ASP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 654 Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 removed outlier: 3.501A pdb=" N MET A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 765 Processing helix chain 'A' and resid 787 through 791 removed outlier: 3.912A pdb=" N LEU A 790 " --> pdb=" O SER A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.566A pdb=" N MET A 846 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 877 removed outlier: 3.653A pdb=" N ILE A 868 " --> pdb=" O GLN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 893 Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.788A pdb=" N SER A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 958 removed outlier: 3.818A pdb=" N THR A 958 " --> pdb=" O SER A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 990 removed outlier: 4.360A pdb=" N VAL A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1027 through 1075 removed outlier: 3.731A pdb=" N ILE A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix removed outlier: 4.061A pdb=" N ALA A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A1064 " --> pdb=" O MET A1060 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A1066 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU A1073 " --> pdb=" O ASN A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1079 removed outlier: 3.507A pdb=" N TYR A1079 " --> pdb=" O LEU A1076 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1079' Processing helix chain 'A' and resid 1081 through 1091 Processing helix chain 'A' and resid 1098 through 1104 Processing helix chain 'A' and resid 1109 through 1116 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.691A pdb=" N LEU A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1168 through 1187 Processing helix chain 'B' and resid 8 through 16 Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.707A pdb=" N PHE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 211 through 233 Processing helix chain 'B' and resid 250 through 260 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 312 through 334 removed outlier: 3.745A pdb=" N THR B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 Processing helix chain 'B' and resid 375 through 381 Processing helix chain 'B' and resid 385 through 405 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 541 through 560 removed outlier: 4.252A pdb=" N ILE B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.987A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.600A pdb=" N LYS B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 603 " --> pdb=" O TRP B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.615A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.944A pdb=" N VAL B 636 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 654 removed outlier: 3.899A pdb=" N LEU B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 707 Processing helix chain 'B' and resid 715 through 729 Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.633A pdb=" N MET B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 767 removed outlier: 3.997A pdb=" N LEU B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 842 through 846 Processing helix chain 'B' and resid 864 through 877 removed outlier: 3.616A pdb=" N ILE B 868 " --> pdb=" O GLN B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 893 removed outlier: 3.659A pdb=" N LEU B 886 " --> pdb=" O LYS B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.514A pdb=" N THR B 958 " --> pdb=" O SER B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 990 Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1075 removed outlier: 3.717A pdb=" N ILE B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 4.021A pdb=" N ALA B1063 " --> pdb=" O ILE B1059 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B1064 " --> pdb=" O MET B1060 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG B1066 " --> pdb=" O THR B1062 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA B1072 " --> pdb=" O ILE B1068 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B1073 " --> pdb=" O ASN B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1091 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1109 through 1117 removed outlier: 3.966A pdb=" N LYS B1116 " --> pdb=" O GLU B1112 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.500A pdb=" N LEU B1133 " --> pdb=" O ALA B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1187 removed outlier: 3.972A pdb=" N TRP B1170 " --> pdb=" O GLY B1166 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180 Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 180 removed outlier: 5.330A pdb=" N GLN A 167 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 157 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 82 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 304 removed outlier: 3.889A pdb=" N LYS A 274 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AA8, first strand: chain 'A' and resid 465 through 469 removed outlier: 3.789A pdb=" N ILE A 468 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 481 through 484 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.667A pdb=" N GLU A 833 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU A 827 " --> pdb=" O ARG A 831 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 849 through 852 removed outlier: 3.545A pdb=" N GLY A 849 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.722A pdb=" N HIS A 909 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR A 917 " --> pdb=" O LEU A1009 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 933 through 934 removed outlier: 3.727A pdb=" N GLU A 962 " --> pdb=" O LYS A 977 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AB9, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AC1, first strand: chain 'B' and resid 179 through 180 removed outlier: 5.330A pdb=" N GLN B 167 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP B 157 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 82 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 299 through 304 removed outlier: 3.889A pdb=" N LYS B 274 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AC4, first strand: chain 'B' and resid 418 through 419 removed outlier: 3.710A pdb=" N ILE B 468 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 481 through 485 Processing sheet with id=AC6, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 737 removed outlier: 3.694A pdb=" N ARG B 736 " --> pdb=" O VAL B 803 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 824 through 827 removed outlier: 3.771A pdb=" N GLU B 833 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU B 827 " --> pdb=" O ARG B 831 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 849 through 852 removed outlier: 3.652A pdb=" N GLY B 849 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 909 through 913 removed outlier: 3.514A pdb=" N TYR B 916 " --> pdb=" O PHE B 913 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 925 through 926 removed outlier: 4.202A pdb=" N ILE B 932 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 962 " --> pdb=" O LYS B 977 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1014 through 1016 895 hydrogen bonds defined for protein. 2523 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 5987 1.34 - 1.47: 5888 1.47 - 1.60: 9060 1.60 - 1.74: 24 1.74 - 1.87: 148 Bond restraints: 21107 Sorted by residual: bond pdb=" C1' DT D 22 " pdb=" N1 DT D 22 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" CD GLU A 106 " pdb=" OE2 GLU A 106 " ideal model delta sigma weight residual 1.249 1.329 -0.080 1.90e-02 2.77e+03 1.79e+01 bond pdb=" CD GLU B 106 " pdb=" OE2 GLU B 106 " ideal model delta sigma weight residual 1.249 1.329 -0.080 1.90e-02 2.77e+03 1.78e+01 bond pdb=" C3' DT C 40 " pdb=" O3' DT C 40 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" N9 DA C 31 " pdb=" C4 DA C 31 " ideal model delta sigma weight residual 1.374 1.351 0.023 6.00e-03 2.78e+04 1.51e+01 ... (remaining 21102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 28486 3.24 - 6.48: 339 6.48 - 9.73: 33 9.73 - 12.97: 2 12.97 - 16.21: 3 Bond angle restraints: 28863 Sorted by residual: angle pdb=" O4' DA C 31 " pdb=" C4' DA C 31 " pdb=" C3' DA C 31 " ideal model delta sigma weight residual 106.00 102.45 3.55 6.00e-01 2.78e+00 3.51e+01 angle pdb=" O4' DT D 18 " pdb=" C4' DT D 18 " pdb=" C3' DT D 18 " ideal model delta sigma weight residual 106.00 102.54 3.46 6.00e-01 2.78e+00 3.33e+01 angle pdb=" O4' DT D 24 " pdb=" C4' DT D 24 " pdb=" C3' DT D 24 " ideal model delta sigma weight residual 106.00 102.84 3.16 6.00e-01 2.78e+00 2.77e+01 angle pdb=" O4' DT C 30 " pdb=" C4' DT C 30 " pdb=" C3' DT C 30 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.43e+01 angle pdb=" C ARG A 929 " pdb=" N ASN A 930 " pdb=" CA ASN A 930 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.22e+01 ... (remaining 28858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12099 35.65 - 71.29: 454 71.29 - 106.93: 14 106.93 - 142.58: 1 142.58 - 178.22: 3 Dihedral angle restraints: 12571 sinusoidal: 5638 harmonic: 6933 Sorted by residual: dihedral pdb=" CA ARG A 247 " pdb=" C ARG A 247 " pdb=" N THR A 248 " pdb=" CA THR A 248 " ideal model delta harmonic sigma weight residual 180.00 -151.97 -28.03 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ARG B 247 " pdb=" C ARG B 247 " pdb=" N THR B 248 " pdb=" CA THR B 248 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR A1062 " pdb=" C THR A1062 " pdb=" N ALA A1063 " pdb=" CA ALA A1063 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 12568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2629 0.077 - 0.153: 531 0.153 - 0.230: 44 0.230 - 0.306: 7 0.306 - 0.383: 4 Chirality restraints: 3215 Sorted by residual: chirality pdb=" C3' DT C 44 " pdb=" C4' DT C 44 " pdb=" O3' DT C 44 " pdb=" C2' DT C 44 " both_signs ideal model delta sigma weight residual False -2.73 -2.35 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB ILE A 963 " pdb=" CA ILE A 963 " pdb=" CG1 ILE A 963 " pdb=" CG2 ILE A 963 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C3' DA C 49 " pdb=" C4' DA C 49 " pdb=" O3' DA C 49 " pdb=" C2' DA C 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 3212 not shown) Planarity restraints: 3397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1170 " -0.026 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP B1170 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP B1170 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1170 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1170 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1170 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1170 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B1170 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1170 " -0.025 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP A1170 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A1170 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A1170 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1170 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1170 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1170 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A1170 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 531 " 0.037 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR A 531 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 531 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 531 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 531 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 531 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 531 " 0.007 2.00e-02 2.50e+03 ... (remaining 3394 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 20 2.18 - 2.86: 6930 2.86 - 3.54: 26878 3.54 - 4.22: 49374 4.22 - 4.90: 83515 Nonbonded interactions: 166717 Sorted by model distance: nonbonded pdb=" N GLY A 855 " pdb=" OP1 DA C 39 " model vdw 1.497 3.120 nonbonded pdb=" NH1 ARG A 344 " pdb=" NH1 ARG B 344 " model vdw 1.624 3.200 nonbonded pdb=" OD1 ASN A 851 " pdb=" O4' DG D 15 " model vdw 1.698 3.040 nonbonded pdb=" OE2 GLU A 854 " pdb=" C5' DC C 38 " model vdw 1.822 3.440 nonbonded pdb=" O TRP A 856 " pdb=" C4' DA C 39 " model vdw 1.883 3.470 ... (remaining 166712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 403 or resid 414 through 1192)) selection = (chain 'B' and (resid 3 through 403 or resid 408 or resid 415 through 1192)) } ncs_group { reference = (chain 'C' and (resid 14 through 18 or resid 20 through 22 or resid 24 through 3 \ 9 or resid 41 through 43 or resid 45 through 49 or resid 51)) selection = (chain 'D' and (resid 4 through 8 or resid 10 through 12 or resid 14 through 29 \ or resid 31 through 33 or resid 35 through 39 or resid 41)) } 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.930 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4475 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 : 0.008 0.080 21107 Z= 0.446 Angle : 0.990 16.211 28863 Z= 0.590 Chirality : 0.060 0.383 3215 Planarity : 0.007 0.077 3397 Dihedral : 16.569 178.224 8109 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.23 % Rotamer: Outliers : 0.68 % Allowed : 7.50 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.15), residues: 2359 helix: -1.95 (0.13), residues: 972 sheet: -1.25 (0.28), residues: 349 loop : -1.91 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B1039 TYR 0.060 0.003 TYR A 531 PHE 0.026 0.003 PHE B 739 TRP 0.071 0.004 TRP B1170 HIS 0.014 0.003 HIS B 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.45 (21107) covalent geometry : angle 0.98973 / 0.59 (28863) hydrogen bonds : bond 0.16766 / 11.51 ( 931) hydrogen bonds : angle 7.03496 / 4.95 ( 2595) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 448 time to evaluate : 0.655 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.8471 (tp) cc_final: 0.8257 (tp) REVERT: A 576 LEU cc_start: 0.7165 (tp) cc_final: 0.6889 (tp) REVERT: A 721 ILE cc_start: 0.9196 (mt) cc_final: 0.8747 (mt) REVERT: A 722 LEU cc_start: 0.9204 (tp) cc_final: 0.8975 (tp) REVERT: A 776 TYR cc_start: 0.7521 (m-80) cc_final: 0.7292 (m-80) REVERT: A 836 TYR cc_start: 0.6422 (p90) cc_final: 0.6220 (p90) REVERT: A 838 VAL cc_start: 0.8600 (t) cc_final: 0.8110 (p) REVERT: A 848 TYR cc_start: 0.5381 (m-80) cc_final: 0.5099 (m-10) REVERT: B 392 MET cc_start: 0.0464 (mmm) cc_final: 0.0234 (mmm) REVERT: B 446 LEU cc_start: 0.8713 (mt) cc_final: 0.8383 (mt) REVERT: B 541 ASP cc_start: 0.7601 (p0) cc_final: 0.7140 (p0) REVERT: B 573 LEU cc_start: 0.7945 (tm) cc_final: 0.7643 (tm) REVERT: B 621 ASP cc_start: 0.8433 (t0) cc_final: 0.8228 (t70) REVERT: B 722 LEU cc_start: 0.9067 (tp) cc_final: 0.8834 (tp) REVERT: B 939 LEU cc_start: 0.8310 (mt) cc_final: 0.7883 (mt) REVERT: B 1181 ILE cc_start: 0.8715 (mt) cc_final: 0.8458 (mm) outliers start: 14 outliers final: 1 residues processed: 462 average time/residue: 0.1680 time to fit residues: 114.5666 Evaluate side-chains 246 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 566 HIS A 677 GLN A 753 HIS A 883 HIS ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 175 GLN B 283 HIS B 483 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 HIS B 692 GLN B 706 GLN B 748 HIS ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 GLN B 892 HIS B 905 ASN B1069 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.079545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.052581 restraints weight = 163806.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054434 restraints weight = 106670.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.055591 restraints weight = 76565.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.056698 restraints weight = 58933.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.057160 restraints weight = 47296.689| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 21107 Z= 0.179 Angle : 0.699 15.389 28863 Z= 0.383 Chirality : 0.047 0.275 3215 Planarity : 0.005 0.051 3397 Dihedral : 17.615 172.730 3463 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.16), residues: 2359 helix: -0.39 (0.16), residues: 979 sheet: -0.55 (0.28), residues: 338 loop : -1.39 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 571 TYR 0.030 0.002 TYR A 698 PHE 0.028 0.002 PHE B 317 TRP 0.028 0.002 TRP B1170 HIS 0.009 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (21107) covalent geometry : angle 0.69858 / 0.38 (28863) hydrogen bonds : bond 0.06514 / 4.41 ( 931) hydrogen bonds : angle 5.44982 / 3.89 ( 2595) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.598 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 MET cc_start: -0.5951 (mmm) cc_final: -0.6346 (mmm) REVERT: A 542 LEU cc_start: 0.9077 (mt) cc_final: 0.8862 (mt) REVERT: A 586 MET cc_start: 0.8839 (mmm) cc_final: 0.8615 (tpp) REVERT: A 629 PHE cc_start: 0.9611 (m-10) cc_final: 0.9320 (m-10) REVERT: A 698 TYR cc_start: 0.9468 (t80) cc_final: 0.8809 (t80) REVERT: A 775 LEU cc_start: 0.9314 (tp) cc_final: 0.8915 (tp) REVERT: A 776 TYR cc_start: 0.9205 (m-80) cc_final: 0.9005 (m-80) REVERT: A 846 MET cc_start: 0.9640 (mtp) cc_final: 0.9363 (mtt) REVERT: A 854 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9074 (mm-30) REVERT: A 897 LEU cc_start: 0.9120 (tp) cc_final: 0.8813 (tp) REVERT: A 957 MET cc_start: 0.9108 (mmp) cc_final: 0.8788 (mmm) REVERT: A 962 GLU cc_start: 0.8409 (tp30) cc_final: 0.8082 (tp30) REVERT: A 988 GLU cc_start: 0.9074 (mp0) cc_final: 0.8457 (pm20) REVERT: A 1078 HIS cc_start: 0.9592 (t70) cc_final: 0.9355 (t70) REVERT: A 1129 GLN cc_start: 0.9205 (mt0) cc_final: 0.9004 (mt0) REVERT: B 18 MET cc_start: -0.0427 (ptt) cc_final: -0.1896 (mmt) REVERT: B 447 ARG cc_start: 0.9310 (mtm-85) cc_final: 0.9103 (ptp90) REVERT: B 502 ASN cc_start: 0.8861 (t0) cc_final: 0.8553 (t0) REVERT: B 573 LEU cc_start: 0.8733 (tt) cc_final: 0.8488 (tp) REVERT: B 576 LEU cc_start: 0.9134 (tp) cc_final: 0.8874 (tp) REVERT: B 586 MET cc_start: 0.8269 (mmm) cc_final: 0.7962 (mmm) REVERT: B 606 LEU cc_start: 0.8569 (tp) cc_final: 0.8273 (mm) REVERT: B 621 ASP cc_start: 0.9677 (t0) cc_final: 0.9439 (t70) REVERT: B 628 MET cc_start: 0.9359 (mtm) cc_final: 0.9124 (mtt) REVERT: B 761 SER cc_start: 0.9817 (m) cc_final: 0.9557 (p) REVERT: B 790 LEU cc_start: 0.9386 (mp) cc_final: 0.8935 (tp) REVERT: B 813 MET cc_start: 0.9528 (tpt) cc_final: 0.8674 (tpp) REVERT: B 846 MET cc_start: 0.9257 (mtm) cc_final: 0.8868 (mtp) REVERT: B 939 LEU cc_start: 0.9396 (mt) cc_final: 0.9086 (mt) REVERT: B 966 TYR cc_start: 0.9044 (m-80) cc_final: 0.8815 (m-80) outliers start: 1 outliers final: 1 residues processed: 284 average time/residue: 0.1487 time to fit residues: 64.0934 Evaluate side-chains 214 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 189 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 2 optimal weight: 40.0000 chunk 149 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 115 optimal weight: 0.0370 chunk 61 optimal weight: 6.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN A 883 HIS ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.075530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.049178 restraints weight = 171956.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.050835 restraints weight = 111825.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.052062 restraints weight = 80742.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.052521 restraints weight = 62597.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.053505 restraints weight = 52667.136| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21107 Z= 0.174 Angle : 0.660 14.175 28863 Z= 0.357 Chirality : 0.047 0.245 3215 Planarity : 0.004 0.042 3397 Dihedral : 17.529 171.331 3463 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2359 helix: 0.43 (0.16), residues: 969 sheet: -0.61 (0.27), residues: 374 loop : -0.95 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 247 TYR 0.022 0.002 TYR A 698 PHE 0.024 0.002 PHE B 317 TRP 0.029 0.002 TRP B1170 HIS 0.008 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (21107) covalent geometry : angle 0.66019 / 0.36 (28863) hydrogen bonds : bond 0.05745 / 3.81 ( 931) hydrogen bonds : angle 5.17645 / 3.70 ( 2595) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.587 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 MET cc_start: -0.5779 (mmm) cc_final: -0.6076 (mmm) REVERT: A 542 LEU cc_start: 0.9135 (mt) cc_final: 0.8907 (mt) REVERT: A 586 MET cc_start: 0.8896 (mmm) cc_final: 0.8652 (tpp) REVERT: A 629 PHE cc_start: 0.9632 (m-10) cc_final: 0.9431 (m-10) REVERT: A 684 ARG cc_start: 0.9721 (mtm180) cc_final: 0.9423 (mmm-85) REVERT: A 698 TYR cc_start: 0.9527 (t80) cc_final: 0.8619 (t80) REVERT: A 704 GLU cc_start: 0.9601 (tp30) cc_final: 0.9160 (tp30) REVERT: A 775 LEU cc_start: 0.9387 (tp) cc_final: 0.9105 (tp) REVERT: A 843 LEU cc_start: 0.9740 (mm) cc_final: 0.9306 (mm) REVERT: A 846 MET cc_start: 0.9584 (mtp) cc_final: 0.9316 (mtt) REVERT: A 854 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8873 (mm-30) REVERT: A 957 MET cc_start: 0.9222 (mmp) cc_final: 0.8801 (mmm) REVERT: A 962 GLU cc_start: 0.8515 (tp30) cc_final: 0.8120 (tp30) REVERT: A 1078 HIS cc_start: 0.9607 (t70) cc_final: 0.9395 (t70) REVERT: A 1128 LEU cc_start: 0.8954 (mt) cc_final: 0.8254 (mm) REVERT: A 1174 ILE cc_start: 0.9650 (mm) cc_final: 0.9279 (mm) REVERT: A 1178 GLU cc_start: 0.9665 (tt0) cc_final: 0.9283 (pt0) REVERT: B 18 MET cc_start: 0.0181 (ptt) cc_final: -0.1627 (mmt) REVERT: B 447 ARG cc_start: 0.9357 (mtm-85) cc_final: 0.9090 (mtt90) REVERT: B 573 LEU cc_start: 0.8777 (tt) cc_final: 0.8355 (tp) REVERT: B 576 LEU cc_start: 0.9089 (tp) cc_final: 0.8703 (tp) REVERT: B 586 MET cc_start: 0.8316 (mmm) cc_final: 0.8021 (mmm) REVERT: B 621 ASP cc_start: 0.9738 (t0) cc_final: 0.9467 (t70) REVERT: B 629 PHE cc_start: 0.9447 (m-80) cc_final: 0.9213 (m-10) REVERT: B 692 GLN cc_start: 0.9402 (pt0) cc_final: 0.9106 (pp30) REVERT: B 704 GLU cc_start: 0.9244 (tm-30) cc_final: 0.9040 (tm-30) REVERT: B 790 LEU cc_start: 0.9417 (mp) cc_final: 0.9075 (tt) REVERT: B 813 MET cc_start: 0.9518 (tpt) cc_final: 0.8693 (tpp) REVERT: B 845 ILE cc_start: 0.9176 (mm) cc_final: 0.8888 (mp) REVERT: B 846 MET cc_start: 0.9344 (mtm) cc_final: 0.8926 (mtp) outliers start: 2 outliers final: 1 residues processed: 251 average time/residue: 0.1373 time to fit residues: 53.4355 Evaluate side-chains 194 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 286 GLN B 506 GLN B 905 ASN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.072577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046623 restraints weight = 175953.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.048189 restraints weight = 113726.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.049435 restraints weight = 82309.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.049843 restraints weight = 63662.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.050733 restraints weight = 53318.793| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21107 Z= 0.190 Angle : 0.670 12.723 28863 Z= 0.358 Chirality : 0.047 0.580 3215 Planarity : 0.004 0.044 3397 Dihedral : 17.538 172.076 3463 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2359 helix: 0.63 (0.16), residues: 972 sheet: -0.61 (0.28), residues: 373 loop : -0.69 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 447 TYR 0.025 0.002 TYR A1079 PHE 0.039 0.002 PHE B 388 TRP 0.015 0.001 TRP B1189 HIS 0.007 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (21107) covalent geometry : angle 0.66977 / 0.36 (28863) hydrogen bonds : bond 0.05404 / 3.57 ( 931) hydrogen bonds : angle 5.14723 / 3.70 ( 2595) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.639 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: A 445 LEU cc_start: 0.9812 (tt) cc_final: 0.9559 (tt) REVERT: A 446 LEU cc_start: 0.9633 (mt) cc_final: 0.9323 (mt) REVERT: A 475 MET cc_start: 0.7509 (mmp) cc_final: 0.6512 (tpp) REVERT: A 483 ASN cc_start: 0.8905 (p0) cc_final: 0.8590 (m-40) REVERT: A 586 MET cc_start: 0.8884 (mmm) cc_final: 0.8653 (tpp) REVERT: A 617 LEU cc_start: 0.9578 (tp) cc_final: 0.8863 (tp) REVERT: A 635 MET cc_start: 0.9470 (ptp) cc_final: 0.9146 (ptp) REVERT: A 684 ARG cc_start: 0.9721 (mtm180) cc_final: 0.9452 (mmm-85) REVERT: A 698 TYR cc_start: 0.9520 (t80) cc_final: 0.8563 (t80) REVERT: A 701 ASP cc_start: 0.9720 (t70) cc_final: 0.9404 (t0) REVERT: A 704 GLU cc_start: 0.9547 (tp30) cc_final: 0.9137 (tp30) REVERT: A 775 LEU cc_start: 0.9465 (tp) cc_final: 0.8854 (tp) REVERT: A 776 TYR cc_start: 0.9287 (m-80) cc_final: 0.8960 (m-80) REVERT: A 843 LEU cc_start: 0.9714 (mm) cc_final: 0.9333 (mm) REVERT: A 846 MET cc_start: 0.9705 (mtp) cc_final: 0.9194 (mtt) REVERT: A 854 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9121 (mm-30) REVERT: A 897 LEU cc_start: 0.9192 (tp) cc_final: 0.8936 (tt) REVERT: A 957 MET cc_start: 0.9244 (mmp) cc_final: 0.8835 (mmm) REVERT: A 962 GLU cc_start: 0.8558 (tp30) cc_final: 0.8137 (tp30) REVERT: A 1042 LEU cc_start: 0.9468 (mt) cc_final: 0.9234 (mt) REVERT: A 1128 LEU cc_start: 0.9025 (mt) cc_final: 0.8396 (mm) REVERT: A 1174 ILE cc_start: 0.9675 (mm) cc_final: 0.9274 (mm) REVERT: A 1178 GLU cc_start: 0.9676 (tt0) cc_final: 0.9300 (pt0) REVERT: B 18 MET cc_start: 0.0510 (ptt) cc_final: -0.1570 (mmp) REVERT: B 447 ARG cc_start: 0.9282 (mtm-85) cc_final: 0.8901 (mtt-85) REVERT: B 505 LEU cc_start: 0.9287 (pp) cc_final: 0.9086 (pp) REVERT: B 573 LEU cc_start: 0.8797 (tt) cc_final: 0.8562 (pp) REVERT: B 576 LEU cc_start: 0.9000 (tp) cc_final: 0.8609 (tp) REVERT: B 586 MET cc_start: 0.8436 (mmm) cc_final: 0.8110 (mmm) REVERT: B 606 LEU cc_start: 0.8577 (tp) cc_final: 0.8064 (mm) REVERT: B 621 ASP cc_start: 0.9745 (t0) cc_final: 0.9479 (t70) REVERT: B 629 PHE cc_start: 0.9477 (m-80) cc_final: 0.9262 (m-10) REVERT: B 764 LYS cc_start: 0.9574 (mtpt) cc_final: 0.9276 (ttpt) REVERT: B 790 LEU cc_start: 0.9399 (mp) cc_final: 0.9067 (tt) REVERT: B 813 MET cc_start: 0.9552 (tpt) cc_final: 0.8666 (tpp) REVERT: B 846 MET cc_start: 0.9354 (mtm) cc_final: 0.8737 (mtp) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.1421 time to fit residues: 51.0281 Evaluate side-chains 181 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 150 optimal weight: 5.9990 chunk 155 optimal weight: 40.0000 chunk 93 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 119 optimal weight: 0.0980 chunk 106 optimal weight: 20.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.070818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.044901 restraints weight = 176178.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.046493 restraints weight = 114471.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047594 restraints weight = 83178.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.047986 restraints weight = 64677.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.048918 restraints weight = 54409.325| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21107 Z= 0.185 Angle : 0.658 12.030 28863 Z= 0.354 Chirality : 0.046 0.325 3215 Planarity : 0.004 0.062 3397 Dihedral : 17.523 170.145 3463 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2359 helix: 0.68 (0.17), residues: 985 sheet: -0.50 (0.28), residues: 382 loop : -0.61 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 683 TYR 0.022 0.002 TYR B 614 PHE 0.028 0.002 PHE B 590 TRP 0.012 0.001 TRP A1170 HIS 0.011 0.001 HIS A 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (21107) covalent geometry : angle 0.65807 / 0.35 (28863) hydrogen bonds : bond 0.05168 / 3.36 ( 931) hydrogen bonds : angle 5.17022 / 3.72 ( 2595) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.3228 (tmm) cc_final: 0.2301 (tmm) REVERT: A 446 LEU cc_start: 0.9707 (mt) cc_final: 0.9480 (mt) REVERT: A 483 ASN cc_start: 0.9021 (p0) cc_final: 0.8598 (m-40) REVERT: A 586 MET cc_start: 0.8947 (mmm) cc_final: 0.8704 (tpp) REVERT: A 617 LEU cc_start: 0.9346 (tp) cc_final: 0.8950 (tp) REVERT: A 698 TYR cc_start: 0.9443 (t80) cc_final: 0.8515 (t80) REVERT: A 701 ASP cc_start: 0.9675 (t70) cc_final: 0.9434 (t0) REVERT: A 704 GLU cc_start: 0.9535 (tp30) cc_final: 0.9059 (tp30) REVERT: A 775 LEU cc_start: 0.9505 (tp) cc_final: 0.8854 (tp) REVERT: A 776 TYR cc_start: 0.9263 (m-80) cc_final: 0.8826 (m-80) REVERT: A 843 LEU cc_start: 0.9669 (mm) cc_final: 0.9332 (mm) REVERT: A 846 MET cc_start: 0.9700 (mtp) cc_final: 0.9158 (mtt) REVERT: A 854 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9075 (mm-30) REVERT: A 897 LEU cc_start: 0.9242 (tp) cc_final: 0.8970 (tt) REVERT: A 957 MET cc_start: 0.9219 (mmp) cc_final: 0.8809 (mmm) REVERT: A 962 GLU cc_start: 0.8615 (tp30) cc_final: 0.8131 (tp30) REVERT: A 1042 LEU cc_start: 0.9488 (mt) cc_final: 0.9227 (mt) REVERT: A 1174 ILE cc_start: 0.9677 (mm) cc_final: 0.9303 (mm) REVERT: A 1178 GLU cc_start: 0.9682 (tt0) cc_final: 0.9316 (pt0) REVERT: B 18 MET cc_start: 0.0329 (ptt) cc_final: -0.1350 (mmt) REVERT: B 447 ARG cc_start: 0.9280 (mtm-85) cc_final: 0.8891 (mtt-85) REVERT: B 502 ASN cc_start: 0.9078 (t0) cc_final: 0.8813 (t0) REVERT: B 541 ASP cc_start: 0.8652 (p0) cc_final: 0.8230 (p0) REVERT: B 573 LEU cc_start: 0.8796 (tt) cc_final: 0.8552 (pp) REVERT: B 576 LEU cc_start: 0.8719 (tp) cc_final: 0.8488 (tp) REVERT: B 586 MET cc_start: 0.8421 (mmm) cc_final: 0.8139 (mmm) REVERT: B 606 LEU cc_start: 0.8608 (tp) cc_final: 0.8172 (mm) REVERT: B 621 ASP cc_start: 0.9729 (t0) cc_final: 0.9479 (t70) REVERT: B 629 PHE cc_start: 0.9451 (m-80) cc_final: 0.9244 (m-10) REVERT: B 755 ASP cc_start: 0.9629 (p0) cc_final: 0.9256 (p0) REVERT: B 790 LEU cc_start: 0.9481 (mp) cc_final: 0.9088 (tt) REVERT: B 813 MET cc_start: 0.9533 (tpt) cc_final: 0.8691 (tpp) REVERT: B 828 ASP cc_start: 0.9304 (m-30) cc_final: 0.8442 (t0) REVERT: B 838 VAL cc_start: 0.9482 (t) cc_final: 0.9190 (p) REVERT: B 846 MET cc_start: 0.9345 (mtm) cc_final: 0.8827 (mtp) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1259 time to fit residues: 43.1604 Evaluate side-chains 175 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 195 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 145 optimal weight: 30.0000 chunk 176 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 chunk 127 optimal weight: 50.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS A 506 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 175 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** 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 = 0.3674 r_free = 0.3674 target = 0.068171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.042804 restraints weight = 181281.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044316 restraints weight = 118366.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.045380 restraints weight = 85222.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.046179 restraints weight = 66298.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046414 restraints weight = 54388.787| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 21107 Z= 0.210 Angle : 0.676 11.118 28863 Z= 0.365 Chirality : 0.047 0.300 3215 Planarity : 0.005 0.115 3397 Dihedral : 17.587 168.892 3463 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.10 % Allowed : 2.23 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2359 helix: 0.60 (0.16), residues: 998 sheet: -0.48 (0.28), residues: 381 loop : -0.50 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 929 TYR 0.020 0.002 TYR A 698 PHE 0.037 0.002 PHE B 596 TRP 0.019 0.002 TRP B1170 HIS 0.008 0.001 HIS B 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (21107) covalent geometry : angle 0.67571 / 0.36 (28863) hydrogen bonds : bond 0.05226 / 3.44 ( 931) hydrogen bonds : angle 5.23190 / 3.76 ( 2595) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.3316 (tmm) cc_final: 0.2935 (tmm) REVERT: A 446 LEU cc_start: 0.9759 (mt) cc_final: 0.9521 (mt) REVERT: A 467 MET cc_start: 0.9363 (mtp) cc_final: 0.9147 (mtt) REVERT: A 483 ASN cc_start: 0.8998 (p0) cc_final: 0.8600 (m-40) REVERT: A 586 MET cc_start: 0.8988 (mmm) cc_final: 0.8762 (tpp) REVERT: A 617 LEU cc_start: 0.9392 (tp) cc_final: 0.9047 (tp) REVERT: A 698 TYR cc_start: 0.9477 (t80) cc_final: 0.8612 (t80) REVERT: A 704 GLU cc_start: 0.9528 (tp30) cc_final: 0.9077 (tp30) REVERT: A 756 MET cc_start: 0.9713 (mpp) cc_final: 0.9260 (tpt) REVERT: A 775 LEU cc_start: 0.9426 (tp) cc_final: 0.9047 (tp) REVERT: A 776 TYR cc_start: 0.9243 (m-80) cc_final: 0.9021 (m-80) REVERT: A 843 LEU cc_start: 0.9677 (mm) cc_final: 0.9356 (mm) REVERT: A 846 MET cc_start: 0.9726 (mtp) cc_final: 0.9267 (mtt) REVERT: A 854 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9127 (mm-30) REVERT: A 957 MET cc_start: 0.9253 (mmp) cc_final: 0.8789 (mmm) REVERT: A 962 GLU cc_start: 0.8669 (tp30) cc_final: 0.8141 (tp30) REVERT: A 1042 LEU cc_start: 0.9521 (mt) cc_final: 0.9268 (mt) REVERT: A 1174 ILE cc_start: 0.9689 (mm) cc_final: 0.9322 (mm) REVERT: A 1178 GLU cc_start: 0.9669 (tt0) cc_final: 0.9352 (pt0) REVERT: B 32 MET cc_start: 0.4546 (tpt) cc_final: 0.3544 (tpt) REVERT: B 447 ARG cc_start: 0.9258 (mtm-85) cc_final: 0.8892 (mtt-85) REVERT: B 475 MET cc_start: 0.6544 (tpt) cc_final: 0.5516 (tpt) REVERT: B 502 ASN cc_start: 0.9155 (t0) cc_final: 0.8885 (t0) REVERT: B 573 LEU cc_start: 0.8855 (tt) cc_final: 0.8620 (pp) REVERT: B 586 MET cc_start: 0.8431 (mmm) cc_final: 0.8143 (mmm) REVERT: B 621 ASP cc_start: 0.9730 (t0) cc_final: 0.9472 (t70) REVERT: B 764 LYS cc_start: 0.9592 (mtpt) cc_final: 0.9372 (ttpt) REVERT: B 790 LEU cc_start: 0.9465 (mp) cc_final: 0.9064 (tt) REVERT: B 813 MET cc_start: 0.9518 (tpt) cc_final: 0.8695 (tpp) REVERT: B 828 ASP cc_start: 0.9362 (m-30) cc_final: 0.8411 (t0) REVERT: B 838 VAL cc_start: 0.9351 (t) cc_final: 0.8989 (p) REVERT: B 846 MET cc_start: 0.9305 (mtm) cc_final: 0.8790 (mtp) REVERT: B 957 MET cc_start: 0.8981 (mmp) cc_final: 0.8722 (mmm) outliers start: 2 outliers final: 2 residues processed: 213 average time/residue: 0.1370 time to fit residues: 46.5489 Evaluate side-chains 164 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 60 optimal weight: 0.0970 chunk 113 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 151 optimal weight: 0.1980 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 208 optimal weight: 0.0040 chunk 19 optimal weight: 40.0000 chunk 141 optimal weight: 30.0000 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.070603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.044498 restraints weight = 171240.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.046030 restraints weight = 111444.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.047202 restraints weight = 80528.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.048044 restraints weight = 62122.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.048417 restraints weight = 50915.160| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21107 Z= 0.128 Angle : 0.610 11.891 28863 Z= 0.325 Chirality : 0.046 0.291 3215 Planarity : 0.004 0.043 3397 Dihedral : 17.496 167.454 3463 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2359 helix: 0.78 (0.17), residues: 1000 sheet: -0.46 (0.27), residues: 395 loop : -0.45 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 683 TYR 0.017 0.001 TYR A 698 PHE 0.044 0.002 PHE B 596 TRP 0.016 0.001 TRP A 157 HIS 0.015 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (21107) covalent geometry : angle 0.61044 / 0.32 (28863) hydrogen bonds : bond 0.04716 / 3.14 ( 931) hydrogen bonds : angle 5.04318 / 3.65 ( 2595) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.784 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: A 18 MET cc_start: 0.3629 (tmm) cc_final: 0.2873 (tmm) REVERT: A 446 LEU cc_start: 0.9793 (mt) cc_final: 0.9567 (mt) REVERT: A 475 MET cc_start: 0.7258 (mmp) cc_final: 0.6155 (tpp) REVERT: A 483 ASN cc_start: 0.8992 (p0) cc_final: 0.8635 (m-40) REVERT: A 586 MET cc_start: 0.8971 (mmm) cc_final: 0.8721 (tpp) REVERT: A 617 LEU cc_start: 0.9362 (tp) cc_final: 0.8959 (tp) REVERT: A 629 PHE cc_start: 0.9572 (m-10) cc_final: 0.9319 (m-10) REVERT: A 698 TYR cc_start: 0.9464 (t80) cc_final: 0.8435 (t80) REVERT: A 701 ASP cc_start: 0.9790 (t0) cc_final: 0.9543 (t0) REVERT: A 704 GLU cc_start: 0.9537 (tp30) cc_final: 0.9018 (tp30) REVERT: A 756 MET cc_start: 0.9718 (mpp) cc_final: 0.9202 (tpp) REVERT: A 764 LYS cc_start: 0.9685 (mtpt) cc_final: 0.9452 (mmmm) REVERT: A 775 LEU cc_start: 0.9421 (tp) cc_final: 0.9174 (tp) REVERT: A 843 LEU cc_start: 0.9727 (mm) cc_final: 0.9364 (mm) REVERT: A 854 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8535 (mm-30) REVERT: A 957 MET cc_start: 0.9254 (mmp) cc_final: 0.8783 (mmm) REVERT: A 962 GLU cc_start: 0.8583 (tp30) cc_final: 0.8047 (tp30) REVERT: A 1042 LEU cc_start: 0.9526 (mt) cc_final: 0.9230 (mt) REVERT: A 1174 ILE cc_start: 0.9692 (mm) cc_final: 0.9304 (mm) REVERT: A 1178 GLU cc_start: 0.9646 (tt0) cc_final: 0.9309 (pt0) REVERT: B 18 MET cc_start: 0.1816 (ppp) cc_final: 0.0042 (mmp) REVERT: B 475 MET cc_start: 0.6661 (tpt) cc_final: 0.5876 (tpt) REVERT: B 502 ASN cc_start: 0.9080 (t0) cc_final: 0.8804 (t0) REVERT: B 573 LEU cc_start: 0.8836 (tt) cc_final: 0.8429 (tp) REVERT: B 586 MET cc_start: 0.8426 (mmm) cc_final: 0.8121 (mmm) REVERT: B 621 ASP cc_start: 0.9738 (t0) cc_final: 0.9517 (t70) REVERT: B 722 LEU cc_start: 0.9706 (mm) cc_final: 0.9457 (mt) REVERT: B 764 LYS cc_start: 0.9578 (mtpt) cc_final: 0.9359 (ttpt) REVERT: B 813 MET cc_start: 0.9539 (tpt) cc_final: 0.8767 (tpp) REVERT: B 828 ASP cc_start: 0.9366 (m-30) cc_final: 0.8299 (t0) REVERT: B 838 VAL cc_start: 0.9284 (t) cc_final: 0.8909 (p) REVERT: B 845 ILE cc_start: 0.9366 (mm) cc_final: 0.9140 (mp) REVERT: B 846 MET cc_start: 0.9285 (mtm) cc_final: 0.8766 (mtp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1455 time to fit residues: 50.3888 Evaluate side-chains 172 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.070616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.044451 restraints weight = 173679.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046023 restraints weight = 112202.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.047196 restraints weight = 80533.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.047585 restraints weight = 62584.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.048545 restraints weight = 52708.545| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21107 Z= 0.124 Angle : 0.596 10.390 28863 Z= 0.317 Chirality : 0.045 0.424 3215 Planarity : 0.004 0.044 3397 Dihedral : 17.413 167.096 3463 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2359 helix: 0.95 (0.17), residues: 993 sheet: -0.45 (0.27), residues: 397 loop : -0.36 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 831 TYR 0.015 0.001 TYR B 824 PHE 0.034 0.001 PHE B 596 TRP 0.016 0.001 TRP B 820 HIS 0.011 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (21107) covalent geometry : angle 0.59576 / 0.32 (28863) hydrogen bonds : bond 0.04583 / 3.04 ( 931) hydrogen bonds : angle 4.98932 / 3.63 ( 2595) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.3676 (tmm) cc_final: 0.3381 (tmm) REVERT: A 446 LEU cc_start: 0.9813 (mt) cc_final: 0.9598 (mt) REVERT: A 474 ILE cc_start: 0.9190 (mp) cc_final: 0.8895 (pt) REVERT: A 475 MET cc_start: 0.7462 (mmp) cc_final: 0.6238 (tpp) REVERT: A 586 MET cc_start: 0.8967 (mmm) cc_final: 0.8714 (tpp) REVERT: A 617 LEU cc_start: 0.9362 (tp) cc_final: 0.8971 (tp) REVERT: A 629 PHE cc_start: 0.9567 (m-10) cc_final: 0.9287 (m-10) REVERT: A 698 TYR cc_start: 0.9452 (t80) cc_final: 0.8411 (t80) REVERT: A 704 GLU cc_start: 0.9525 (tp30) cc_final: 0.9011 (tp30) REVERT: A 756 MET cc_start: 0.9726 (mpp) cc_final: 0.9223 (tpp) REVERT: A 764 LYS cc_start: 0.9667 (mtpt) cc_final: 0.9429 (mmmm) REVERT: A 775 LEU cc_start: 0.9420 (tp) cc_final: 0.8934 (tp) REVERT: A 776 TYR cc_start: 0.8865 (m-80) cc_final: 0.8506 (m-80) REVERT: A 846 MET cc_start: 0.9624 (mtm) cc_final: 0.9282 (mtt) REVERT: A 854 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9085 (mm-30) REVERT: A 957 MET cc_start: 0.9246 (mmp) cc_final: 0.8763 (mmm) REVERT: A 962 GLU cc_start: 0.8575 (tp30) cc_final: 0.8029 (tp30) REVERT: A 1174 ILE cc_start: 0.9681 (mm) cc_final: 0.9298 (mm) REVERT: A 1178 GLU cc_start: 0.9661 (tt0) cc_final: 0.9326 (pt0) REVERT: B 32 MET cc_start: 0.4835 (tpt) cc_final: 0.4088 (tpp) REVERT: B 447 ARG cc_start: 0.9281 (mtm-85) cc_final: 0.9068 (mtm-85) REVERT: B 467 MET cc_start: 0.9156 (mtm) cc_final: 0.8793 (mpp) REVERT: B 475 MET cc_start: 0.6590 (tpt) cc_final: 0.6048 (tpt) REVERT: B 502 ASN cc_start: 0.9053 (t0) cc_final: 0.8802 (t0) REVERT: B 573 LEU cc_start: 0.8833 (tt) cc_final: 0.8444 (tp) REVERT: B 586 MET cc_start: 0.8441 (mmm) cc_final: 0.8125 (mmm) REVERT: B 621 ASP cc_start: 0.9736 (t0) cc_final: 0.9520 (t70) REVERT: B 722 LEU cc_start: 0.9642 (mm) cc_final: 0.9393 (mt) REVERT: B 764 LYS cc_start: 0.9586 (mtpt) cc_final: 0.9363 (ttpt) REVERT: B 813 MET cc_start: 0.9525 (tpt) cc_final: 0.8753 (tpp) REVERT: B 828 ASP cc_start: 0.9369 (m-30) cc_final: 0.8285 (t0) REVERT: B 838 VAL cc_start: 0.9322 (t) cc_final: 0.8952 (p) REVERT: B 846 MET cc_start: 0.9305 (mtm) cc_final: 0.8760 (mtp) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1350 time to fit residues: 46.4293 Evaluate side-chains 171 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 174 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 158 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 300 HIS A 381 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 381 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B1099 HIS ** 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 = 0.3697 r_free = 0.3697 target = 0.069139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.043476 restraints weight = 178151.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.045003 restraints weight = 115402.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046094 restraints weight = 82860.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.046480 restraints weight = 64536.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.047411 restraints weight = 54305.843| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21107 Z= 0.151 Angle : 0.607 10.893 28863 Z= 0.326 Chirality : 0.045 0.371 3215 Planarity : 0.004 0.040 3397 Dihedral : 17.404 168.236 3463 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2359 helix: 0.92 (0.17), residues: 993 sheet: -0.37 (0.27), residues: 391 loop : -0.31 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 578 TYR 0.018 0.001 TYR B 698 PHE 0.039 0.002 PHE B 590 TRP 0.014 0.001 TRP A 157 HIS 0.010 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (21107) covalent geometry : angle 0.60699 / 0.33 (28863) hydrogen bonds : bond 0.04644 / 3.05 ( 931) hydrogen bonds : angle 5.00467 / 3.65 ( 2595) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.841 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: A 18 MET cc_start: 0.3902 (tmm) cc_final: 0.3630 (tmm) REVERT: A 446 LEU cc_start: 0.9811 (mt) cc_final: 0.9581 (mt) REVERT: A 475 MET cc_start: 0.7804 (mmp) cc_final: 0.6711 (tpp) REVERT: A 483 ASN cc_start: 0.8973 (p0) cc_final: 0.8602 (m-40) REVERT: A 586 MET cc_start: 0.8998 (mmm) cc_final: 0.8758 (tpp) REVERT: A 617 LEU cc_start: 0.9390 (tp) cc_final: 0.9034 (tp) REVERT: A 629 PHE cc_start: 0.9584 (m-10) cc_final: 0.9311 (m-10) REVERT: A 698 TYR cc_start: 0.9479 (t80) cc_final: 0.8564 (t80) REVERT: A 704 GLU cc_start: 0.9519 (tp30) cc_final: 0.8999 (tp30) REVERT: A 756 MET cc_start: 0.9730 (mpp) cc_final: 0.9238 (tpp) REVERT: A 764 LYS cc_start: 0.9672 (mtpt) cc_final: 0.9463 (mmmm) REVERT: A 775 LEU cc_start: 0.9384 (tp) cc_final: 0.9110 (tp) REVERT: A 854 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9151 (mm-30) REVERT: A 957 MET cc_start: 0.9234 (mmp) cc_final: 0.8740 (mmm) REVERT: A 962 GLU cc_start: 0.8555 (tp30) cc_final: 0.8029 (tp30) REVERT: A 1042 LEU cc_start: 0.9584 (mt) cc_final: 0.9366 (mt) REVERT: A 1174 ILE cc_start: 0.9686 (mm) cc_final: 0.9331 (mm) REVERT: A 1178 GLU cc_start: 0.9669 (tt0) cc_final: 0.9333 (pt0) REVERT: B 32 MET cc_start: 0.4876 (tpt) cc_final: 0.4090 (tpp) REVERT: B 447 ARG cc_start: 0.9261 (mtm-85) cc_final: 0.8902 (mtt-85) REVERT: B 475 MET cc_start: 0.7039 (tpt) cc_final: 0.6277 (tpt) REVERT: B 502 ASN cc_start: 0.9084 (t0) cc_final: 0.8816 (t0) REVERT: B 541 ASP cc_start: 0.8703 (p0) cc_final: 0.8387 (p0) REVERT: B 573 LEU cc_start: 0.8842 (tt) cc_final: 0.8467 (tp) REVERT: B 586 MET cc_start: 0.8450 (mmm) cc_final: 0.8121 (mmm) REVERT: B 621 ASP cc_start: 0.9726 (t0) cc_final: 0.9488 (t70) REVERT: B 698 TYR cc_start: 0.9567 (t80) cc_final: 0.9232 (t80) REVERT: B 764 LYS cc_start: 0.9604 (mtpt) cc_final: 0.9359 (ttpt) REVERT: B 813 MET cc_start: 0.9490 (tpt) cc_final: 0.8709 (tpp) REVERT: B 828 ASP cc_start: 0.9375 (m-30) cc_final: 0.8270 (t0) REVERT: B 838 VAL cc_start: 0.9371 (t) cc_final: 0.9017 (p) REVERT: B 841 LEU cc_start: 0.9821 (tp) cc_final: 0.9601 (tp) REVERT: B 845 ILE cc_start: 0.9231 (mm) cc_final: 0.8862 (mp) REVERT: B 846 MET cc_start: 0.9363 (mtm) cc_final: 0.8910 (mpp) REVERT: B 957 MET cc_start: 0.8962 (mmp) cc_final: 0.8700 (mmm) REVERT: B 1153 ASP cc_start: 0.9536 (t0) cc_final: 0.9199 (m-30) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1387 time to fit residues: 46.3323 Evaluate side-chains 162 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 92 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 144 optimal weight: 50.0000 chunk 170 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 115 optimal weight: 0.0020 chunk 225 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 176 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 overall best weight: 3.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.067293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.042013 restraints weight = 181011.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.043560 restraints weight = 118251.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044043 restraints weight = 85622.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.045159 restraints weight = 70153.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045498 restraints weight = 57478.907| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21107 Z= 0.181 Angle : 0.644 11.099 28863 Z= 0.346 Chirality : 0.046 0.320 3215 Planarity : 0.004 0.044 3397 Dihedral : 17.482 169.322 3463 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2359 helix: 0.87 (0.17), residues: 998 sheet: -0.42 (0.27), residues: 386 loop : -0.32 (0.22), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 683 TYR 0.024 0.002 TYR B 614 PHE 0.024 0.002 PHE B 590 TRP 0.014 0.002 TRP A1170 HIS 0.010 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (21107) covalent geometry : angle 0.64403 / 0.35 (28863) hydrogen bonds : bond 0.04802 / 3.13 ( 931) hydrogen bonds : angle 5.08044 / 3.72 ( 2595) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.3924 (tmm) cc_final: 0.3620 (tmm) REVERT: A 446 LEU cc_start: 0.9809 (mt) cc_final: 0.9539 (mt) REVERT: A 475 MET cc_start: 0.8118 (mmp) cc_final: 0.7505 (tpp) REVERT: A 617 LEU cc_start: 0.9346 (tp) cc_final: 0.8974 (tp) REVERT: A 629 PHE cc_start: 0.9602 (m-10) cc_final: 0.9350 (m-80) REVERT: A 698 TYR cc_start: 0.9457 (t80) cc_final: 0.8499 (t80) REVERT: A 701 ASP cc_start: 0.9774 (t0) cc_final: 0.9502 (t0) REVERT: A 704 GLU cc_start: 0.9502 (tp30) cc_final: 0.9008 (tp30) REVERT: A 756 MET cc_start: 0.9727 (mpp) cc_final: 0.9245 (tpp) REVERT: A 775 LEU cc_start: 0.9392 (tp) cc_final: 0.9102 (tp) REVERT: A 854 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9159 (mm-30) REVERT: A 957 MET cc_start: 0.9219 (mmp) cc_final: 0.8745 (mmm) REVERT: A 1042 LEU cc_start: 0.9585 (mt) cc_final: 0.9368 (mt) REVERT: B 32 MET cc_start: 0.5131 (tpt) cc_final: 0.4216 (tpp) REVERT: B 447 ARG cc_start: 0.9246 (mtm-85) cc_final: 0.8822 (mtt-85) REVERT: B 467 MET cc_start: 0.9260 (mtm) cc_final: 0.8822 (mpp) REVERT: B 475 MET cc_start: 0.7072 (tpt) cc_final: 0.6449 (tpt) REVERT: B 502 ASN cc_start: 0.9281 (t0) cc_final: 0.9020 (t0) REVERT: B 573 LEU cc_start: 0.8870 (tt) cc_final: 0.8524 (tp) REVERT: B 586 MET cc_start: 0.8517 (mmm) cc_final: 0.8174 (mmm) REVERT: B 621 ASP cc_start: 0.9719 (t0) cc_final: 0.9466 (t70) REVERT: B 813 MET cc_start: 0.9474 (tpt) cc_final: 0.8743 (tpp) REVERT: B 828 ASP cc_start: 0.9275 (m-30) cc_final: 0.8430 (t70) REVERT: B 838 VAL cc_start: 0.9407 (t) cc_final: 0.9061 (p) REVERT: B 845 ILE cc_start: 0.9296 (mm) cc_final: 0.9038 (pt) REVERT: B 846 MET cc_start: 0.9320 (mtm) cc_final: 0.8905 (mtp) REVERT: B 957 MET cc_start: 0.8957 (mmp) cc_final: 0.8745 (mmm) REVERT: B 1148 MET cc_start: 0.8898 (ptt) cc_final: 0.8593 (ptt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1420 time to fit residues: 45.8194 Evaluate side-chains 159 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 105 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 239 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.067711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.042430 restraints weight = 180748.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.043687 restraints weight = 117035.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.044899 restraints weight = 85955.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.045301 restraints weight = 66343.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.046123 restraints weight = 56091.888| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21107 Z= 0.143 Angle : 0.614 10.518 28863 Z= 0.330 Chirality : 0.045 0.309 3215 Planarity : 0.004 0.043 3397 Dihedral : 17.495 169.017 3463 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2359 helix: 0.88 (0.17), residues: 1012 sheet: -0.33 (0.28), residues: 387 loop : -0.39 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B1151 TYR 0.030 0.002 TYR B 698 PHE 0.019 0.002 PHE B 388 TRP 0.014 0.001 TRP A 157 HIS 0.008 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (21107) covalent geometry : angle 0.61408 / 0.33 (28863) hydrogen bonds : bond 0.04614 / 3.04 ( 931) hydrogen bonds : angle 5.02060 / 3.65 ( 2595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4032.83 seconds wall clock time: 70 minutes 33.31 seconds (4233.31 seconds total)