Starting phenix.real_space_refine on Sat May 24 14:30:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgm_37226/05_2025/8kgm_37226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgm_37226/05_2025/8kgm_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_37226/05_2025/8kgm_37226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgm_37226/05_2025/8kgm_37226.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgm_37226/05_2025/8kgm_37226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgm_37226/05_2025/8kgm_37226.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.59s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.90, per 1000 atoms: 0.58 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: 5.06 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 7.72 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: 10.13 Time building geometry restraints manager: 5.84 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=" 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=" CA ARG B 344 " pdb=" C ARG B 344 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.37e-02 5.33e+03 8.60e+00 bond pdb=" CA ARG A 344 " pdb=" C ARG A 344 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.37e-02 5.33e+03 8.34e+00 bond pdb=" CA PHE B 4 " pdb=" C PHE B 4 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.23e-02 6.61e+03 7.22e+00 ... (remaining 21102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 28494 3.24 - 6.48: 333 6.48 - 9.73: 31 9.73 - 12.97: 2 12.97 - 16.21: 3 Bond angle restraints: 28863 Sorted by residual: 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 angle pdb=" N ARG A 344 " pdb=" CA ARG A 344 " pdb=" C ARG A 344 " ideal model delta sigma weight residual 112.23 106.46 5.77 1.26e+00 6.30e-01 2.10e+01 angle pdb=" N ARG B 344 " pdb=" CA ARG B 344 " pdb=" C ARG B 344 " ideal model delta sigma weight residual 112.23 106.49 5.74 1.26e+00 6.30e-01 2.08e+01 angle pdb=" N ASP B 408 " pdb=" CA ASP B 408 " pdb=" C ASP B 408 " ideal model delta sigma weight residual 112.92 107.49 5.43 1.23e+00 6.61e-01 1.95e+01 angle pdb=" CA LEU A 261 " pdb=" CB LEU A 261 " pdb=" CG LEU A 261 " ideal model delta sigma weight residual 116.30 101.05 15.25 3.50e+00 8.16e-02 1.90e+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 - 0.075: 2626 0.075 - 0.151: 538 0.151 - 0.226: 42 0.226 - 0.301: 6 0.301 - 0.377: 3 Chirality restraints: 3215 Sorted by residual: 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=" CB ILE B 963 " pdb=" CA ILE B 963 " pdb=" CG1 ILE B 963 " pdb=" CG2 ILE B 963 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 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 -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.44e+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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 53.570 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4648 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= 0.374 Angle : 0.982 16.211 28863 Z= 0.544 Chirality : 0.059 0.377 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (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 TRP 0.071 0.004 TRP B1170 HIS 0.014 0.003 HIS B 892 PHE 0.026 0.003 PHE B 739 TYR 0.060 0.003 TYR A 531 ARG 0.018 0.002 ARG B1039 Details of bonding type rmsd hydrogen bonds : bond 0.16766 ( 931) hydrogen bonds : angle 7.03496 ( 2595) covalent geometry : bond 0.00836 (21107) covalent geometry : angle 0.98192 (28863) *********************** 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 : 2.186 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: 0.8256 (tp) REVERT: A 576 LEU cc_start: 0.7165 (tp) cc_final: 0.6911 (tp) REVERT: A 721 ILE cc_start: 0.9196 (mt) cc_final: 0.8755 (mt) REVERT: A 722 LEU cc_start: 0.9204 (tp) cc_final: 0.8975 (tp) REVERT: A 776 TYR cc_start: 0.7521 (m-80) cc_final: 0.7290 (m-80) REVERT: A 838 VAL cc_start: 0.8600 (t) cc_final: 0.8105 (p) REVERT: A 848 TYR cc_start: 0.5381 (m-80) cc_final: 0.5095 (m-10) REVERT: B 446 LEU cc_start: 0.8713 (mt) cc_final: 0.8382 (mt) REVERT: B 541 ASP cc_start: 0.7602 (p0) cc_final: 0.7139 (p0) REVERT: B 573 LEU cc_start: 0.7945 (tm) cc_final: 0.7643 (tm) REVERT: B 621 ASP cc_start: 0.8433 (t0) cc_final: 0.8230 (t70) REVERT: B 722 LEU cc_start: 0.9066 (tp) cc_final: 0.8824 (tp) REVERT: B 939 LEU cc_start: 0.8310 (mt) cc_final: 0.7875 (mt) REVERT: B 1181 ILE cc_start: 0.8715 (mt) cc_final: 0.8457 (mm) outliers start: 14 outliers final: 1 residues processed: 462 average time/residue: 0.3654 time to fit residues: 245.7754 Evaluate side-chains 245 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 123 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 283 HIS A 402 GLN A 566 HIS A 677 GLN ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 ASN B 125 HIS B 175 GLN B 283 HIS B 483 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 566 HIS B 692 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 GLN B 892 HIS B 905 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.079872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.052689 restraints weight = 162990.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.054407 restraints weight = 105685.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.055795 restraints weight = 76620.438| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21107 Z= 0.150 Angle : 0.647 13.964 28863 Z= 0.350 Chirality : 0.045 0.214 3215 Planarity : 0.005 0.047 3397 Dihedral : 17.495 174.063 3463 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2359 helix: -0.27 (0.16), residues: 982 sheet: -0.51 (0.28), residues: 338 loop : -1.37 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B1170 HIS 0.008 0.001 HIS B 650 PHE 0.027 0.002 PHE B 317 TYR 0.022 0.002 TYR A 698 ARG 0.007 0.001 ARG A 571 Details of bonding type rmsd hydrogen bonds : bond 0.05832 ( 931) hydrogen bonds : angle 5.22993 ( 2595) covalent geometry : bond 0.00315 (21107) covalent geometry : angle 0.64657 (28863) *********************** 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 291 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 2.147 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: A 392 MET cc_start: -0.5702 (mmm) cc_final: -0.6146 (mmm) REVERT: A 473 VAL cc_start: 0.8319 (t) cc_final: 0.8104 (t) REVERT: A 475 MET cc_start: 0.7260 (mmp) cc_final: 0.6808 (tpp) REVERT: A 537 CYS cc_start: 0.9190 (m) cc_final: 0.8931 (p) REVERT: A 586 MET cc_start: 0.8861 (mmm) cc_final: 0.8627 (tpp) REVERT: A 629 PHE cc_start: 0.9594 (m-10) cc_final: 0.9353 (m-10) REVERT: A 684 ARG cc_start: 0.9724 (mtm180) cc_final: 0.9412 (mmm-85) REVERT: A 698 TYR cc_start: 0.9448 (t80) cc_final: 0.8606 (t80) REVERT: A 737 LYS cc_start: 0.8794 (tppt) cc_final: 0.8543 (tppp) REVERT: A 739 PHE cc_start: 0.9410 (p90) cc_final: 0.9125 (p90) REVERT: A 760 THR cc_start: 0.9663 (m) cc_final: 0.9453 (p) REVERT: A 775 LEU cc_start: 0.9303 (tp) cc_final: 0.8919 (tp) REVERT: A 776 TYR cc_start: 0.9194 (m-80) cc_final: 0.8988 (m-80) REVERT: A 827 GLU cc_start: 0.8760 (tp30) cc_final: 0.8122 (tp30) REVERT: A 843 LEU cc_start: 0.9583 (mt) cc_final: 0.9360 (mm) REVERT: A 846 MET cc_start: 0.9574 (mtp) cc_final: 0.9348 (mtt) REVERT: A 854 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8525 (tp30) REVERT: A 957 MET cc_start: 0.9122 (mmp) cc_final: 0.8753 (mmm) REVERT: A 962 GLU cc_start: 0.8486 (tp30) cc_final: 0.8135 (tp30) REVERT: A 988 GLU cc_start: 0.9149 (mp0) cc_final: 0.8507 (pm20) REVERT: A 1078 HIS cc_start: 0.9608 (t70) cc_final: 0.9384 (t70) REVERT: B 18 MET cc_start: -0.0199 (ptt) cc_final: -0.1843 (mmt) REVERT: B 450 LEU cc_start: 0.9243 (tp) cc_final: 0.8857 (tp) REVERT: B 467 MET cc_start: 0.9198 (mtm) cc_final: 0.8747 (mtt) REVERT: B 502 ASN cc_start: 0.8843 (t0) cc_final: 0.8509 (t0) REVERT: B 573 LEU cc_start: 0.8773 (tt) cc_final: 0.8538 (tp) REVERT: B 586 MET cc_start: 0.8254 (mmm) cc_final: 0.7934 (mmm) REVERT: B 606 LEU cc_start: 0.8572 (tp) cc_final: 0.8278 (mm) REVERT: B 628 MET cc_start: 0.9363 (mtm) cc_final: 0.9141 (mtt) REVERT: B 714 MET cc_start: 0.8740 (ppp) cc_final: 0.8451 (tmm) REVERT: B 813 MET cc_start: 0.9581 (tpt) cc_final: 0.8774 (tpp) REVERT: B 846 MET cc_start: 0.9247 (mtm) cc_final: 0.8892 (mtm) REVERT: B 939 LEU cc_start: 0.9419 (mt) cc_final: 0.9128 (mt) REVERT: B 962 GLU cc_start: 0.9242 (tt0) cc_final: 0.9032 (tm-30) REVERT: B 966 TYR cc_start: 0.9077 (m-80) cc_final: 0.8745 (m-80) outliers start: 2 outliers final: 1 residues processed: 291 average time/residue: 0.3495 time to fit residues: 153.1169 Evaluate side-chains 215 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 29 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 HIS ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.072255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.046577 restraints weight = 174534.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.048123 restraints weight = 115395.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.049233 restraints weight = 84412.911| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21107 Z= 0.218 Angle : 0.664 12.427 28863 Z= 0.359 Chirality : 0.044 0.234 3215 Planarity : 0.004 0.044 3397 Dihedral : 17.378 175.170 3463 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2359 helix: 0.60 (0.16), residues: 976 sheet: -0.68 (0.28), residues: 379 loop : -0.82 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1170 HIS 0.008 0.001 HIS A 892 PHE 0.034 0.002 PHE B 785 TYR 0.018 0.002 TYR A 698 ARG 0.007 0.001 ARG B 788 Details of bonding type rmsd hydrogen bonds : bond 0.05429 ( 931) hydrogen bonds : angle 5.11293 ( 2595) covalent geometry : bond 0.00447 (21107) covalent geometry : angle 0.66428 (28863) *********************** 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 233 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 MET cc_start: -0.5294 (mmm) cc_final: -0.5656 (mmm) REVERT: A 446 LEU cc_start: 0.9755 (mt) cc_final: 0.9458 (mt) REVERT: A 475 MET cc_start: 0.8201 (mmp) cc_final: 0.7911 (tpp) REVERT: A 586 MET cc_start: 0.8898 (mmm) cc_final: 0.8681 (tpp) REVERT: A 684 ARG cc_start: 0.9728 (mtm180) cc_final: 0.9447 (mmm-85) REVERT: A 698 TYR cc_start: 0.9531 (t80) cc_final: 0.8604 (t80) REVERT: A 704 GLU cc_start: 0.9612 (tp30) cc_final: 0.9197 (tp30) REVERT: A 714 MET cc_start: 0.9584 (ttt) cc_final: 0.8982 (ttp) REVERT: A 775 LEU cc_start: 0.9412 (tp) cc_final: 0.9166 (tp) REVERT: A 843 LEU cc_start: 0.9618 (mt) cc_final: 0.9400 (mt) REVERT: A 846 MET cc_start: 0.9619 (mtp) cc_final: 0.9353 (mtt) REVERT: A 854 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9054 (mm-30) REVERT: A 957 MET cc_start: 0.9184 (mmp) cc_final: 0.8803 (mmm) REVERT: A 962 GLU cc_start: 0.8627 (tp30) cc_final: 0.8225 (tp30) REVERT: A 1128 LEU cc_start: 0.8744 (mt) cc_final: 0.8169 (mm) REVERT: B 32 MET cc_start: 0.3985 (tpt) cc_final: 0.3621 (tpt) REVERT: B 573 LEU cc_start: 0.8851 (tt) cc_final: 0.8595 (pp) REVERT: B 576 LEU cc_start: 0.9067 (tp) cc_final: 0.8709 (tp) REVERT: B 586 MET cc_start: 0.8438 (mmm) cc_final: 0.8092 (mmm) REVERT: B 621 ASP cc_start: 0.9723 (t0) cc_final: 0.9430 (t70) REVERT: B 755 ASP cc_start: 0.9621 (p0) cc_final: 0.9307 (p0) REVERT: B 790 LEU cc_start: 0.9428 (mp) cc_final: 0.8984 (tp) REVERT: B 813 MET cc_start: 0.9602 (tpt) cc_final: 0.8682 (tpp) REVERT: B 838 VAL cc_start: 0.9463 (t) cc_final: 0.9143 (p) REVERT: B 845 ILE cc_start: 0.9331 (mm) cc_final: 0.9115 (mm) REVERT: B 846 MET cc_start: 0.9348 (mtm) cc_final: 0.8830 (mtp) REVERT: B 962 GLU cc_start: 0.9331 (tt0) cc_final: 0.9115 (tm-30) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3444 time to fit residues: 124.5427 Evaluate side-chains 176 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 191 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN A 381 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 557 HIS B 905 ASN ** B 909 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 = 0.3772 r_free = 0.3772 target = 0.072633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.046331 restraints weight = 175139.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.047983 restraints weight = 113488.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.049165 restraints weight = 81415.755| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21107 Z= 0.141 Angle : 0.588 11.805 28863 Z= 0.316 Chirality : 0.045 0.736 3215 Planarity : 0.004 0.043 3397 Dihedral : 17.293 173.763 3463 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2359 helix: 0.86 (0.17), residues: 982 sheet: -0.49 (0.27), residues: 387 loop : -0.62 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1170 HIS 0.005 0.001 HIS A 892 PHE 0.032 0.001 PHE B 596 TYR 0.020 0.002 TYR B 837 ARG 0.004 0.000 ARG B 912 Details of bonding type rmsd hydrogen bonds : bond 0.04842 ( 931) hydrogen bonds : angle 4.92364 ( 2595) covalent geometry : bond 0.00299 (21107) covalent geometry : angle 0.58830 (28863) *********************** 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 232 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 2.254 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 446 LEU cc_start: 0.9817 (mt) cc_final: 0.9573 (mt) REVERT: A 483 ASN cc_start: 0.8966 (p0) cc_final: 0.8537 (m-40) REVERT: A 503 LYS cc_start: 0.9525 (ptmm) cc_final: 0.9264 (ptmm) REVERT: A 586 MET cc_start: 0.8908 (mmm) cc_final: 0.8674 (tpp) REVERT: A 617 LEU cc_start: 0.9591 (tp) cc_final: 0.9064 (tp) REVERT: A 684 ARG cc_start: 0.9727 (mtm180) cc_final: 0.9470 (mmm-85) REVERT: A 698 TYR cc_start: 0.9409 (t80) cc_final: 0.8429 (t80) REVERT: A 701 ASP cc_start: 0.9808 (t0) cc_final: 0.9605 (t70) REVERT: A 704 GLU cc_start: 0.9537 (tp30) cc_final: 0.9060 (tp30) REVERT: A 775 LEU cc_start: 0.9533 (tp) cc_final: 0.8897 (tp) REVERT: A 846 MET cc_start: 0.9719 (mtp) cc_final: 0.9212 (mtt) REVERT: A 854 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8961 (mm-30) REVERT: A 897 LEU cc_start: 0.9103 (tp) cc_final: 0.8877 (tp) REVERT: A 957 MET cc_start: 0.9226 (mmp) cc_final: 0.8900 (mmm) REVERT: A 962 GLU cc_start: 0.8634 (tp30) cc_final: 0.8194 (tp30) REVERT: A 1042 LEU cc_start: 0.9498 (mt) cc_final: 0.9232 (mt) REVERT: B 32 MET cc_start: 0.3321 (tpt) cc_final: 0.2868 (tpp) REVERT: B 502 ASN cc_start: 0.9036 (t0) cc_final: 0.8767 (t0) REVERT: B 573 LEU cc_start: 0.8863 (tt) cc_final: 0.8477 (tp) REVERT: B 586 MET cc_start: 0.8474 (mmm) cc_final: 0.8107 (mmm) REVERT: B 606 LEU cc_start: 0.8577 (tp) cc_final: 0.8222 (mm) REVERT: B 621 ASP cc_start: 0.9715 (t0) cc_final: 0.9459 (t70) REVERT: B 790 LEU cc_start: 0.9436 (mp) cc_final: 0.8957 (tp) REVERT: B 813 MET cc_start: 0.9621 (tpt) cc_final: 0.8765 (tpp) REVERT: B 828 ASP cc_start: 0.9315 (m-30) cc_final: 0.8343 (t0) REVERT: B 838 VAL cc_start: 0.9385 (t) cc_final: 0.9050 (p) REVERT: B 846 MET cc_start: 0.9389 (mtm) cc_final: 0.8768 (mtp) REVERT: B 962 GLU cc_start: 0.9329 (tt0) cc_final: 0.9120 (tm-30) REVERT: B 966 TYR cc_start: 0.9354 (m-80) cc_final: 0.8953 (m-80) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.3425 time to fit residues: 121.2537 Evaluate side-chains 181 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 14 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 35 optimal weight: 40.0000 chunk 179 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN A 506 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 175 GLN B 381 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3653 r_free = 0.3653 target = 0.067041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.041730 restraints weight = 180766.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.043157 restraints weight = 119465.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.044197 restraints weight = 87769.162| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 21107 Z= 0.242 Angle : 0.694 11.635 28863 Z= 0.372 Chirality : 0.048 1.058 3215 Planarity : 0.005 0.069 3397 Dihedral : 17.489 173.728 3463 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2359 helix: 0.78 (0.16), residues: 997 sheet: -0.62 (0.27), residues: 394 loop : -0.56 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1170 HIS 0.010 0.001 HIS A 892 PHE 0.021 0.002 PHE B 596 TYR 0.029 0.002 TYR B 837 ARG 0.010 0.001 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 931) hydrogen bonds : angle 5.15607 ( 2595) covalent geometry : bond 0.00507 (21107) covalent geometry : angle 0.69371 (28863) *********************** 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 202 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 2.299 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: A 446 LEU cc_start: 0.9845 (mt) cc_final: 0.9644 (mt) REVERT: A 483 ASN cc_start: 0.9008 (p0) cc_final: 0.8598 (m-40) REVERT: A 586 MET cc_start: 0.9028 (mmm) cc_final: 0.8811 (tpp) REVERT: A 684 ARG cc_start: 0.9722 (mtm180) cc_final: 0.9446 (mmm-85) REVERT: A 698 TYR cc_start: 0.9469 (t80) cc_final: 0.8486 (t80) REVERT: A 701 ASP cc_start: 0.9774 (t0) cc_final: 0.9565 (t0) REVERT: A 704 GLU cc_start: 0.9565 (tp30) cc_final: 0.9088 (tp30) REVERT: A 843 LEU cc_start: 0.9660 (mm) cc_final: 0.9324 (mm) REVERT: A 854 GLU cc_start: 0.9511 (mm-30) cc_final: 0.8594 (mm-30) REVERT: A 957 MET cc_start: 0.9248 (mmp) cc_final: 0.8823 (mmm) REVERT: A 962 GLU cc_start: 0.8776 (tp30) cc_final: 0.8247 (tp30) REVERT: A 1042 LEU cc_start: 0.9568 (mt) cc_final: 0.9338 (mt) REVERT: B 475 MET cc_start: 0.7791 (mmm) cc_final: 0.7578 (mmm) REVERT: B 573 LEU cc_start: 0.8935 (tt) cc_final: 0.8691 (pp) REVERT: B 586 MET cc_start: 0.8515 (mmm) cc_final: 0.8165 (mmm) REVERT: B 621 ASP cc_start: 0.9732 (t0) cc_final: 0.9450 (t70) REVERT: B 755 ASP cc_start: 0.9654 (p0) cc_final: 0.9437 (p0) REVERT: B 813 MET cc_start: 0.9599 (tpt) cc_final: 0.8711 (tpp) REVERT: B 828 ASP cc_start: 0.9371 (m-30) cc_final: 0.8405 (t0) REVERT: B 838 VAL cc_start: 0.9504 (t) cc_final: 0.9206 (p) REVERT: B 846 MET cc_start: 0.9362 (mtm) cc_final: 0.8741 (mtp) REVERT: B 957 MET cc_start: 0.8934 (mmp) cc_final: 0.8684 (mmm) REVERT: B 962 GLU cc_start: 0.9344 (tt0) cc_final: 0.9116 (tm-30) REVERT: B 1148 MET cc_start: 0.8895 (ptt) cc_final: 0.8552 (ptt) outliers start: 2 outliers final: 1 residues processed: 202 average time/residue: 0.3560 time to fit residues: 111.8026 Evaluate side-chains 159 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 28 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 152 optimal weight: 30.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 402 GLN ** 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 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN 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 = 0.3651 r_free = 0.3651 target = 0.066829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.041565 restraints weight = 179203.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.042911 restraints weight = 117909.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.043985 restraints weight = 86711.269| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21107 Z= 0.192 Angle : 0.637 10.295 28863 Z= 0.340 Chirality : 0.047 1.075 3215 Planarity : 0.004 0.042 3397 Dihedral : 17.544 173.304 3463 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.05 % Allowed : 1.21 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2359 helix: 0.87 (0.17), residues: 995 sheet: -0.56 (0.28), residues: 391 loop : -0.53 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1170 HIS 0.022 0.001 HIS B 172 PHE 0.030 0.002 PHE B 596 TYR 0.019 0.002 TYR B 837 ARG 0.008 0.001 ARG B1040 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 931) hydrogen bonds : angle 5.09894 ( 2595) covalent geometry : bond 0.00402 (21107) covalent geometry : angle 0.63714 (28863) *********************** 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 204 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7726 (mmp) cc_final: 0.6967 (tpp) REVERT: A 483 ASN cc_start: 0.8986 (p0) cc_final: 0.8638 (m-40) REVERT: A 531 TYR cc_start: 0.9190 (p90) cc_final: 0.8878 (p90) REVERT: A 684 ARG cc_start: 0.9729 (mtm180) cc_final: 0.9494 (ttp80) REVERT: A 698 TYR cc_start: 0.9472 (t80) cc_final: 0.8574 (t80) REVERT: A 704 GLU cc_start: 0.9547 (tp30) cc_final: 0.9046 (tp30) REVERT: A 714 MET cc_start: 0.9761 (tpp) cc_final: 0.9515 (tpp) REVERT: A 756 MET cc_start: 0.9743 (mpp) cc_final: 0.9257 (tpp) REVERT: A 854 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9095 (mm-30) REVERT: A 858 TYR cc_start: 0.9015 (t80) cc_final: 0.8728 (t80) REVERT: A 957 MET cc_start: 0.9252 (mmp) cc_final: 0.8783 (mmm) REVERT: A 962 GLU cc_start: 0.8729 (tp30) cc_final: 0.8174 (tp30) REVERT: A 1042 LEU cc_start: 0.9608 (mt) cc_final: 0.9390 (mt) REVERT: B 42 MET cc_start: 0.8938 (pmm) cc_final: 0.8550 (pmm) REVERT: B 447 ARG cc_start: 0.9371 (mtm-85) cc_final: 0.8989 (mtt180) REVERT: B 475 MET cc_start: 0.8030 (mmm) cc_final: 0.7541 (mmm) REVERT: B 573 LEU cc_start: 0.8948 (tt) cc_final: 0.8594 (tp) REVERT: B 586 MET cc_start: 0.8527 (mmm) cc_final: 0.8195 (mmm) REVERT: B 621 ASP cc_start: 0.9728 (t0) cc_final: 0.9462 (t70) REVERT: B 628 MET cc_start: 0.9185 (mtm) cc_final: 0.8982 (mtt) REVERT: B 813 MET cc_start: 0.9590 (tpt) cc_final: 0.8753 (tpp) REVERT: B 828 ASP cc_start: 0.9392 (m-30) cc_final: 0.8426 (t0) REVERT: B 838 VAL cc_start: 0.9502 (t) cc_final: 0.9194 (p) REVERT: B 841 LEU cc_start: 0.9791 (tp) cc_final: 0.9587 (tp) REVERT: B 845 ILE cc_start: 0.9335 (mm) cc_final: 0.9071 (mm) REVERT: B 846 MET cc_start: 0.9342 (mtm) cc_final: 0.8910 (mpp) REVERT: B 957 MET cc_start: 0.8937 (mmp) cc_final: 0.8686 (mmm) REVERT: B 962 GLU cc_start: 0.9353 (tt0) cc_final: 0.9131 (tm-30) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.3162 time to fit residues: 100.8097 Evaluate side-chains 165 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 198 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 chunk 107 optimal weight: 2.9990 chunk 127 optimal weight: 50.0000 chunk 57 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A 402 GLN ** 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.063919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039424 restraints weight = 182562.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040710 restraints weight = 121173.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.041695 restraints weight = 90076.640| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.6471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21107 Z= 0.230 Angle : 0.681 10.542 28863 Z= 0.366 Chirality : 0.047 0.929 3215 Planarity : 0.004 0.043 3397 Dihedral : 17.686 174.944 3463 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2359 helix: 0.63 (0.16), residues: 1005 sheet: -0.63 (0.28), residues: 390 loop : -0.55 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1170 HIS 0.010 0.001 HIS B 172 PHE 0.033 0.002 PHE B 596 TYR 0.026 0.002 TYR B 837 ARG 0.007 0.001 ARG B1040 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 931) hydrogen bonds : angle 5.25671 ( 2595) covalent geometry : bond 0.00476 (21107) covalent geometry : angle 0.68112 (28863) *********************** 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 191 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 ASN cc_start: 0.8984 (p0) cc_final: 0.8572 (m-40) REVERT: A 531 TYR cc_start: 0.9195 (p90) cc_final: 0.8875 (p90) REVERT: A 586 MET cc_start: 0.9060 (mmp) cc_final: 0.8539 (tpp) REVERT: A 698 TYR cc_start: 0.9486 (t80) cc_final: 0.8495 (t80) REVERT: A 701 ASP cc_start: 0.9730 (t70) cc_final: 0.9362 (t0) REVERT: A 704 GLU cc_start: 0.9550 (tp30) cc_final: 0.9076 (tp30) REVERT: A 714 MET cc_start: 0.9743 (tpp) cc_final: 0.9468 (tpp) REVERT: A 854 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9329 (mm-30) REVERT: A 858 TYR cc_start: 0.9083 (t80) cc_final: 0.8862 (t80) REVERT: A 957 MET cc_start: 0.9243 (mmp) cc_final: 0.8775 (mmm) REVERT: A 1042 LEU cc_start: 0.9619 (mt) cc_final: 0.9300 (mt) REVERT: B 32 MET cc_start: 0.4826 (tpt) cc_final: 0.4607 (tpt) REVERT: B 42 MET cc_start: 0.8973 (pmm) cc_final: 0.8567 (pmm) REVERT: B 447 ARG cc_start: 0.9355 (mtm-85) cc_final: 0.9088 (mtm-85) REVERT: B 475 MET cc_start: 0.8386 (mmm) cc_final: 0.8140 (mmt) REVERT: B 573 LEU cc_start: 0.8990 (tt) cc_final: 0.8716 (tp) REVERT: B 576 LEU cc_start: 0.8847 (tp) cc_final: 0.8559 (tp) REVERT: B 586 MET cc_start: 0.8648 (mmm) cc_final: 0.8325 (mmm) REVERT: B 621 ASP cc_start: 0.9700 (t0) cc_final: 0.9434 (t70) REVERT: B 698 TYR cc_start: 0.9592 (t80) cc_final: 0.9318 (t80) REVERT: B 813 MET cc_start: 0.9539 (tpt) cc_final: 0.8792 (tpp) REVERT: B 838 VAL cc_start: 0.9490 (t) cc_final: 0.9190 (p) REVERT: B 845 ILE cc_start: 0.9285 (mm) cc_final: 0.9029 (mp) REVERT: B 846 MET cc_start: 0.9345 (mtm) cc_final: 0.8768 (mtp) REVERT: B 858 TYR cc_start: 0.9092 (t80) cc_final: 0.8532 (t80) REVERT: B 957 MET cc_start: 0.8892 (mmp) cc_final: 0.8670 (mmm) REVERT: B 962 GLU cc_start: 0.9406 (tt0) cc_final: 0.9181 (tm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3177 time to fit residues: 95.5905 Evaluate side-chains 143 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 121 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 154 optimal weight: 40.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 GLN ** 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 = 0.3560 r_free = 0.3560 target = 0.062477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.038424 restraints weight = 189214.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.039752 restraints weight = 124627.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040718 restraints weight = 90993.637| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21107 Z= 0.242 Angle : 0.692 10.797 28863 Z= 0.373 Chirality : 0.046 0.519 3215 Planarity : 0.005 0.052 3397 Dihedral : 17.833 175.609 3463 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2359 helix: 0.46 (0.16), residues: 1015 sheet: -0.85 (0.27), residues: 388 loop : -0.67 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1189 HIS 0.008 0.001 HIS B 172 PHE 0.023 0.002 PHE B1107 TYR 0.024 0.002 TYR B 824 ARG 0.005 0.001 ARG B1131 Details of bonding type rmsd hydrogen bonds : bond 0.05159 ( 931) hydrogen bonds : angle 5.35705 ( 2595) covalent geometry : bond 0.00503 (21107) covalent geometry : angle 0.69187 (28863) *********************** 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 178 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.101 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 483 ASN cc_start: 0.9007 (p0) cc_final: 0.8703 (t0) REVERT: A 531 TYR cc_start: 0.9172 (p90) cc_final: 0.8822 (p90) REVERT: A 586 MET cc_start: 0.9048 (mmp) cc_final: 0.8765 (tpp) REVERT: A 635 MET cc_start: 0.9483 (pmm) cc_final: 0.8941 (pmm) REVERT: A 698 TYR cc_start: 0.9462 (t80) cc_final: 0.8497 (t80) REVERT: A 701 ASP cc_start: 0.9631 (t70) cc_final: 0.9385 (t0) REVERT: A 704 GLU cc_start: 0.9486 (tp30) cc_final: 0.9051 (tp30) REVERT: A 714 MET cc_start: 0.9753 (tpp) cc_final: 0.9451 (tpp) REVERT: A 756 MET cc_start: 0.9729 (mpp) cc_final: 0.9214 (tpp) REVERT: A 775 LEU cc_start: 0.9521 (tp) cc_final: 0.9295 (tp) REVERT: A 854 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9223 (mm-30) REVERT: A 858 TYR cc_start: 0.9023 (t80) cc_final: 0.8674 (t80) REVERT: A 957 MET cc_start: 0.9203 (mmp) cc_final: 0.8707 (mmm) REVERT: A 1042 LEU cc_start: 0.9602 (mt) cc_final: 0.9299 (mt) REVERT: B 32 MET cc_start: 0.4719 (tpt) cc_final: 0.4478 (tpt) REVERT: B 42 MET cc_start: 0.8916 (pmm) cc_final: 0.8514 (pmm) REVERT: B 576 LEU cc_start: 0.8925 (tp) cc_final: 0.8674 (tp) REVERT: B 586 MET cc_start: 0.8743 (mmm) cc_final: 0.8135 (mmm) REVERT: B 621 ASP cc_start: 0.9682 (t0) cc_final: 0.9437 (t70) REVERT: B 643 ASP cc_start: 0.9265 (m-30) cc_final: 0.8897 (p0) REVERT: B 698 TYR cc_start: 0.9492 (t80) cc_final: 0.9166 (t80) REVERT: B 813 MET cc_start: 0.9492 (tpt) cc_final: 0.8793 (tpp) REVERT: B 838 VAL cc_start: 0.9455 (t) cc_final: 0.9149 (p) REVERT: B 845 ILE cc_start: 0.9328 (mm) cc_final: 0.9122 (pt) REVERT: B 846 MET cc_start: 0.9264 (mtm) cc_final: 0.8969 (mtp) REVERT: B 858 TYR cc_start: 0.9044 (t80) cc_final: 0.8387 (t80) REVERT: B 1153 ASP cc_start: 0.9562 (t0) cc_final: 0.9251 (m-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3075 time to fit residues: 87.4894 Evaluate side-chains 140 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 230 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 557 HIS ** 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 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 GLN ** 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 = 0.3600 r_free = 0.3600 target = 0.064204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.039606 restraints weight = 185226.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040909 restraints weight = 119676.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041969 restraints weight = 86901.560| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21107 Z= 0.155 Angle : 0.616 10.101 28863 Z= 0.329 Chirality : 0.046 0.733 3215 Planarity : 0.004 0.049 3397 Dihedral : 17.744 176.068 3463 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2359 helix: 0.69 (0.16), residues: 1007 sheet: -0.74 (0.28), residues: 379 loop : -0.54 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.008 0.001 HIS B 172 PHE 0.033 0.002 PHE B 596 TYR 0.024 0.002 TYR B 698 ARG 0.005 0.001 ARG A 736 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 931) hydrogen bonds : angle 5.16786 ( 2595) covalent geometry : bond 0.00331 (21107) covalent geometry : angle 0.61650 (28863) *********************** 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 185 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 2.348 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 475 MET cc_start: 0.8460 (mmp) cc_final: 0.8202 (mmp) REVERT: A 483 ASN cc_start: 0.9032 (p0) cc_final: 0.8641 (t0) REVERT: A 586 MET cc_start: 0.9025 (mmp) cc_final: 0.8706 (tpp) REVERT: A 635 MET cc_start: 0.9505 (pmm) cc_final: 0.8904 (pmm) REVERT: A 698 TYR cc_start: 0.9446 (t80) cc_final: 0.8530 (t80) REVERT: A 704 GLU cc_start: 0.9471 (tp30) cc_final: 0.9019 (tp30) REVERT: A 714 MET cc_start: 0.9769 (tpp) cc_final: 0.9352 (tpp) REVERT: A 756 MET cc_start: 0.9717 (mpp) cc_final: 0.9234 (tpp) REVERT: A 854 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9297 (mm-30) REVERT: A 858 TYR cc_start: 0.8980 (t80) cc_final: 0.8677 (t80) REVERT: A 957 MET cc_start: 0.9189 (mmp) cc_final: 0.8682 (mmm) REVERT: A 1042 LEU cc_start: 0.9572 (mt) cc_final: 0.9298 (mt) REVERT: B 32 MET cc_start: 0.4353 (tpt) cc_final: 0.4140 (tpt) REVERT: B 42 MET cc_start: 0.8834 (pmm) cc_final: 0.8478 (pmm) REVERT: B 447 ARG cc_start: 0.9313 (mtm-85) cc_final: 0.8964 (mtt-85) REVERT: B 576 LEU cc_start: 0.8871 (tp) cc_final: 0.8551 (tp) REVERT: B 586 MET cc_start: 0.8736 (mmm) cc_final: 0.8141 (mmm) REVERT: B 621 ASP cc_start: 0.9701 (t0) cc_final: 0.9465 (t70) REVERT: B 643 ASP cc_start: 0.9270 (m-30) cc_final: 0.8953 (p0) REVERT: B 698 TYR cc_start: 0.9533 (t80) cc_final: 0.9253 (t80) REVERT: B 813 MET cc_start: 0.9516 (tpt) cc_final: 0.8789 (tpp) REVERT: B 845 ILE cc_start: 0.9252 (mm) cc_final: 0.9003 (pt) REVERT: B 846 MET cc_start: 0.9234 (mtm) cc_final: 0.8833 (mtp) REVERT: B 858 TYR cc_start: 0.8938 (t80) cc_final: 0.8650 (t80) REVERT: B 865 LEU cc_start: 0.9488 (mm) cc_final: 0.9253 (pp) REVERT: B 1153 ASP cc_start: 0.9545 (t0) cc_final: 0.9242 (m-30) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3203 time to fit residues: 94.8034 Evaluate side-chains 143 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 32 optimal weight: 0.4980 chunk 239 optimal weight: 7.9990 chunk 15 optimal weight: 40.0000 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 ASN ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 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 = 0.3595 r_free = 0.3595 target = 0.064005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039446 restraints weight = 183856.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.040843 restraints weight = 119424.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041889 restraints weight = 86045.360| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21107 Z= 0.156 Angle : 0.622 10.513 28863 Z= 0.330 Chirality : 0.045 0.739 3215 Planarity : 0.004 0.054 3397 Dihedral : 17.682 176.659 3463 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2359 helix: 0.72 (0.16), residues: 1008 sheet: -0.74 (0.27), residues: 386 loop : -0.50 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1170 HIS 0.008 0.001 HIS B 172 PHE 0.029 0.002 PHE B 596 TYR 0.021 0.002 TYR B 698 ARG 0.006 0.001 ARG B1131 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 931) hydrogen bonds : angle 5.12732 ( 2595) covalent geometry : bond 0.00333 (21107) covalent geometry : angle 0.62183 (28863) ********************** 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 180 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 2.168 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 483 ASN cc_start: 0.9083 (p0) cc_final: 0.8706 (t0) REVERT: A 531 TYR cc_start: 0.9083 (p90) cc_final: 0.8698 (p90) REVERT: A 586 MET cc_start: 0.9114 (mmp) cc_final: 0.8773 (tpp) REVERT: A 635 MET cc_start: 0.9507 (pmm) cc_final: 0.8959 (pmm) REVERT: A 698 TYR cc_start: 0.9454 (t80) cc_final: 0.8508 (t80) REVERT: A 704 GLU cc_start: 0.9541 (tp30) cc_final: 0.9070 (tp30) REVERT: A 714 MET cc_start: 0.9749 (tpp) cc_final: 0.9409 (tpp) REVERT: A 756 MET cc_start: 0.9733 (mpp) cc_final: 0.9242 (tpp) REVERT: A 854 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9187 (mm-30) REVERT: A 858 TYR cc_start: 0.9005 (t80) cc_final: 0.8695 (t80) REVERT: A 957 MET cc_start: 0.9194 (mmp) cc_final: 0.8687 (mmm) REVERT: A 1042 LEU cc_start: 0.9570 (mt) cc_final: 0.9301 (mt) REVERT: B 42 MET cc_start: 0.8849 (pmm) cc_final: 0.8496 (pmm) REVERT: B 517 ASN cc_start: 0.9447 (m110) cc_final: 0.9131 (p0) REVERT: B 576 LEU cc_start: 0.8897 (tp) cc_final: 0.8593 (tp) REVERT: B 586 MET cc_start: 0.8728 (mmm) cc_final: 0.8160 (mmm) REVERT: B 621 ASP cc_start: 0.9690 (t0) cc_final: 0.9468 (t70) REVERT: B 643 ASP cc_start: 0.9312 (m-30) cc_final: 0.9001 (p0) REVERT: B 698 TYR cc_start: 0.9539 (t80) cc_final: 0.9243 (t80) REVERT: B 813 MET cc_start: 0.9488 (tpt) cc_final: 0.8771 (tpp) REVERT: B 845 ILE cc_start: 0.9295 (mm) cc_final: 0.9046 (pt) REVERT: B 846 MET cc_start: 0.9268 (mtm) cc_final: 0.8868 (mtp) REVERT: B 858 TYR cc_start: 0.8932 (t80) cc_final: 0.8668 (t80) REVERT: B 865 LEU cc_start: 0.9520 (mm) cc_final: 0.9291 (pp) REVERT: B 957 MET cc_start: 0.8857 (mmp) cc_final: 0.8655 (mmm) REVERT: B 1153 ASP cc_start: 0.9543 (t0) cc_final: 0.9255 (m-30) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3032 time to fit residues: 87.3164 Evaluate side-chains 138 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 172 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.063881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039399 restraints weight = 186302.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.040783 restraints weight = 120579.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041808 restraints weight = 86781.979| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21107 Z= 0.157 Angle : 0.621 9.769 28863 Z= 0.331 Chirality : 0.045 0.671 3215 Planarity : 0.004 0.048 3397 Dihedral : 17.673 177.681 3463 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2359 helix: 0.70 (0.16), residues: 1012 sheet: -0.70 (0.27), residues: 386 loop : -0.48 (0.21), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1170 HIS 0.007 0.001 HIS B 172 PHE 0.028 0.002 PHE B 596 TYR 0.021 0.002 TYR B 698 ARG 0.014 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 931) hydrogen bonds : angle 5.14869 ( 2595) covalent geometry : bond 0.00335 (21107) covalent geometry : angle 0.62087 (28863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7068.41 seconds wall clock time: 124 minutes 59.35 seconds (7499.35 seconds total)