Starting phenix.real_space_refine on Sun Jun 22 04:39:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgm_37226/06_2025/8kgm_37226.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgm_37226/06_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_37226/06_2025/8kgm_37226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgm_37226/06_2025/8kgm_37226.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgm_37226/06_2025/8kgm_37226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgm_37226/06_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): 1.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.00, per 1000 atoms: 0.59 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: 4.64 Conformation dependent library (CDL) restraints added in 2.3 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: 7.89 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: 10.52 Time building geometry restraints manager: 5.59 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 53.750 Find NCS groups from input model: 0.900 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.310 ------------------------------------------------------------------------------- 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 : 2.231 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: 0.3857 time to fit residues: 260.5184 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 : 2.235 ------------------------------------------------------------------------------- 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 = 62)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.052687 restraints weight = 162990.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.054542 restraints weight = 105688.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.055867 restraints weight = 75622.582| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 2.051 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: -0.5796 (mmm) cc_final: -0.6230 (mmm) REVERT: A 473 VAL cc_start: 0.8311 (t) cc_final: 0.8095 (t) REVERT: A 475 MET cc_start: 0.7258 (mmp) cc_final: 0.6808 (tpp) REVERT: A 537 CYS cc_start: 0.9185 (m) cc_final: 0.8929 (p) REVERT: A 586 MET cc_start: 0.8863 (mmm) cc_final: 0.8629 (tpp) REVERT: A 629 PHE cc_start: 0.9588 (m-10) cc_final: 0.9349 (m-10) REVERT: A 684 ARG cc_start: 0.9722 (mtm180) cc_final: 0.9409 (mmm-85) REVERT: A 698 TYR cc_start: 0.9450 (t80) cc_final: 0.8608 (t80) REVERT: A 737 LYS cc_start: 0.8797 (tppt) cc_final: 0.8547 (tppp) REVERT: A 739 PHE cc_start: 0.9411 (p90) cc_final: 0.9126 (p90) REVERT: A 760 THR cc_start: 0.9662 (m) cc_final: 0.9451 (p) REVERT: A 775 LEU cc_start: 0.9303 (tp) cc_final: 0.8920 (tp) REVERT: A 776 TYR cc_start: 0.9193 (m-80) cc_final: 0.8988 (m-80) REVERT: A 827 GLU cc_start: 0.8749 (tp30) cc_final: 0.8107 (tp30) REVERT: A 843 LEU cc_start: 0.9585 (mt) cc_final: 0.9361 (mm) REVERT: A 846 MET cc_start: 0.9572 (mtp) cc_final: 0.9347 (mtt) REVERT: A 854 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8524 (tp30) REVERT: A 957 MET cc_start: 0.9122 (mmp) cc_final: 0.8754 (mmm) REVERT: A 962 GLU cc_start: 0.8491 (tp30) cc_final: 0.8140 (tp30) REVERT: A 988 GLU cc_start: 0.9143 (mp0) cc_final: 0.8502 (pm20) REVERT: A 1078 HIS cc_start: 0.9607 (t70) cc_final: 0.9380 (t70) REVERT: B 18 MET cc_start: -0.0245 (ptt) cc_final: -0.1859 (mmt) REVERT: B 450 LEU cc_start: 0.9241 (tp) cc_final: 0.8855 (tp) REVERT: B 467 MET cc_start: 0.9199 (mtm) cc_final: 0.8748 (mtt) REVERT: B 502 ASN cc_start: 0.8844 (t0) cc_final: 0.8510 (t0) REVERT: B 573 LEU cc_start: 0.8771 (tt) cc_final: 0.8534 (tp) REVERT: B 586 MET cc_start: 0.8250 (mmm) cc_final: 0.7929 (mmm) REVERT: B 606 LEU cc_start: 0.8575 (tp) cc_final: 0.8282 (mm) REVERT: B 628 MET cc_start: 0.9360 (mtm) cc_final: 0.9139 (mtt) REVERT: B 714 MET cc_start: 0.8741 (ppp) cc_final: 0.8454 (tmm) REVERT: B 813 MET cc_start: 0.9577 (tpt) cc_final: 0.8772 (tpp) REVERT: B 846 MET cc_start: 0.9247 (mtm) cc_final: 0.8892 (mtm) REVERT: B 939 LEU cc_start: 0.9420 (mt) cc_final: 0.9130 (mt) REVERT: B 962 GLU cc_start: 0.9241 (tt0) cc_final: 0.9030 (tm-30) REVERT: B 966 TYR cc_start: 0.9076 (m-80) cc_final: 0.8744 (m-80) outliers start: 2 outliers final: 1 residues processed: 291 average time/residue: 0.3483 time to fit residues: 154.8290 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 : 2.453 ------------------------------------------------------------------------------- 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: 8.9990 chunk 204 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN A 402 GLN A 506 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS A1149 GLN ** 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 905 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.070833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.045303 restraints weight = 176619.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.046811 restraints weight = 117044.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047890 restraints weight = 85425.321| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21107 Z= 0.229 Angle : 0.699 12.134 28863 Z= 0.375 Chirality : 0.045 0.191 3215 Planarity : 0.005 0.054 3397 Dihedral : 17.439 175.349 3463 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % 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: -0.40 (0.17), residues: 2359 helix: 0.53 (0.16), residues: 983 sheet: -0.65 (0.27), residues: 387 loop : -0.80 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1170 HIS 0.009 0.002 HIS A 892 PHE 0.034 0.002 PHE B 785 TYR 0.020 0.002 TYR B 837 ARG 0.011 0.001 ARG B 571 Details of bonding type rmsd hydrogen bonds : bond 0.05605 ( 931) hydrogen bonds : angle 5.18723 ( 2595) covalent geometry : bond 0.00476 (21107) covalent geometry : angle 0.69872 (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 228 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 2.729 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: A 392 MET cc_start: -0.5323 (mmm) cc_final: -0.5682 (mmm) REVERT: A 542 LEU cc_start: 0.9276 (mt) cc_final: 0.9044 (mt) REVERT: A 586 MET cc_start: 0.8916 (mmm) cc_final: 0.8703 (tpp) REVERT: A 684 ARG cc_start: 0.9702 (mtm180) cc_final: 0.9434 (mmm-85) REVERT: A 698 TYR cc_start: 0.9512 (t80) cc_final: 0.8484 (t80) REVERT: A 701 ASP cc_start: 0.9701 (t70) cc_final: 0.9477 (t0) REVERT: A 704 GLU cc_start: 0.9568 (tp30) cc_final: 0.9167 (tp30) REVERT: A 714 MET cc_start: 0.9567 (ttt) cc_final: 0.9029 (ttp) REVERT: A 775 LEU cc_start: 0.9414 (tp) cc_final: 0.9172 (tp) REVERT: A 776 TYR cc_start: 0.9296 (m-80) cc_final: 0.9067 (m-80) REVERT: A 854 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9080 (mm-30) REVERT: A 957 MET cc_start: 0.9186 (mmp) cc_final: 0.8814 (mmm) REVERT: A 962 GLU cc_start: 0.8617 (tp30) cc_final: 0.8183 (tp30) REVERT: A 1042 LEU cc_start: 0.9517 (mt) cc_final: 0.9293 (mt) REVERT: B 257 MET cc_start: -0.0704 (tmm) cc_final: -0.1825 (ttp) REVERT: B 573 LEU cc_start: 0.8890 (tt) cc_final: 0.8630 (pp) REVERT: B 576 LEU cc_start: 0.9069 (tp) cc_final: 0.8696 (tp) REVERT: B 586 MET cc_start: 0.8532 (mmm) cc_final: 0.8169 (mmm) REVERT: B 621 ASP cc_start: 0.9712 (t0) cc_final: 0.9408 (t70) REVERT: B 755 ASP cc_start: 0.9644 (p0) cc_final: 0.9103 (p0) REVERT: B 790 LEU cc_start: 0.9406 (mp) cc_final: 0.8982 (tp) REVERT: B 813 MET cc_start: 0.9595 (tpt) cc_final: 0.8649 (tpp) REVERT: B 828 ASP cc_start: 0.9233 (m-30) cc_final: 0.8478 (t0) REVERT: B 838 VAL cc_start: 0.9492 (t) cc_final: 0.9184 (p) REVERT: B 845 ILE cc_start: 0.9269 (mm) cc_final: 0.9059 (mm) REVERT: B 846 MET cc_start: 0.9359 (mtm) cc_final: 0.8803 (mtp) REVERT: B 962 GLU cc_start: 0.9327 (tt0) cc_final: 0.9106 (tm-30) REVERT: B 1048 MET cc_start: 0.9503 (ptt) cc_final: 0.9149 (mmt) outliers start: 1 outliers final: 1 residues processed: 228 average time/residue: 0.3279 time to fit residues: 115.5945 Evaluate side-chains 169 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 2.216 ------------------------------------------------------------------------------- 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: 0.8980 chunk 67 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 51 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 70 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 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 381 HIS A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS B 175 GLN B 557 HIS B 759 ASN B 905 ASN ** B 909 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 = 0.3786 r_free = 0.3786 target = 0.073216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046684 restraints weight = 174195.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.048411 restraints weight = 112118.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.049631 restraints weight = 79677.421| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21107 Z= 0.123 Angle : 0.588 11.462 28863 Z= 0.311 Chirality : 0.043 0.284 3215 Planarity : 0.004 0.047 3397 Dihedral : 17.291 173.304 3463 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % 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: -0.05 (0.18), residues: 2359 helix: 0.84 (0.17), residues: 981 sheet: -0.54 (0.27), residues: 386 loop : -0.61 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.005 0.001 HIS A 620 PHE 0.015 0.001 PHE B 785 TYR 0.017 0.001 TYR B 837 ARG 0.013 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 931) hydrogen bonds : angle 4.84961 ( 2595) covalent geometry : bond 0.00259 (21107) covalent geometry : angle 0.58849 (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 238 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 LEU cc_start: 0.9806 (mt) cc_final: 0.9595 (mt) REVERT: A 483 ASN cc_start: 0.8931 (p0) cc_final: 0.8520 (m-40) REVERT: A 503 LYS cc_start: 0.9518 (ptmm) cc_final: 0.9258 (ptmm) REVERT: A 586 MET cc_start: 0.8931 (mmm) cc_final: 0.8701 (tpp) REVERT: A 684 ARG cc_start: 0.9750 (mtm180) cc_final: 0.9482 (mmm-85) REVERT: A 698 TYR cc_start: 0.9470 (t80) cc_final: 0.8516 (t80) REVERT: A 704 GLU cc_start: 0.9578 (tp30) cc_final: 0.9074 (tp30) REVERT: A 775 LEU cc_start: 0.9455 (tp) cc_final: 0.9148 (tp) REVERT: A 776 TYR cc_start: 0.9250 (m-80) cc_final: 0.8858 (m-80) REVERT: A 854 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8792 (mm-30) REVERT: A 957 MET cc_start: 0.9257 (mmp) cc_final: 0.8818 (mmm) REVERT: A 962 GLU cc_start: 0.8636 (tp30) cc_final: 0.8188 (tp30) REVERT: B 32 MET cc_start: 0.3559 (tpt) cc_final: 0.3175 (tpp) REVERT: B 502 ASN cc_start: 0.8982 (t0) cc_final: 0.8749 (t0) REVERT: B 573 LEU cc_start: 0.8862 (tt) cc_final: 0.8489 (tp) REVERT: B 576 LEU cc_start: 0.9019 (tp) cc_final: 0.8605 (tp) REVERT: B 586 MET cc_start: 0.8490 (mmm) cc_final: 0.8142 (mmm) REVERT: B 606 LEU cc_start: 0.8491 (tp) cc_final: 0.8235 (mm) REVERT: B 621 ASP cc_start: 0.9716 (t0) cc_final: 0.9482 (t70) REVERT: B 755 ASP cc_start: 0.9407 (p0) cc_final: 0.9178 (p0) REVERT: B 790 LEU cc_start: 0.9407 (mp) cc_final: 0.8941 (tp) REVERT: B 813 MET cc_start: 0.9620 (tpt) cc_final: 0.8767 (tpp) REVERT: B 838 VAL cc_start: 0.9408 (t) cc_final: 0.9084 (p) REVERT: B 846 MET cc_start: 0.9441 (mtm) cc_final: 0.8782 (mtp) REVERT: B 962 GLU cc_start: 0.9337 (tt0) cc_final: 0.9131 (tm-30) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.4450 time to fit residues: 166.5970 Evaluate side-chains 182 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 2.897 ------------------------------------------------------------------------------- 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: 10.0000 chunk 167 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 217 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 chunk 35 optimal weight: 50.0000 chunk 179 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS ** A1051 HIS ** 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 767 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.070287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.044238 restraints weight = 174786.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.045777 restraints weight = 115047.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046906 restraints weight = 83801.373| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21107 Z= 0.172 Angle : 0.606 11.771 28863 Z= 0.325 Chirality : 0.043 0.380 3215 Planarity : 0.004 0.044 3397 Dihedral : 17.301 172.921 3463 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.18), residues: 2359 helix: 1.07 (0.17), residues: 982 sheet: -0.44 (0.27), residues: 393 loop : -0.48 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1170 HIS 0.013 0.001 HIS B 172 PHE 0.022 0.002 PHE B 590 TYR 0.018 0.002 TYR B 837 ARG 0.009 0.001 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 931) hydrogen bonds : angle 4.87259 ( 2595) covalent geometry : bond 0.00368 (21107) covalent geometry : angle 0.60568 (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 213 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 2.375 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 475 MET cc_start: 0.6698 (mmp) cc_final: 0.5564 (tpp) REVERT: A 483 ASN cc_start: 0.8948 (p0) cc_final: 0.8534 (m-40) REVERT: A 586 MET cc_start: 0.8961 (mmm) cc_final: 0.8733 (tpp) REVERT: A 684 ARG cc_start: 0.9715 (mtm180) cc_final: 0.9476 (mmm-85) REVERT: A 698 TYR cc_start: 0.9423 (t80) cc_final: 0.8446 (t80) REVERT: A 701 ASP cc_start: 0.9737 (t70) cc_final: 0.9484 (t0) REVERT: A 704 GLU cc_start: 0.9534 (tp30) cc_final: 0.9024 (tp30) REVERT: A 749 MET cc_start: 0.9230 (mmp) cc_final: 0.8170 (mmm) REVERT: A 843 LEU cc_start: 0.9706 (mm) cc_final: 0.9355 (mm) REVERT: A 846 MET cc_start: 0.9591 (mtp) cc_final: 0.9239 (mtt) REVERT: A 854 GLU cc_start: 0.9547 (mm-30) cc_final: 0.8585 (mm-30) REVERT: A 957 MET cc_start: 0.9214 (mmp) cc_final: 0.8759 (mmm) REVERT: A 962 GLU cc_start: 0.8650 (tp30) cc_final: 0.8164 (tp30) REVERT: A 1042 LEU cc_start: 0.9552 (mt) cc_final: 0.9330 (mt) REVERT: B 257 MET cc_start: -0.0149 (tmm) cc_final: -0.0790 (ttp) REVERT: B 475 MET cc_start: 0.6388 (tpt) cc_final: 0.5951 (tpt) REVERT: B 502 ASN cc_start: 0.9024 (t0) cc_final: 0.8764 (t0) REVERT: B 541 ASP cc_start: 0.8668 (p0) cc_final: 0.8294 (p0) REVERT: B 573 LEU cc_start: 0.8890 (tt) cc_final: 0.8515 (tp) REVERT: B 586 MET cc_start: 0.8498 (mmm) cc_final: 0.8166 (mmm) REVERT: B 621 ASP cc_start: 0.9711 (t0) cc_final: 0.9431 (t70) REVERT: B 813 MET cc_start: 0.9612 (tpt) cc_final: 0.8719 (tpp) REVERT: B 828 ASP cc_start: 0.9319 (m-30) cc_final: 0.8346 (t0) REVERT: B 838 VAL cc_start: 0.9456 (t) cc_final: 0.9117 (p) REVERT: B 846 MET cc_start: 0.9408 (mtm) cc_final: 0.8796 (mtp) REVERT: B 957 MET cc_start: 0.8914 (mmp) cc_final: 0.8700 (mmm) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.4315 time to fit residues: 142.6782 Evaluate side-chains 170 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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: 0.9990 chunk 100 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 chunk 18 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 152 optimal weight: 30.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 HIS ** 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 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.071074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.044842 restraints weight = 172158.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.046416 restraints weight = 111868.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047540 restraints weight = 80861.323| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21107 Z= 0.124 Angle : 0.588 13.522 28863 Z= 0.309 Chirality : 0.043 0.316 3215 Planarity : 0.004 0.048 3397 Dihedral : 17.230 173.218 3463 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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 : 0.00 % 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: 0.27 (0.18), residues: 2359 helix: 1.10 (0.17), residues: 983 sheet: -0.26 (0.28), residues: 394 loop : -0.48 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1170 HIS 0.009 0.001 HIS B 172 PHE 0.038 0.001 PHE B 596 TYR 0.015 0.001 TYR A 169 ARG 0.014 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 931) hydrogen bonds : angle 4.76281 ( 2595) covalent geometry : bond 0.00265 (21107) covalent geometry : angle 0.58799 (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 219 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 3.782 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 467 MET cc_start: 0.9614 (mtt) cc_final: 0.7990 (mmp) REVERT: A 475 MET cc_start: 0.6859 (mmp) cc_final: 0.5774 (tpp) REVERT: A 483 ASN cc_start: 0.8978 (p0) cc_final: 0.8609 (m-40) REVERT: A 493 MET cc_start: 0.9637 (tpp) cc_final: 0.9359 (tpp) REVERT: A 572 LEU cc_start: 0.9342 (tp) cc_final: 0.9119 (tt) REVERT: A 586 MET cc_start: 0.8952 (mmm) cc_final: 0.8713 (tpp) REVERT: A 684 ARG cc_start: 0.9717 (mtm180) cc_final: 0.9472 (mmm-85) REVERT: A 698 TYR cc_start: 0.9424 (t80) cc_final: 0.8392 (t80) REVERT: A 701 ASP cc_start: 0.9732 (t70) cc_final: 0.9451 (t70) REVERT: A 704 GLU cc_start: 0.9517 (tp30) cc_final: 0.9020 (tp30) REVERT: A 749 MET cc_start: 0.9166 (mmp) cc_final: 0.8713 (mmm) REVERT: A 756 MET cc_start: 0.9721 (mpp) cc_final: 0.9276 (tpt) REVERT: A 776 TYR cc_start: 0.8939 (m-80) cc_final: 0.8512 (m-80) REVERT: A 843 LEU cc_start: 0.9702 (mm) cc_final: 0.9321 (mm) REVERT: A 854 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9084 (mm-30) REVERT: A 957 MET cc_start: 0.9225 (mmp) cc_final: 0.8760 (mmm) REVERT: A 962 GLU cc_start: 0.8625 (tp30) cc_final: 0.8124 (tp30) REVERT: A 1042 LEU cc_start: 0.9549 (mt) cc_final: 0.9317 (mt) REVERT: B 502 ASN cc_start: 0.8976 (t0) cc_final: 0.8774 (t0) REVERT: B 541 ASP cc_start: 0.8743 (p0) cc_final: 0.8432 (p0) REVERT: B 573 LEU cc_start: 0.8865 (tt) cc_final: 0.8503 (tp) REVERT: B 586 MET cc_start: 0.8499 (mmm) cc_final: 0.8173 (mmm) REVERT: B 621 ASP cc_start: 0.9723 (t0) cc_final: 0.9481 (t70) REVERT: B 764 LYS cc_start: 0.9621 (mtpt) cc_final: 0.9352 (ttpt) REVERT: B 813 MET cc_start: 0.9615 (tpt) cc_final: 0.8774 (tpp) REVERT: B 828 ASP cc_start: 0.9295 (m-30) cc_final: 0.8352 (t0) REVERT: B 831 ARG cc_start: 0.8867 (mtt-85) cc_final: 0.8632 (mtt180) REVERT: B 838 VAL cc_start: 0.9422 (t) cc_final: 0.9087 (p) REVERT: B 846 MET cc_start: 0.9358 (mtm) cc_final: 0.8761 (mtp) REVERT: B 957 MET cc_start: 0.8892 (mmp) cc_final: 0.8658 (mmm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.4999 time to fit residues: 170.6864 Evaluate side-chains 175 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 2.209 ------------------------------------------------------------------------------- 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: 5.9990 chunk 207 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 chunk 107 optimal weight: 2.9990 chunk 127 optimal weight: 50.0000 chunk 57 optimal weight: 0.0370 chunk 211 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 381 HIS A 402 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 381 HIS B 759 ASN ** B 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1099 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.066758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.041486 restraints weight = 179493.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.042826 restraints weight = 118380.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043898 restraints weight = 87501.615| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21107 Z= 0.200 Angle : 0.657 11.394 28863 Z= 0.350 Chirality : 0.044 0.269 3215 Planarity : 0.004 0.066 3397 Dihedral : 17.426 174.740 3463 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.18), residues: 2359 helix: 0.93 (0.17), residues: 990 sheet: -0.32 (0.28), residues: 385 loop : -0.39 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 820 HIS 0.010 0.001 HIS A 631 PHE 0.019 0.002 PHE B 785 TYR 0.026 0.002 TYR B 837 ARG 0.007 0.001 ARG A 736 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 931) hydrogen bonds : angle 4.99271 ( 2595) covalent geometry : bond 0.00420 (21107) covalent geometry : angle 0.65684 (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 202 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7938 (mmp) cc_final: 0.6806 (tpp) REVERT: A 483 ASN cc_start: 0.8966 (p0) cc_final: 0.8647 (m-40) REVERT: A 493 MET cc_start: 0.9682 (tpp) cc_final: 0.9465 (tpp) REVERT: A 698 TYR cc_start: 0.9437 (t80) cc_final: 0.8491 (t80) REVERT: A 701 ASP cc_start: 0.9677 (t70) cc_final: 0.9418 (t0) REVERT: A 704 GLU cc_start: 0.9515 (tp30) cc_final: 0.9025 (tp30) REVERT: A 714 MET cc_start: 0.9526 (tpt) cc_final: 0.9284 (tpp) REVERT: A 749 MET cc_start: 0.9064 (mmp) cc_final: 0.8743 (mmm) REVERT: A 756 MET cc_start: 0.9725 (mpp) cc_final: 0.9272 (tpp) REVERT: A 775 LEU cc_start: 0.9441 (tp) cc_final: 0.8874 (tp) REVERT: A 846 MET cc_start: 0.9572 (mtm) cc_final: 0.9138 (mtt) REVERT: A 854 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9188 (mm-30) REVERT: A 957 MET cc_start: 0.9197 (mmp) cc_final: 0.8727 (mmm) REVERT: A 962 GLU cc_start: 0.8640 (tp30) cc_final: 0.8097 (tp30) REVERT: A 1042 LEU cc_start: 0.9582 (mt) cc_final: 0.9269 (mt) REVERT: B 32 MET cc_start: 0.4477 (tpt) cc_final: 0.3869 (tpp) REVERT: B 475 MET cc_start: 0.7757 (mmm) cc_final: 0.7276 (mmm) REVERT: B 541 ASP cc_start: 0.8814 (p0) cc_final: 0.8551 (p0) REVERT: B 573 LEU cc_start: 0.8906 (tt) cc_final: 0.8698 (pp) REVERT: B 586 MET cc_start: 0.8491 (mmm) cc_final: 0.8140 (mmm) REVERT: B 621 ASP cc_start: 0.9698 (t0) cc_final: 0.9407 (t70) REVERT: B 813 MET cc_start: 0.9524 (tpt) cc_final: 0.8677 (tpp) REVERT: B 838 VAL cc_start: 0.9467 (t) cc_final: 0.9141 (p) REVERT: B 845 ILE cc_start: 0.9294 (mm) cc_final: 0.8992 (pt) REVERT: B 846 MET cc_start: 0.9404 (mtm) cc_final: 0.8966 (mtp) REVERT: B 858 TYR cc_start: 0.8991 (t80) cc_final: 0.8769 (t80) REVERT: B 1153 ASP cc_start: 0.9531 (t0) cc_final: 0.9238 (m-30) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3321 time to fit residues: 104.5011 Evaluate side-chains 160 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.201 ------------------------------------------------------------------------------- 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: 0.8980 chunk 133 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 154 optimal weight: 30.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 620 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** ** A1051 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 286 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1099 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.064879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040069 restraints weight = 183530.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041486 restraints weight = 119761.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.042473 restraints weight = 86668.817| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.6542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21107 Z= 0.212 Angle : 0.656 9.709 28863 Z= 0.351 Chirality : 0.044 0.245 3215 Planarity : 0.004 0.053 3397 Dihedral : 17.511 174.216 3463 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 0.05 (0.18), residues: 2359 helix: 0.83 (0.16), residues: 997 sheet: -0.63 (0.27), residues: 392 loop : -0.36 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1189 HIS 0.007 0.001 HIS B 172 PHE 0.026 0.002 PHE B 596 TYR 0.022 0.002 TYR B 837 ARG 0.034 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04808 ( 931) hydrogen bonds : angle 5.10590 ( 2595) covalent geometry : bond 0.00443 (21107) covalent geometry : angle 0.65569 (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 199 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 2.311 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: 0.8979 (p0) cc_final: 0.8667 (m-40) REVERT: A 531 TYR cc_start: 0.9094 (p90) cc_final: 0.8775 (p90) REVERT: A 586 MET cc_start: 0.9049 (mmp) cc_final: 0.8732 (tpp) REVERT: A 698 TYR cc_start: 0.9454 (t80) cc_final: 0.8658 (t80) REVERT: A 704 GLU cc_start: 0.9485 (tp30) cc_final: 0.9019 (tp30) REVERT: A 749 MET cc_start: 0.9177 (mmp) cc_final: 0.8860 (mmm) REVERT: A 756 MET cc_start: 0.9733 (mpp) cc_final: 0.9270 (tpp) REVERT: A 775 LEU cc_start: 0.9516 (tp) cc_final: 0.9316 (tp) REVERT: A 846 MET cc_start: 0.9733 (mtm) cc_final: 0.9502 (mtt) REVERT: A 854 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9290 (mm-30) REVERT: A 957 MET cc_start: 0.9194 (mmp) cc_final: 0.8698 (mmm) REVERT: A 1042 LEU cc_start: 0.9586 (mt) cc_final: 0.9224 (mt) REVERT: B 32 MET cc_start: 0.4490 (tpt) cc_final: 0.4102 (tpp) REVERT: B 475 MET cc_start: 0.8160 (mmm) cc_final: 0.7808 (mmm) REVERT: B 573 LEU cc_start: 0.8957 (tt) cc_final: 0.8735 (pp) REVERT: B 586 MET cc_start: 0.8589 (mmm) cc_final: 0.8232 (mmm) REVERT: B 621 ASP cc_start: 0.9699 (t0) cc_final: 0.9442 (t70) REVERT: B 813 MET cc_start: 0.9533 (tpt) cc_final: 0.8713 (tpp) REVERT: B 831 ARG cc_start: 0.8898 (mtt-85) cc_final: 0.8656 (mtt180) REVERT: B 838 VAL cc_start: 0.9440 (t) cc_final: 0.9129 (p) REVERT: B 845 ILE cc_start: 0.9404 (mm) cc_final: 0.8923 (pt) REVERT: B 846 MET cc_start: 0.9369 (mtm) cc_final: 0.8936 (mpp) REVERT: B 858 TYR cc_start: 0.9076 (t80) cc_final: 0.8600 (t80) REVERT: B 865 LEU cc_start: 0.9607 (mm) cc_final: 0.9292 (pp) REVERT: B 957 MET cc_start: 0.8932 (mmp) cc_final: 0.8712 (mmm) REVERT: B 1153 ASP cc_start: 0.9547 (t0) cc_final: 0.9257 (m-30) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.3249 time to fit residues: 102.0642 Evaluate side-chains 156 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 2.261 ------------------------------------------------------------------------------- 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: 9.9990 chunk 146 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.065835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.040826 restraints weight = 181214.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.042178 restraints weight = 118391.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.043252 restraints weight = 86331.904| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21107 Z= 0.157 Angle : 0.612 10.566 28863 Z= 0.325 Chirality : 0.044 0.268 3215 Planarity : 0.004 0.054 3397 Dihedral : 17.486 174.945 3463 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.04 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: 0.10 (0.18), residues: 2359 helix: 0.88 (0.16), residues: 1010 sheet: -0.60 (0.27), residues: 395 loop : -0.38 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1170 HIS 0.007 0.001 HIS B 172 PHE 0.020 0.002 PHE B 388 TYR 0.017 0.002 TYR B1067 ARG 0.013 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 931) hydrogen bonds : angle 4.96379 ( 2595) covalent geometry : bond 0.00335 (21107) covalent geometry : angle 0.61211 (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 200 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8324 (mmp) cc_final: 0.7429 (mmm) REVERT: A 483 ASN cc_start: 0.9070 (p0) cc_final: 0.8629 (t0) REVERT: A 531 TYR cc_start: 0.9058 (p90) cc_final: 0.8674 (p90) REVERT: A 586 MET cc_start: 0.9073 (mmp) cc_final: 0.8756 (tpp) REVERT: A 635 MET cc_start: 0.9499 (pmm) cc_final: 0.9049 (pmm) REVERT: A 704 GLU cc_start: 0.9506 (tp30) cc_final: 0.9038 (tp30) REVERT: A 714 MET cc_start: 0.9600 (tpt) cc_final: 0.9144 (tpp) REVERT: A 749 MET cc_start: 0.9127 (mmp) cc_final: 0.8820 (mmm) REVERT: A 957 MET cc_start: 0.9195 (mmp) cc_final: 0.8687 (mmm) REVERT: A 1042 LEU cc_start: 0.9610 (mt) cc_final: 0.9366 (mt) REVERT: B 32 MET cc_start: 0.4380 (tpt) cc_final: 0.3979 (tpp) REVERT: B 42 MET cc_start: 0.8955 (pmm) cc_final: 0.8713 (pmm) REVERT: B 257 MET cc_start: -0.1481 (ttt) cc_final: -0.1704 (ttt) REVERT: B 573 LEU cc_start: 0.8965 (tt) cc_final: 0.8651 (tp) REVERT: B 586 MET cc_start: 0.8705 (mmm) cc_final: 0.8363 (mmm) REVERT: B 621 ASP cc_start: 0.9701 (t0) cc_final: 0.9435 (t70) REVERT: B 643 ASP cc_start: 0.9256 (m-30) cc_final: 0.8885 (p0) REVERT: B 698 TYR cc_start: 0.9444 (t80) cc_final: 0.9099 (t80) REVERT: B 764 LYS cc_start: 0.9572 (mtpt) cc_final: 0.9349 (ttpt) REVERT: B 845 ILE cc_start: 0.9378 (mm) cc_final: 0.9073 (pt) REVERT: B 846 MET cc_start: 0.9347 (mtm) cc_final: 0.8922 (mtp) REVERT: B 858 TYR cc_start: 0.9006 (t80) cc_final: 0.8559 (t80) REVERT: B 865 LEU cc_start: 0.9564 (mm) cc_final: 0.9301 (pp) REVERT: B 1153 ASP cc_start: 0.9535 (t0) cc_final: 0.9261 (m-30) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3257 time to fit residues: 103.2658 Evaluate side-chains 155 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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: 10.0000 chunk 239 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 164 optimal weight: 0.1980 chunk 216 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 0.4980 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 603 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 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 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.064438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039872 restraints weight = 184341.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.041258 restraints weight = 120651.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.042261 restraints weight = 88057.417| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21107 Z= 0.195 Angle : 0.648 10.244 28863 Z= 0.347 Chirality : 0.044 0.201 3215 Planarity : 0.004 0.077 3397 Dihedral : 17.577 175.823 3463 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 0.04 (0.18), residues: 2359 helix: 0.84 (0.16), residues: 1008 sheet: -0.67 (0.27), residues: 392 loop : -0.39 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 820 HIS 0.007 0.001 HIS B 172 PHE 0.058 0.002 PHE B 809 TYR 0.020 0.002 TYR A1067 ARG 0.011 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 931) hydrogen bonds : angle 5.06690 ( 2595) covalent geometry : bond 0.00411 (21107) covalent geometry : angle 0.64753 (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 187 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 ASN cc_start: 0.9027 (p0) cc_final: 0.8732 (t0) REVERT: A 531 TYR cc_start: 0.9079 (p90) cc_final: 0.8690 (p90) REVERT: A 586 MET cc_start: 0.9024 (mmp) cc_final: 0.8715 (tpp) REVERT: A 684 ARG cc_start: 0.9377 (tmm160) cc_final: 0.9140 (ptm-80) REVERT: A 698 TYR cc_start: 0.9466 (t80) cc_final: 0.8590 (t80) REVERT: A 701 ASP cc_start: 0.9728 (t70) cc_final: 0.9502 (t0) REVERT: A 704 GLU cc_start: 0.9457 (tp30) cc_final: 0.8998 (tp30) REVERT: A 714 MET cc_start: 0.9614 (tpt) cc_final: 0.9236 (tpp) REVERT: A 749 MET cc_start: 0.9160 (mmp) cc_final: 0.8372 (mmm) REVERT: A 756 MET cc_start: 0.9737 (mpp) cc_final: 0.9262 (tpp) REVERT: A 858 TYR cc_start: 0.9051 (t80) cc_final: 0.8792 (t80) REVERT: A 957 MET cc_start: 0.9200 (mmp) cc_final: 0.8707 (mmm) REVERT: A 1042 LEU cc_start: 0.9585 (mt) cc_final: 0.9269 (mt) REVERT: B 32 MET cc_start: 0.4388 (tpt) cc_final: 0.3965 (tpp) REVERT: B 42 MET cc_start: 0.8959 (pmm) cc_final: 0.8702 (pmm) REVERT: B 573 LEU cc_start: 0.8961 (tt) cc_final: 0.8702 (tp) REVERT: B 576 LEU cc_start: 0.8654 (tp) cc_final: 0.8429 (tp) REVERT: B 586 MET cc_start: 0.8717 (mmm) cc_final: 0.8381 (mmm) REVERT: B 621 ASP cc_start: 0.9675 (t0) cc_final: 0.9422 (t70) REVERT: B 643 ASP cc_start: 0.9281 (m-30) cc_final: 0.8919 (p0) REVERT: B 698 TYR cc_start: 0.9509 (t80) cc_final: 0.9061 (t80) REVERT: B 764 LYS cc_start: 0.9571 (mtpt) cc_final: 0.9371 (ttpt) REVERT: B 831 ARG cc_start: 0.8871 (mtt-85) cc_final: 0.8632 (mtt180) REVERT: B 845 ILE cc_start: 0.9407 (mm) cc_final: 0.8962 (pt) REVERT: B 846 MET cc_start: 0.9313 (mtm) cc_final: 0.8919 (mpp) REVERT: B 858 TYR cc_start: 0.9030 (t80) cc_final: 0.8492 (t80) REVERT: B 865 LEU cc_start: 0.9613 (mm) cc_final: 0.9287 (pp) REVERT: B 1153 ASP cc_start: 0.9572 (t0) cc_final: 0.9307 (m-30) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3825 time to fit residues: 114.9134 Evaluate side-chains 152 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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: 0.6980 chunk 204 optimal weight: 4.9990 chunk 120 optimal weight: 40.0000 chunk 18 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 880 ASN ** 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 349 ASN B 804 GLN ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.065725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.040763 restraints weight = 182248.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.042247 restraints weight = 117767.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.043275 restraints weight = 85302.129| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21107 Z= 0.141 Angle : 0.610 10.838 28863 Z= 0.323 Chirality : 0.044 0.180 3215 Planarity : 0.004 0.056 3397 Dihedral : 17.534 176.779 3463 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.15 (0.18), residues: 2359 helix: 0.98 (0.17), residues: 1016 sheet: -0.69 (0.27), residues: 404 loop : -0.36 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.006 0.001 HIS B 172 PHE 0.045 0.002 PHE B 809 TYR 0.015 0.001 TYR A 169 ARG 0.014 0.001 ARG B 447 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 931) hydrogen bonds : angle 4.93927 ( 2595) covalent geometry : bond 0.00304 (21107) covalent geometry : angle 0.60999 (28863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9239.95 seconds wall clock time: 167 minutes 2.20 seconds (10022.20 seconds total)