Starting phenix.real_space_refine on Sat Aug 8 03:04:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgm_37226/08_2026/8kgm_37226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgm_37226/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2026/8kgm_37226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2026/8kgm_37226.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2026/8kgm_37226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgm_37226/08_2026/8kgm_37226.cif" } 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-2.2rc3-6140/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: 4.54, per 1000 atoms: 0.22 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: 1.50 Conformation dependent library (CDL) restraints added in 941.5 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: 2.42 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: 4.78 Time building geometry restraints manager: 2.07 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.050 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- 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= 0.447 Angle : 0.991 16.211 28863 Z= 0.591 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 0.99056 / 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 : 0.815 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: A 434 LEU cc_start: 0.8471 (tp) cc_final: 0.8255 (tp) REVERT: A 576 LEU cc_start: 0.7165 (tp) cc_final: 0.6888 (tp) REVERT: A 721 ILE cc_start: 0.9196 (mt) cc_final: 0.8778 (mt) REVERT: A 722 LEU cc_start: 0.9204 (tp) cc_final: 0.8989 (tp) REVERT: A 776 TYR cc_start: 0.7521 (m-80) cc_final: 0.7288 (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: 0.8071 (p) REVERT: A 848 TYR cc_start: 0.5381 (m-80) cc_final: 0.5095 (m-10) REVERT: B 392 MET cc_start: 0.0464 (mmm) cc_final: 0.0229 (mmm) REVERT: B 446 LEU cc_start: 0.8713 (mt) cc_final: 0.8379 (mt) REVERT: B 541 ASP cc_start: 0.7601 (p0) cc_final: 0.7130 (p0) REVERT: B 573 LEU cc_start: 0.7945 (tm) cc_final: 0.7641 (tm) REVERT: B 574 THR cc_start: 0.8134 (p) cc_final: 0.7932 (t) REVERT: B 722 LEU cc_start: 0.9067 (tp) cc_final: 0.8844 (tp) REVERT: B 939 LEU cc_start: 0.8310 (mt) cc_final: 0.7888 (mt) REVERT: B 1181 ILE cc_start: 0.8715 (mt) cc_final: 0.8456 (mm) outliers start: 14 outliers final: 1 residues processed: 462 average time/residue: 0.1817 time to fit residues: 123.9723 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 : 0.755 ------------------------------------------------------------------------------- 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 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3907 r_free = 0.3907 target = 0.079633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.052198 restraints weight = 164197.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.054070 restraints weight = 106963.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055400 restraints weight = 76963.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.056293 restraints weight = 59106.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.056743 restraints weight = 47751.160| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 0.105 21107 Z= 0.180 Angle : 0.703 15.396 28863 Z= 0.384 Chirality : 0.048 0.296 3215 Planarity : 0.005 0.053 3397 Dihedral : 17.591 172.973 3463 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % 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: -1.30 (0.16), residues: 2359 helix: -0.37 (0.16), residues: 976 sheet: -0.61 (0.28), residues: 350 loop : -1.34 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 788 TYR 0.030 0.002 TYR A 698 PHE 0.028 0.002 PHE B 317 TRP 0.026 0.002 TRP B1170 HIS 0.008 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (21107) covalent geometry : angle 0.70328 / 0.38 (28863) hydrogen bonds : bond 0.06445 / 4.37 ( 931) hydrogen bonds : angle 5.42563 / 3.88 ( 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 281 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.713 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: -0.5936 (mmm) cc_final: -0.6335 (mmm) REVERT: A 475 MET cc_start: 0.8074 (tpp) cc_final: 0.7738 (tpp) REVERT: A 542 LEU cc_start: 0.9085 (mt) cc_final: 0.8850 (mt) REVERT: A 586 MET cc_start: 0.8862 (mmm) cc_final: 0.8636 (tpp) REVERT: A 628 MET cc_start: 0.9117 (mtm) cc_final: 0.8912 (mtt) REVERT: A 629 PHE cc_start: 0.9636 (m-10) cc_final: 0.9334 (m-10) REVERT: A 698 TYR cc_start: 0.9508 (t80) cc_final: 0.8780 (t80) REVERT: A 775 LEU cc_start: 0.9329 (tp) cc_final: 0.8922 (tp) REVERT: A 776 TYR cc_start: 0.9235 (m-80) cc_final: 0.9033 (m-80) REVERT: A 827 GLU cc_start: 0.8719 (tp30) cc_final: 0.8087 (tp30) REVERT: A 846 MET cc_start: 0.9653 (mtp) cc_final: 0.9367 (mtt) REVERT: A 854 GLU cc_start: 0.9363 (mm-30) cc_final: 0.8906 (tp30) REVERT: A 897 LEU cc_start: 0.9119 (tp) cc_final: 0.8806 (tp) REVERT: A 957 MET cc_start: 0.9083 (mmp) cc_final: 0.8770 (mmm) REVERT: A 962 GLU cc_start: 0.8505 (tp30) cc_final: 0.8156 (tp30) REVERT: A 988 GLU cc_start: 0.9103 (mp0) cc_final: 0.8481 (pm20) REVERT: A 1078 HIS cc_start: 0.9613 (t70) cc_final: 0.9371 (t70) REVERT: A 1129 GLN cc_start: 0.9234 (mt0) cc_final: 0.9032 (mt0) REVERT: B 18 MET cc_start: -0.0330 (ptt) cc_final: -0.1890 (mmt) REVERT: B 447 ARG cc_start: 0.9318 (mtm-85) cc_final: 0.9107 (ptp90) REVERT: B 573 LEU cc_start: 0.8798 (tt) cc_final: 0.8590 (pp) REVERT: B 574 THR cc_start: 0.9698 (p) cc_final: 0.9465 (t) REVERT: B 576 LEU cc_start: 0.9148 (tp) cc_final: 0.8875 (tp) REVERT: B 586 MET cc_start: 0.8234 (mmm) cc_final: 0.7929 (mmm) REVERT: B 606 LEU cc_start: 0.8546 (tp) cc_final: 0.8255 (mm) REVERT: B 628 MET cc_start: 0.9444 (mtm) cc_final: 0.9140 (mtt) REVERT: B 629 PHE cc_start: 0.9408 (m-10) cc_final: 0.9207 (m-10) REVERT: B 790 LEU cc_start: 0.9408 (mp) cc_final: 0.9012 (tp) REVERT: B 813 MET cc_start: 0.9545 (tpt) cc_final: 0.8706 (tpp) REVERT: B 846 MET cc_start: 0.9247 (mtm) cc_final: 0.8851 (mtp) REVERT: B 939 LEU cc_start: 0.9400 (mt) cc_final: 0.9101 (mt) REVERT: B 966 TYR cc_start: 0.9037 (m-80) cc_final: 0.8806 (m-80) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.1664 time to fit residues: 71.3981 Evaluate side-chains 211 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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: 5.9990 chunk 154 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 186 optimal weight: 0.4980 chunk 2 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 HIS A 476 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 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 B1186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.073590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047729 restraints weight = 174757.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.049279 restraints weight = 114447.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.050405 restraints weight = 84024.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050823 restraints weight = 65299.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.051833 restraints weight = 55059.309| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21107 Z= 0.206 Angle : 0.695 14.159 28863 Z= 0.374 Chirality : 0.047 0.232 3215 Planarity : 0.005 0.043 3397 Dihedral : 17.549 171.227 3463 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.19 % Allowed : 3.43 % Favored : 96.37 % 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: -0.52 (0.17), residues: 2359 helix: 0.40 (0.16), residues: 973 sheet: -0.64 (0.27), residues: 376 loop : -0.85 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 571 TYR 0.034 0.002 TYR A 614 PHE 0.025 0.002 PHE B 785 TRP 0.016 0.002 TRP A1170 HIS 0.009 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (21107) covalent geometry : angle 0.69472 / 0.37 (28863) hydrogen bonds : bond 0.05684 / 3.78 ( 931) hydrogen bonds : angle 5.24016 / 3.75 ( 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 247 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 243 time to evaluate : 0.691 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: A 257 MET cc_start: 0.3121 (ptm) cc_final: 0.2832 (ptm) REVERT: A 392 MET cc_start: -0.5774 (mmm) cc_final: -0.6097 (mmm) REVERT: A 475 MET cc_start: 0.8369 (tpp) cc_final: 0.8037 (tpp) REVERT: A 586 MET cc_start: 0.8875 (mmm) cc_final: 0.8638 (tpp) REVERT: A 617 LEU cc_start: 0.9596 (tp) cc_final: 0.9167 (tp) REVERT: A 684 ARG cc_start: 0.9686 (mtm180) cc_final: 0.9401 (mmm-85) REVERT: A 698 TYR cc_start: 0.9539 (t80) cc_final: 0.8696 (t80) REVERT: A 775 LEU cc_start: 0.9370 (tp) cc_final: 0.9094 (tp) REVERT: A 776 TYR cc_start: 0.9300 (m-80) cc_final: 0.9051 (m-80) REVERT: A 854 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9165 (mm-30) REVERT: A 957 MET cc_start: 0.9186 (mmp) cc_final: 0.8793 (mmm) REVERT: A 962 GLU cc_start: 0.8500 (tp30) cc_final: 0.8086 (tp30) REVERT: A 1128 LEU cc_start: 0.8999 (mt) cc_final: 0.8411 (mm) REVERT: A 1174 ILE cc_start: 0.9648 (mm) cc_final: 0.9284 (mm) REVERT: A 1178 GLU cc_start: 0.9681 (tt0) cc_final: 0.9293 (pt0) REVERT: B 18 MET cc_start: 0.0370 (ptt) cc_final: -0.1512 (mmt) REVERT: B 447 ARG cc_start: 0.9338 (mtm-85) cc_final: 0.9083 (mtt180) REVERT: B 573 LEU cc_start: 0.8881 (tt) cc_final: 0.8636 (pp) REVERT: B 574 THR cc_start: 0.9705 (p) cc_final: 0.9484 (t) REVERT: B 576 LEU cc_start: 0.9092 (tp) cc_final: 0.8690 (tp) REVERT: B 586 MET cc_start: 0.8399 (mmm) cc_final: 0.8086 (mmm) REVERT: B 628 MET cc_start: 0.9377 (mtm) cc_final: 0.9126 (mtt) REVERT: B 755 ASP cc_start: 0.9600 (p0) cc_final: 0.9383 (p0) REVERT: B 790 LEU cc_start: 0.9404 (mp) cc_final: 0.8987 (tp) REVERT: B 813 MET cc_start: 0.9538 (tpt) cc_final: 0.8683 (tpp) REVERT: B 845 ILE cc_start: 0.9152 (mm) cc_final: 0.8894 (mp) REVERT: B 846 MET cc_start: 0.9309 (mtm) cc_final: 0.8841 (mtp) outliers start: 4 outliers final: 2 residues processed: 247 average time/residue: 0.1543 time to fit residues: 59.5084 Evaluate side-chains 181 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 30.0000 chunk 48 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 69 optimal weight: 0.0970 chunk 237 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS A 476 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.075119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.048969 restraints weight = 171907.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.050638 restraints weight = 110185.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051907 restraints weight = 78440.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.052341 restraints weight = 59941.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.053273 restraints weight = 49818.594| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21107 Z= 0.135 Angle : 0.636 12.730 28863 Z= 0.337 Chirality : 0.054 1.642 3215 Planarity : 0.004 0.045 3397 Dihedral : 17.431 171.629 3463 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.10 % Allowed : 1.98 % Favored : 97.92 % 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: -0.32 (0.17), residues: 2359 helix: 0.57 (0.16), residues: 974 sheet: -0.62 (0.28), residues: 368 loop : -0.71 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 736 TYR 0.020 0.001 TYR A1079 PHE 0.040 0.001 PHE B 388 TRP 0.012 0.001 TRP B1189 HIS 0.006 0.001 HIS B1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (21107) covalent geometry : angle 0.63597 / 0.34 (28863) hydrogen bonds : bond 0.05208 / 3.51 ( 931) hydrogen bonds : angle 5.07158 / 3.66 ( 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 241 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 0.801 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 257 MET cc_start: 0.3239 (ptm) cc_final: 0.2691 (ptm) REVERT: A 446 LEU cc_start: 0.9731 (mt) cc_final: 0.9458 (mt) REVERT: A 467 MET cc_start: 0.9544 (mtt) cc_final: 0.9212 (mtt) REVERT: A 475 MET cc_start: 0.8362 (tpp) cc_final: 0.8065 (tpp) REVERT: A 483 ASN cc_start: 0.8876 (p0) cc_final: 0.8604 (m-40) REVERT: A 503 LYS cc_start: 0.9520 (ptmm) cc_final: 0.9275 (ptmm) REVERT: A 542 LEU cc_start: 0.9215 (mt) cc_final: 0.9005 (mt) REVERT: A 586 MET cc_start: 0.8849 (mmm) cc_final: 0.8620 (tpp) REVERT: A 617 LEU cc_start: 0.9397 (tp) cc_final: 0.9043 (tp) REVERT: A 629 PHE cc_start: 0.9544 (m-80) cc_final: 0.9275 (m-10) REVERT: A 698 TYR cc_start: 0.9483 (t80) cc_final: 0.8494 (t80) REVERT: A 701 ASP cc_start: 0.9691 (t70) cc_final: 0.9438 (t70) REVERT: A 704 GLU cc_start: 0.9464 (tp30) cc_final: 0.8994 (tp30) REVERT: A 775 LEU cc_start: 0.9384 (tp) cc_final: 0.9017 (tp) REVERT: A 776 TYR cc_start: 0.9249 (m-80) cc_final: 0.8980 (m-80) REVERT: A 843 LEU cc_start: 0.9699 (mm) cc_final: 0.9303 (mm) REVERT: A 846 MET cc_start: 0.9569 (mtp) cc_final: 0.9284 (mtt) REVERT: A 854 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8458 (mm-30) REVERT: A 957 MET cc_start: 0.9204 (mmp) cc_final: 0.8821 (mmm) REVERT: A 962 GLU cc_start: 0.8357 (tp30) cc_final: 0.7973 (tp30) REVERT: A 1042 LEU cc_start: 0.9433 (mt) cc_final: 0.9198 (mt) REVERT: A 1060 MET cc_start: 0.9114 (ptp) cc_final: 0.8888 (ptp) REVERT: A 1128 LEU cc_start: 0.8927 (mt) cc_final: 0.8138 (mm) REVERT: A 1174 ILE cc_start: 0.9678 (mm) cc_final: 0.9281 (mm) REVERT: A 1178 GLU cc_start: 0.9658 (tt0) cc_final: 0.9255 (pt0) REVERT: B 18 MET cc_start: 0.0213 (ptt) cc_final: -0.1634 (mmt) REVERT: B 447 ARG cc_start: 0.9270 (mtm-85) cc_final: 0.8959 (mtm-85) REVERT: B 573 LEU cc_start: 0.8823 (tt) cc_final: 0.8530 (pp) REVERT: B 574 THR cc_start: 0.9748 (p) cc_final: 0.9531 (t) REVERT: B 586 MET cc_start: 0.8437 (mmm) cc_final: 0.8102 (mmm) REVERT: B 606 LEU cc_start: 0.8652 (tp) cc_final: 0.8357 (mm) REVERT: B 629 PHE cc_start: 0.9384 (m-80) cc_final: 0.9109 (m-10) REVERT: B 755 ASP cc_start: 0.9540 (p0) cc_final: 0.9336 (p0) REVERT: B 790 LEU cc_start: 0.9404 (mp) cc_final: 0.9030 (tt) REVERT: B 813 MET cc_start: 0.9532 (tpt) cc_final: 0.8710 (tpp) REVERT: B 846 MET cc_start: 0.9325 (mtm) cc_final: 0.8827 (mtp) outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.1508 time to fit residues: 56.7304 Evaluate side-chains 184 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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: 6.9990 chunk 155 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 154 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS A 476 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 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 286 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 HIS B 905 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 ASN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.071808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.045660 restraints weight = 172772.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047139 restraints weight = 113861.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.048304 restraints weight = 83660.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.048704 restraints weight = 65237.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.049389 restraints weight = 55140.232| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21107 Z= 0.182 Angle : 0.640 12.200 28863 Z= 0.344 Chirality : 0.049 1.069 3215 Planarity : 0.004 0.040 3397 Dihedral : 17.471 170.967 3463 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.15 % Allowed : 2.08 % Favored : 97.77 % 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: -0.09 (0.18), residues: 2359 helix: 0.76 (0.17), residues: 982 sheet: -0.45 (0.28), residues: 379 loop : -0.62 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 831 TYR 0.019 0.002 TYR B 917 PHE 0.031 0.002 PHE B 826 TRP 0.011 0.001 TRP A 157 HIS 0.009 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (21107) covalent geometry : angle 0.64031 / 0.34 (28863) hydrogen bonds : bond 0.05098 / 3.37 ( 931) hydrogen bonds : angle 5.05812 / 3.62 ( 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 218 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.873 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: A 446 LEU cc_start: 0.9773 (mt) cc_final: 0.9511 (mt) REVERT: A 467 MET cc_start: 0.9489 (mtt) cc_final: 0.8216 (mmt) REVERT: A 483 ASN cc_start: 0.8967 (p0) cc_final: 0.8626 (t0) REVERT: A 542 LEU cc_start: 0.9268 (mt) cc_final: 0.9029 (mt) REVERT: A 586 MET cc_start: 0.8897 (mmm) cc_final: 0.8656 (tpp) REVERT: A 617 LEU cc_start: 0.9387 (tp) cc_final: 0.9064 (tp) REVERT: A 635 MET cc_start: 0.9514 (ptp) cc_final: 0.9159 (ptp) REVERT: A 684 ARG cc_start: 0.9694 (mtm180) cc_final: 0.9434 (mmm-85) REVERT: A 698 TYR cc_start: 0.9517 (t80) cc_final: 0.8619 (t80) REVERT: A 704 GLU cc_start: 0.9536 (tp30) cc_final: 0.8999 (tp30) REVERT: A 775 LEU cc_start: 0.9428 (tp) cc_final: 0.9195 (tp) REVERT: A 776 TYR cc_start: 0.9244 (m-80) cc_final: 0.9043 (m-80) REVERT: A 843 LEU cc_start: 0.9726 (mm) cc_final: 0.9334 (mm) REVERT: A 846 MET cc_start: 0.9612 (mtp) cc_final: 0.9296 (mtt) REVERT: A 854 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9084 (mm-30) REVERT: A 957 MET cc_start: 0.9249 (mmp) cc_final: 0.8903 (mmm) REVERT: A 962 GLU cc_start: 0.8625 (tp30) cc_final: 0.8183 (tp30) REVERT: A 1042 LEU cc_start: 0.9466 (mt) cc_final: 0.9208 (mt) REVERT: A 1174 ILE cc_start: 0.9670 (mm) cc_final: 0.9291 (mm) REVERT: A 1178 GLU cc_start: 0.9681 (tt0) cc_final: 0.9311 (pt0) REVERT: B 18 MET cc_start: 0.0226 (ptt) cc_final: -0.1386 (mmt) REVERT: B 32 MET cc_start: 0.3045 (tpt) cc_final: 0.2476 (tpp) REVERT: B 447 ARG cc_start: 0.9289 (mtm-85) cc_final: 0.8906 (mtt-85) REVERT: B 475 MET cc_start: 0.6278 (tpt) cc_final: 0.5669 (tpt) REVERT: B 502 ASN cc_start: 0.8866 (t0) cc_final: 0.8596 (t0) REVERT: B 573 LEU cc_start: 0.8889 (tt) cc_final: 0.8600 (pp) REVERT: B 586 MET cc_start: 0.8402 (mmm) cc_final: 0.8096 (mmm) REVERT: B 621 ASP cc_start: 0.9731 (t0) cc_final: 0.9457 (t70) REVERT: B 755 ASP cc_start: 0.9625 (p0) cc_final: 0.9195 (p0) REVERT: B 790 LEU cc_start: 0.9447 (mp) cc_final: 0.9067 (tp) REVERT: B 813 MET cc_start: 0.9547 (tpt) cc_final: 0.8654 (tpp) REVERT: B 828 ASP cc_start: 0.9255 (m-30) cc_final: 0.8175 (t0) REVERT: B 838 VAL cc_start: 0.9392 (t) cc_final: 0.9057 (p) REVERT: B 846 MET cc_start: 0.9341 (mtm) cc_final: 0.8724 (mtp) outliers start: 3 outliers final: 0 residues processed: 218 average time/residue: 0.1532 time to fit residues: 52.7109 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 : 0.752 ------------------------------------------------------------------------------- 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: 9.9990 chunk 151 optimal weight: 0.0000 chunk 145 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 21 optimal weight: 40.0000 chunk 127 optimal weight: 20.0000 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS A 476 ASN A 506 GLN ** 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 172 HIS B 175 GLN ** B 506 GLN ** 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 759 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 = 0.3690 r_free = 0.3690 target = 0.068964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.043404 restraints weight = 176062.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044834 restraints weight = 116679.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.045934 restraints weight = 85520.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.046318 restraints weight = 66823.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047249 restraints weight = 56546.634| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 21107 Z= 0.215 Angle : 0.675 12.599 28863 Z= 0.363 Chirality : 0.051 1.233 3215 Planarity : 0.005 0.114 3397 Dihedral : 17.535 170.011 3463 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.15 % Allowed : 1.84 % Favored : 98.02 % 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: -0.05 (0.18), residues: 2359 helix: 0.69 (0.17), residues: 986 sheet: -0.40 (0.28), residues: 383 loop : -0.49 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 683 TYR 0.021 0.002 TYR A 698 PHE 0.045 0.002 PHE B 596 TRP 0.019 0.002 TRP B 599 HIS 0.012 0.001 HIS A 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (21107) covalent geometry : angle 0.67478 / 0.36 (28863) hydrogen bonds : bond 0.05227 / 3.44 ( 931) hydrogen bonds : angle 5.21905 / 3.77 ( 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 209 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 206 time to evaluate : 0.789 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 257 MET cc_start: 0.3142 (ptm) cc_final: 0.2611 (ptm) REVERT: A 446 LEU cc_start: 0.9805 (mt) cc_final: 0.9590 (mt) REVERT: A 483 ASN cc_start: 0.8966 (p0) cc_final: 0.8598 (m-40) REVERT: A 493 MET cc_start: 0.9310 (tpt) cc_final: 0.9096 (tpt) REVERT: A 586 MET cc_start: 0.8988 (mmm) cc_final: 0.8759 (tpp) REVERT: A 617 LEU cc_start: 0.9420 (tp) cc_final: 0.9076 (tp) REVERT: A 698 TYR cc_start: 0.9541 (t80) cc_final: 0.8498 (t80) REVERT: A 701 ASP cc_start: 0.9690 (t70) cc_final: 0.9387 (t70) REVERT: A 704 GLU cc_start: 0.9554 (tp30) cc_final: 0.9027 (tp30) REVERT: A 843 LEU cc_start: 0.9727 (mm) cc_final: 0.9370 (mm) REVERT: A 846 MET cc_start: 0.9603 (mtp) cc_final: 0.9286 (mtt) REVERT: A 854 GLU cc_start: 0.9501 (mm-30) cc_final: 0.8729 (mm-30) REVERT: A 957 MET cc_start: 0.9232 (mmp) cc_final: 0.8791 (mmm) REVERT: A 962 GLU cc_start: 0.8718 (tp30) cc_final: 0.8208 (tp30) REVERT: A 1042 LEU cc_start: 0.9515 (mt) cc_final: 0.9246 (mt) REVERT: B 257 MET cc_start: -0.0498 (tmm) cc_final: -0.0704 (ttt) REVERT: B 447 ARG cc_start: 0.9272 (mtm-85) cc_final: 0.8911 (mtt-85) REVERT: B 475 MET cc_start: 0.6952 (tpt) cc_final: 0.6617 (tpt) REVERT: B 502 ASN cc_start: 0.9043 (t0) cc_final: 0.8842 (t0) REVERT: B 573 LEU cc_start: 0.8870 (tt) cc_final: 0.8631 (pp) REVERT: B 586 MET cc_start: 0.8465 (mmm) cc_final: 0.8159 (mmm) REVERT: B 621 ASP cc_start: 0.9756 (t0) cc_final: 0.9489 (t70) REVERT: B 755 ASP cc_start: 0.9616 (p0) cc_final: 0.9336 (p0) REVERT: B 790 LEU cc_start: 0.9477 (mp) cc_final: 0.9092 (tp) REVERT: B 813 MET cc_start: 0.9557 (tpt) cc_final: 0.8659 (tpp) REVERT: B 828 ASP cc_start: 0.9298 (m-30) cc_final: 0.8155 (t0) REVERT: B 838 VAL cc_start: 0.9464 (t) cc_final: 0.9162 (p) REVERT: B 846 MET cc_start: 0.9334 (mtm) cc_final: 0.8761 (mtp) REVERT: B 957 MET cc_start: 0.8954 (mmp) cc_final: 0.8714 (mmm) outliers start: 3 outliers final: 2 residues processed: 209 average time/residue: 0.1429 time to fit residues: 47.8139 Evaluate side-chains 161 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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: 10.0000 chunk 113 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 chunk 19 optimal weight: 50.0000 chunk 141 optimal weight: 30.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 ASN A 381 HIS A 476 ASN ** 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 175 GLN 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 = 0.3694 r_free = 0.3694 target = 0.069108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043374 restraints weight = 176755.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044920 restraints weight = 115039.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.045984 restraints weight = 83220.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.046377 restraints weight = 65046.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047275 restraints weight = 55183.605| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 21107 Z= 0.160 Angle : 0.626 10.874 28863 Z= 0.336 Chirality : 0.051 1.348 3215 Planarity : 0.004 0.060 3397 Dihedral : 17.497 168.797 3463 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.05 % Allowed : 1.11 % Favored : 98.84 % 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: 0.05 (0.18), residues: 2359 helix: 0.78 (0.17), residues: 994 sheet: -0.49 (0.28), residues: 387 loop : -0.39 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1040 TYR 0.017 0.002 TYR A 698 PHE 0.035 0.002 PHE B 596 TRP 0.015 0.001 TRP A 157 HIS 0.018 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (21107) covalent geometry : angle 0.62590 / 0.34 (28863) hydrogen bonds : bond 0.04859 / 3.22 ( 931) hydrogen bonds : angle 5.11933 / 3.69 ( 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 214 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.712 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: A 257 MET cc_start: 0.3092 (ptm) cc_final: 0.2672 (ptm) REVERT: A 446 LEU cc_start: 0.9834 (mt) cc_final: 0.9576 (mt) REVERT: A 467 MET cc_start: 0.9619 (mtt) cc_final: 0.9328 (ttt) REVERT: A 483 ASN cc_start: 0.8914 (p0) cc_final: 0.8508 (m-40) REVERT: A 493 MET cc_start: 0.9328 (tpt) cc_final: 0.9044 (tpt) REVERT: A 542 LEU cc_start: 0.9333 (mt) cc_final: 0.9066 (mt) REVERT: A 586 MET cc_start: 0.8977 (mmm) cc_final: 0.8741 (tpp) REVERT: A 617 LEU cc_start: 0.9439 (tp) cc_final: 0.9088 (tp) REVERT: A 698 TYR cc_start: 0.9513 (t80) cc_final: 0.8478 (t80) REVERT: A 701 ASP cc_start: 0.9627 (t70) cc_final: 0.9420 (t0) REVERT: A 704 GLU cc_start: 0.9498 (tp30) cc_final: 0.8941 (tp30) REVERT: A 756 MET cc_start: 0.9717 (mpp) cc_final: 0.9210 (tpp) REVERT: A 775 LEU cc_start: 0.9474 (tp) cc_final: 0.8767 (tp) REVERT: A 776 TYR cc_start: 0.8992 (m-80) cc_final: 0.8702 (m-80) REVERT: A 843 LEU cc_start: 0.9669 (mm) cc_final: 0.9365 (mm) REVERT: A 846 MET cc_start: 0.9737 (mtp) cc_final: 0.9367 (mtt) REVERT: A 854 GLU cc_start: 0.9529 (mm-30) cc_final: 0.8737 (mm-30) REVERT: A 957 MET cc_start: 0.9225 (mmp) cc_final: 0.8768 (mmm) REVERT: A 962 GLU cc_start: 0.8618 (tp30) cc_final: 0.8058 (tp30) REVERT: A 1042 LEU cc_start: 0.9527 (mt) cc_final: 0.9227 (mt) REVERT: A 1174 ILE cc_start: 0.9690 (mm) cc_final: 0.9273 (mm) REVERT: A 1178 GLU cc_start: 0.9674 (tt0) cc_final: 0.9326 (pt0) REVERT: B 18 MET cc_start: 0.1927 (ppp) cc_final: 0.0126 (mmp) REVERT: B 257 MET cc_start: -0.0491 (tmm) cc_final: -0.0736 (ttp) REVERT: B 447 ARG cc_start: 0.9275 (mtm-85) cc_final: 0.8904 (mtt-85) REVERT: B 475 MET cc_start: 0.6656 (tpt) cc_final: 0.6394 (tpt) REVERT: B 502 ASN cc_start: 0.9066 (t0) cc_final: 0.8830 (t0) REVERT: B 573 LEU cc_start: 0.8887 (tt) cc_final: 0.8645 (pp) REVERT: B 586 MET cc_start: 0.8460 (mmm) cc_final: 0.8140 (mmm) REVERT: B 621 ASP cc_start: 0.9754 (t0) cc_final: 0.9506 (t70) REVERT: B 755 ASP cc_start: 0.9598 (p0) cc_final: 0.9376 (p0) REVERT: B 790 LEU cc_start: 0.9473 (mp) cc_final: 0.9076 (tp) REVERT: B 813 MET cc_start: 0.9542 (tpt) cc_final: 0.8680 (tpp) REVERT: B 828 ASP cc_start: 0.9299 (m-30) cc_final: 0.8118 (t0) REVERT: B 845 ILE cc_start: 0.9323 (mm) cc_final: 0.9099 (mp) REVERT: B 846 MET cc_start: 0.9293 (mtm) cc_final: 0.8753 (mtp) REVERT: B 957 MET cc_start: 0.8940 (mmp) cc_final: 0.8690 (mmm) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.1426 time to fit residues: 48.6266 Evaluate side-chains 163 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 476 ASN ** A 620 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 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 HIS B 603 GLN ** 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 = 0.3639 r_free = 0.3639 target = 0.066476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041465 restraints weight = 182099.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.042894 restraints weight = 120264.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.043950 restraints weight = 87805.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.044709 restraints weight = 68746.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045279 restraints weight = 56550.493| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21107 Z= 0.215 Angle : 0.693 14.338 28863 Z= 0.372 Chirality : 0.053 1.394 3215 Planarity : 0.005 0.103 3397 Dihedral : 17.549 168.879 3463 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.05 % Allowed : 0.92 % Favored : 99.03 % 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: -0.11 (0.18), residues: 2359 helix: 0.61 (0.16), residues: 999 sheet: -0.57 (0.28), residues: 376 loop : -0.43 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1039 TYR 0.026 0.002 TYR B 698 PHE 0.037 0.002 PHE B 596 TRP 0.015 0.002 TRP A1170 HIS 0.010 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (21107) covalent geometry : angle 0.69256 / 0.37 (28863) hydrogen bonds : bond 0.05258 / 3.44 ( 931) hydrogen bonds : angle 5.24544 / 3.77 ( 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 208 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.792 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: A 257 MET cc_start: 0.3187 (ptm) cc_final: 0.2703 (ptm) REVERT: A 446 LEU cc_start: 0.9836 (mt) cc_final: 0.9599 (mt) REVERT: A 483 ASN cc_start: 0.8945 (p0) cc_final: 0.8453 (t0) REVERT: A 493 MET cc_start: 0.9234 (tpt) cc_final: 0.8955 (tpt) REVERT: A 531 TYR cc_start: 0.9128 (p90) cc_final: 0.8842 (p90) REVERT: A 617 LEU cc_start: 0.9467 (tp) cc_final: 0.9108 (tp) REVERT: A 698 TYR cc_start: 0.9557 (t80) cc_final: 0.8555 (t80) REVERT: A 701 ASP cc_start: 0.9657 (t70) cc_final: 0.9422 (t70) REVERT: A 704 GLU cc_start: 0.9510 (tp30) cc_final: 0.8947 (tp30) REVERT: A 756 MET cc_start: 0.9740 (mpp) cc_final: 0.9261 (tpp) REVERT: A 775 LEU cc_start: 0.9477 (tp) cc_final: 0.8914 (tp) REVERT: A 776 TYR cc_start: 0.9078 (m-80) cc_final: 0.8839 (m-80) REVERT: A 843 LEU cc_start: 0.9662 (mm) cc_final: 0.9366 (mm) REVERT: A 846 MET cc_start: 0.9719 (mtp) cc_final: 0.9150 (mtt) REVERT: A 854 GLU cc_start: 0.9560 (mm-30) cc_final: 0.9242 (mm-30) REVERT: A 957 MET cc_start: 0.9234 (mmp) cc_final: 0.8774 (mmm) REVERT: B 42 MET cc_start: 0.8862 (pmm) cc_final: 0.8660 (pmm) REVERT: B 447 ARG cc_start: 0.9230 (mtm-85) cc_final: 0.8866 (mtt-85) REVERT: B 475 MET cc_start: 0.7302 (tpt) cc_final: 0.6968 (tpt) REVERT: B 586 MET cc_start: 0.8525 (mmm) cc_final: 0.8197 (mmm) REVERT: B 621 ASP cc_start: 0.9745 (t0) cc_final: 0.9469 (t70) REVERT: B 698 TYR cc_start: 0.9571 (t80) cc_final: 0.9357 (t80) REVERT: B 755 ASP cc_start: 0.9676 (p0) cc_final: 0.9450 (p0) REVERT: B 813 MET cc_start: 0.9500 (tpt) cc_final: 0.8654 (tpp) REVERT: B 828 ASP cc_start: 0.9158 (m-30) cc_final: 0.8145 (t0) REVERT: B 846 MET cc_start: 0.9300 (mtm) cc_final: 0.8784 (mtp) REVERT: B 957 MET cc_start: 0.8967 (mmp) cc_final: 0.8759 (mmm) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1381 time to fit residues: 45.9207 Evaluate side-chains 155 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 0.0570 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 HIS A 476 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 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 175 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN B1099 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.068969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.043348 restraints weight = 176174.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.044851 restraints weight = 113521.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.045937 restraints weight = 81609.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046757 restraints weight = 63088.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.047391 restraints weight = 51126.304| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21107 Z= 0.131 Angle : 0.628 10.773 28863 Z= 0.332 Chirality : 0.049 0.913 3215 Planarity : 0.004 0.056 3397 Dihedral : 17.459 168.267 3463 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.52 % 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: 0.85 (0.16), residues: 998 sheet: -0.55 (0.28), residues: 388 loop : -0.31 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 684 TYR 0.020 0.001 TYR B 698 PHE 0.023 0.002 PHE B 596 TRP 0.014 0.001 TRP A 157 HIS 0.009 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (21107) covalent geometry : angle 0.62792 / 0.33 (28863) hydrogen bonds : bond 0.04753 / 3.15 ( 931) hydrogen bonds : angle 4.99274 / 3.64 ( 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 217 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.693 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: A 257 MET cc_start: 0.3115 (ptm) cc_final: 0.2710 (ptm) REVERT: A 467 MET cc_start: 0.9620 (mtt) cc_final: 0.9079 (ttt) REVERT: A 483 ASN cc_start: 0.8964 (p0) cc_final: 0.8511 (t0) REVERT: A 493 MET cc_start: 0.9232 (tpt) cc_final: 0.8948 (tpt) REVERT: A 586 MET cc_start: 0.9053 (mmp) cc_final: 0.8723 (tpp) REVERT: A 617 LEU cc_start: 0.9442 (tp) cc_final: 0.9079 (tp) REVERT: A 698 TYR cc_start: 0.9535 (t80) cc_final: 0.8604 (t80) REVERT: A 704 GLU cc_start: 0.9466 (tp30) cc_final: 0.8924 (tp30) REVERT: A 756 MET cc_start: 0.9719 (mpp) cc_final: 0.9212 (tpp) REVERT: A 775 LEU cc_start: 0.9385 (tp) cc_final: 0.8720 (tp) REVERT: A 776 TYR cc_start: 0.8687 (m-80) cc_final: 0.8326 (m-80) REVERT: A 843 LEU cc_start: 0.9696 (mm) cc_final: 0.9399 (mm) REVERT: A 846 MET cc_start: 0.9753 (mtp) cc_final: 0.9269 (mtt) REVERT: A 854 GLU cc_start: 0.9540 (mm-30) cc_final: 0.9181 (mm-30) REVERT: A 957 MET cc_start: 0.9241 (mmp) cc_final: 0.8761 (mmm) REVERT: A 1042 LEU cc_start: 0.9596 (mt) cc_final: 0.9384 (mt) REVERT: A 1174 ILE cc_start: 0.9687 (mm) cc_final: 0.9294 (mm) REVERT: A 1178 GLU cc_start: 0.9652 (tt0) cc_final: 0.9320 (pt0) REVERT: B 467 MET cc_start: 0.9193 (mtm) cc_final: 0.8738 (mpp) REVERT: B 475 MET cc_start: 0.6947 (tpt) cc_final: 0.6694 (tpt) REVERT: B 502 ASN cc_start: 0.9102 (t0) cc_final: 0.8897 (t0) REVERT: B 586 MET cc_start: 0.8524 (mmm) cc_final: 0.8202 (mmm) REVERT: B 621 ASP cc_start: 0.9751 (t0) cc_final: 0.9505 (t70) REVERT: B 698 TYR cc_start: 0.9504 (t80) cc_final: 0.9213 (t80) REVERT: B 755 ASP cc_start: 0.9560 (p0) cc_final: 0.9257 (p0) REVERT: B 813 MET cc_start: 0.9525 (tpt) cc_final: 0.8710 (tpp) REVERT: B 820 TRP cc_start: 0.9529 (m100) cc_final: 0.9329 (m100) REVERT: B 828 ASP cc_start: 0.9169 (m-30) cc_final: 0.8121 (t70) REVERT: B 845 ILE cc_start: 0.9258 (mm) cc_final: 0.8890 (pt) REVERT: B 846 MET cc_start: 0.9334 (mtm) cc_final: 0.8872 (mpp) REVERT: B 865 LEU cc_start: 0.9492 (mm) cc_final: 0.9174 (pp) REVERT: B 957 MET cc_start: 0.8921 (mmp) cc_final: 0.8714 (mmm) REVERT: B 1151 ARG cc_start: 0.9473 (tpm170) cc_final: 0.9200 (tpm170) REVERT: B 1153 ASP cc_start: 0.9490 (t0) cc_final: 0.9205 (m-30) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1328 time to fit residues: 46.6492 Evaluate side-chains 167 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 10.0000 chunk 147 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 84 optimal weight: 0.3980 chunk 115 optimal weight: 0.1980 chunk 225 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 176 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 381 HIS A 476 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 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 = 0.3672 r_free = 0.3672 target = 0.067968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042638 restraints weight = 178850.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.044185 restraints weight = 116066.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.045256 restraints weight = 83328.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.045646 restraints weight = 65016.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.046493 restraints weight = 55288.871| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21107 Z= 0.146 Angle : 0.627 10.564 28863 Z= 0.334 Chirality : 0.047 0.609 3215 Planarity : 0.004 0.053 3397 Dihedral : 17.406 168.659 3463 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % 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: 0.09 (0.18), residues: 2359 helix: 0.82 (0.16), residues: 1006 sheet: -0.69 (0.28), residues: 378 loop : -0.28 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1151 TYR 0.024 0.002 TYR A 614 PHE 0.031 0.002 PHE B 596 TRP 0.013 0.001 TRP A 157 HIS 0.010 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (21107) covalent geometry : angle 0.62740 / 0.33 (28863) hydrogen bonds : bond 0.04715 / 3.10 ( 931) hydrogen bonds : angle 5.04051 / 3.66 ( 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 210 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.780 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: A 257 MET cc_start: 0.3345 (ptm) cc_final: 0.2847 (ptm) REVERT: A 483 ASN cc_start: 0.8960 (p0) cc_final: 0.8510 (t0) REVERT: A 493 MET cc_start: 0.9213 (tpt) cc_final: 0.8916 (tpt) REVERT: A 586 MET cc_start: 0.9062 (mmp) cc_final: 0.8747 (tpp) REVERT: A 617 LEU cc_start: 0.9385 (tp) cc_final: 0.9030 (tp) REVERT: A 698 TYR cc_start: 0.9495 (t80) cc_final: 0.8584 (t80) REVERT: A 701 ASP cc_start: 0.9791 (t0) cc_final: 0.9555 (t0) REVERT: A 704 GLU cc_start: 0.9503 (tp30) cc_final: 0.8962 (tp30) REVERT: A 756 MET cc_start: 0.9731 (mpp) cc_final: 0.9234 (tpp) REVERT: A 775 LEU cc_start: 0.9410 (tp) cc_final: 0.8783 (tp) REVERT: A 776 TYR cc_start: 0.8720 (m-80) cc_final: 0.8311 (m-80) REVERT: A 843 LEU cc_start: 0.9703 (mm) cc_final: 0.9396 (mm) REVERT: A 846 MET cc_start: 0.9764 (mtp) cc_final: 0.9289 (mtt) REVERT: A 854 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9204 (mm-30) REVERT: A 957 MET cc_start: 0.9230 (mmp) cc_final: 0.8723 (mmm) REVERT: A 1042 LEU cc_start: 0.9601 (mt) cc_final: 0.9374 (mt) REVERT: A 1174 ILE cc_start: 0.9694 (mm) cc_final: 0.9297 (mm) REVERT: A 1178 GLU cc_start: 0.9668 (tt0) cc_final: 0.9346 (pt0) REVERT: B 257 MET cc_start: -0.0330 (ttt) cc_final: -0.0540 (ttt) REVERT: B 447 ARG cc_start: 0.9245 (mtm-85) cc_final: 0.8811 (mtt-85) REVERT: B 467 MET cc_start: 0.9270 (mtm) cc_final: 0.8788 (mpp) REVERT: B 475 MET cc_start: 0.7078 (tpt) cc_final: 0.6799 (tpt) REVERT: B 502 ASN cc_start: 0.9104 (t0) cc_final: 0.8884 (t0) REVERT: B 586 MET cc_start: 0.8494 (mmm) cc_final: 0.8186 (mmm) REVERT: B 621 ASP cc_start: 0.9745 (t0) cc_final: 0.9498 (t70) REVERT: B 698 TYR cc_start: 0.9519 (t80) cc_final: 0.9215 (t80) REVERT: B 755 ASP cc_start: 0.9672 (p0) cc_final: 0.9410 (p0) REVERT: B 813 MET cc_start: 0.9523 (tpt) cc_final: 0.8741 (tpp) REVERT: B 845 ILE cc_start: 0.9318 (mm) cc_final: 0.9057 (pt) REVERT: B 846 MET cc_start: 0.9368 (mtm) cc_final: 0.8848 (mtp) REVERT: B 865 LEU cc_start: 0.9515 (mm) cc_final: 0.9238 (pp) REVERT: B 957 MET cc_start: 0.8930 (mmp) cc_final: 0.8721 (mmm) REVERT: B 1151 ARG cc_start: 0.9461 (tpm170) cc_final: 0.9247 (tpm170) REVERT: B 1153 ASP cc_start: 0.9549 (t0) cc_final: 0.9326 (m-30) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.1319 time to fit residues: 44.2260 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 : 0.662 ------------------------------------------------------------------------------- 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: 5.9990 chunk 154 optimal weight: 50.0000 chunk 75 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 6 optimal weight: 30.0000 chunk 201 optimal weight: 0.0980 chunk 239 optimal weight: 30.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.064344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040022 restraints weight = 185943.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041362 restraints weight = 121747.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.042360 restraints weight = 89363.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.042689 restraints weight = 70178.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043523 restraints weight = 60345.513| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21107 Z= 0.228 Angle : 0.717 10.875 28863 Z= 0.384 Chirality : 0.048 0.482 3215 Planarity : 0.005 0.075 3397 Dihedral : 17.562 171.126 3463 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: -0.20 (0.18), residues: 2359 helix: 0.59 (0.16), residues: 999 sheet: -0.79 (0.27), residues: 392 loop : -0.45 (0.22), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1039 TYR 0.025 0.002 TYR B 837 PHE 0.045 0.003 PHE B 559 TRP 0.020 0.002 TRP B 861 HIS 0.008 0.002 HIS B 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.23 (21107) covalent geometry : angle 0.71741 / 0.38 (28863) hydrogen bonds : bond 0.05215 / 3.45 ( 931) hydrogen bonds : angle 5.26609 / 3.83 ( 2595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.27 seconds wall clock time: 72 minutes 56.01 seconds (4376.01 seconds total)