Starting phenix.real_space_refine on Fri Feb 6 08:26:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ec0_47898/02_2026/9ec0_47898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ec0_47898/02_2026/9ec0_47898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ec0_47898/02_2026/9ec0_47898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ec0_47898/02_2026/9ec0_47898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ec0_47898/02_2026/9ec0_47898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ec0_47898/02_2026/9ec0_47898.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 14654 2.51 5 N 4100 2.21 5 O 4508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23388 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7539 Classifications: {'peptide': 971} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 938} Chain breaks: 2 Chain: "C" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2206 Classifications: {'peptide': 271} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 260} Chain: "D" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1949 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 238} Restraints were copied for chains: B, E, F Time building chain proxies: 9.84, per 1000 atoms: 0.42 Number of scatterers: 23388 At special positions: 0 Unit cell: (156.114, 155.288, 123.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4508 8.00 N 4100 7.00 C 14654 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: 2.06 Conformation dependent library (CDL) restraints added in 980.3 milliseconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5644 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 14 sheets defined 48.3% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 99 through 118 removed outlier: 3.810A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 148 removed outlier: 4.083A pdb=" N LEU A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 6.159A pdb=" N SER A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.810A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 4.121A pdb=" N ILE A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.545A pdb=" N ALA A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.703A pdb=" N GLY A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.756A pdb=" N ARG A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 4.130A pdb=" N LYS A 417 " --> pdb=" O PRO A 413 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 466 through 477 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 506 removed outlier: 4.286A pdb=" N VAL A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 Processing helix chain 'A' and resid 556 through 559 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 584 through 596 removed outlier: 3.741A pdb=" N MET A 590 " --> pdb=" O MET A 586 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 removed outlier: 3.513A pdb=" N PHE A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.923A pdb=" N GLN A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 667 removed outlier: 3.611A pdb=" N ASN A 664 " --> pdb=" O TYR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 705 removed outlier: 3.741A pdb=" N ARG A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR A 686 " --> pdb=" O ILE A 682 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 729 removed outlier: 3.524A pdb=" N ASP A 726 " --> pdb=" O ARG A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 754 through 775 removed outlier: 3.952A pdb=" N LEU A 760 " --> pdb=" O ILE A 756 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU A 761 " --> pdb=" O GLN A 757 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 767 " --> pdb=" O MET A 763 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.784A pdb=" N VAL A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 812 removed outlier: 3.947A pdb=" N GLU A 809 " --> pdb=" O HIS A 805 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.898A pdb=" N VAL A 818 " --> pdb=" O PRO A 814 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 870 removed outlier: 4.130A pdb=" N VAL A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 918 through 924 removed outlier: 3.690A pdb=" N ILE A 924 " --> pdb=" O LYS A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 removed outlier: 4.445A pdb=" N CYS A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1020 removed outlier: 3.751A pdb=" N MET A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 removed outlier: 3.930A pdb=" N PHE A1030 " --> pdb=" O VAL A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1037 Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.809A pdb=" N VAL B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 148 removed outlier: 4.083A pdb=" N LEU B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 171 removed outlier: 6.160A pdb=" N SER B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.810A pdb=" N GLN B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 4.121A pdb=" N ILE B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.546A pdb=" N ALA B 263 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.703A pdb=" N GLY B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 378 through 390 removed outlier: 3.756A pdb=" N ARG B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 4.131A pdb=" N LYS B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 466 through 477 Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 506 removed outlier: 4.287A pdb=" N VAL B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 506 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 Processing helix chain 'B' and resid 556 through 559 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 584 through 596 removed outlier: 3.741A pdb=" N MET B 590 " --> pdb=" O MET B 586 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 removed outlier: 3.514A pdb=" N PHE B 616 " --> pdb=" O THR B 612 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.923A pdb=" N GLN B 641 " --> pdb=" O TYR B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 667 removed outlier: 3.611A pdb=" N ASN B 664 " --> pdb=" O TYR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 705 removed outlier: 3.741A pdb=" N ARG B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.524A pdb=" N ASP B 726 " --> pdb=" O ARG B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 754 through 775 removed outlier: 3.952A pdb=" N LEU B 760 " --> pdb=" O ILE B 756 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER B 762 " --> pdb=" O GLU B 758 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 767 " --> pdb=" O MET B 763 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 773 " --> pdb=" O ARG B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 removed outlier: 3.785A pdb=" N VAL B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP B 784 " --> pdb=" O GLU B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 812 removed outlier: 3.948A pdb=" N GLU B 809 " --> pdb=" O HIS B 805 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.898A pdb=" N VAL B 818 " --> pdb=" O PRO B 814 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 819 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 822 " --> pdb=" O VAL B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 870 removed outlier: 4.131A pdb=" N VAL B 850 " --> pdb=" O SER B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 918 through 924 removed outlier: 3.690A pdb=" N ILE B 924 " --> pdb=" O LYS B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1005 removed outlier: 4.445A pdb=" N CYS B1004 " --> pdb=" O GLN B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1020 removed outlier: 3.751A pdb=" N MET B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 removed outlier: 3.930A pdb=" N PHE B1030 " --> pdb=" O VAL B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1037 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 28 through 41 Processing helix chain 'C' and resid 42 through 62 removed outlier: 4.077A pdb=" N ALA C 51 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 117 through 136 removed outlier: 3.708A pdb=" N ARG C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 128 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 259 removed outlier: 5.693A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 20 through 32 removed outlier: 4.313A pdb=" N SER D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 43 removed outlier: 3.669A pdb=" N SER D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 112 removed outlier: 3.525A pdb=" N PHE D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 233 Processing helix chain 'D' and resid 234 through 244 removed outlier: 3.645A pdb=" N ARG D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 23 Processing helix chain 'E' and resid 28 through 41 Processing helix chain 'E' and resid 42 through 62 removed outlier: 4.076A pdb=" N ALA E 51 " --> pdb=" O ARG E 47 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 116 No H-bonds generated for 'chain 'E' and resid 114 through 116' Processing helix chain 'E' and resid 117 through 136 removed outlier: 3.707A pdb=" N ARG E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU E 128 " --> pdb=" O CYS E 124 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR E 136 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 259 removed outlier: 5.694A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LYS E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 20 through 32 removed outlier: 4.313A pdb=" N SER F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 43 removed outlier: 3.669A pdb=" N SER F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 112 removed outlier: 3.525A pdb=" N PHE F 112 " --> pdb=" O ARG F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 233 Processing helix chain 'F' and resid 234 through 244 removed outlier: 3.645A pdb=" N ARG F 244 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 69 removed outlier: 6.906A pdb=" N LEU A 64 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 57 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 30 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 28 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 94 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.302A pdb=" N LEU A 223 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU A 254 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER A 225 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 397 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL A 457 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 514 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 549 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 69 removed outlier: 6.906A pdb=" N LEU B 64 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR B 57 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 30 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 28 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 94 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.302A pdb=" N LEU B 223 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU B 254 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER B 225 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 397 " --> pdb=" O ASN B 430 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL B 457 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 514 " --> pdb=" O SER B 550 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 549 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 89 removed outlier: 4.505A pdb=" N LYS C 97 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP C 107 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP C 99 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA C 105 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 139 through 148 removed outlier: 3.829A pdb=" N GLN C 164 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP C 169 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN C 187 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 194 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 208 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN C 205 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY D 190 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 207 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN D 188 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS C 209 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR D 186 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET D 187 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 179 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET D 197 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 169 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 178 " --> pdb=" O LYS D 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 49 through 51 Processing sheet with id=AA9, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.674A pdb=" N SER D 70 " --> pdb=" O ASP D 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.505A pdb=" N LYS E 97 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP E 107 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP E 99 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ALA E 105 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 139 through 148 removed outlier: 3.829A pdb=" N GLN E 164 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP E 169 " --> pdb=" O GLN E 164 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN E 187 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE E 194 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER E 208 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN E 205 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY F 190 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL E 207 " --> pdb=" O ASN F 188 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN F 188 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS E 209 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR F 186 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET F 187 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 179 " --> pdb=" O MET F 187 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET F 197 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 169 " --> pdb=" O MET F 197 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN F 178 " --> pdb=" O LYS F 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AB5, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.673A pdb=" N SER F 70 " --> pdb=" O ASP F 67 " (cutoff:3.500A) 1210 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7744 1.35 - 1.47: 4908 1.47 - 1.59: 10918 1.59 - 1.71: 0 1.71 - 1.83: 196 Bond restraints: 23766 Sorted by residual: bond pdb=" CB TRP A 169 " pdb=" CG TRP A 169 " ideal model delta sigma weight residual 1.498 1.576 -0.078 3.10e-02 1.04e+03 6.36e+00 bond pdb=" CB TRP B 169 " pdb=" CG TRP B 169 " ideal model delta sigma weight residual 1.498 1.576 -0.078 3.10e-02 1.04e+03 6.30e+00 bond pdb=" CA ASN E 138 " pdb=" CB ASN E 138 " ideal model delta sigma weight residual 1.526 1.566 -0.041 1.68e-02 3.54e+03 5.86e+00 bond pdb=" CA ASN C 138 " pdb=" CB ASN C 138 " ideal model delta sigma weight residual 1.526 1.565 -0.040 1.68e-02 3.54e+03 5.57e+00 bond pdb=" CB LYS C 256 " pdb=" CG LYS C 256 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.48e+00 ... (remaining 23761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 31777 4.56 - 9.11: 243 9.11 - 13.67: 44 13.67 - 18.22: 22 18.22 - 22.78: 8 Bond angle restraints: 32094 Sorted by residual: angle pdb=" N ASN C 138 " pdb=" CA ASN C 138 " pdb=" C ASN C 138 " ideal model delta sigma weight residual 110.44 101.46 8.98 1.20e+00 6.94e-01 5.60e+01 angle pdb=" N ASN E 138 " pdb=" CA ASN E 138 " pdb=" C ASN E 138 " ideal model delta sigma weight residual 110.44 101.50 8.94 1.20e+00 6.94e-01 5.56e+01 angle pdb=" CA MET B 914 " pdb=" CB MET B 914 " pdb=" CG MET B 914 " ideal model delta sigma weight residual 114.10 128.29 -14.19 2.00e+00 2.50e-01 5.03e+01 angle pdb=" CA MET A 914 " pdb=" CB MET A 914 " pdb=" CG MET A 914 " ideal model delta sigma weight residual 114.10 128.22 -14.12 2.00e+00 2.50e-01 4.98e+01 angle pdb=" CA MET A 763 " pdb=" CB MET A 763 " pdb=" CG MET A 763 " ideal model delta sigma weight residual 114.10 128.12 -14.02 2.00e+00 2.50e-01 4.91e+01 ... (remaining 32089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 12417 15.62 - 31.24: 1684 31.24 - 46.87: 417 46.87 - 62.49: 108 62.49 - 78.11: 26 Dihedral angle restraints: 14652 sinusoidal: 5974 harmonic: 8678 Sorted by residual: dihedral pdb=" CA GLY F 234 " pdb=" C GLY F 234 " pdb=" N LYS F 235 " pdb=" CA LYS F 235 " ideal model delta harmonic sigma weight residual -180.00 -147.74 -32.26 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA GLY D 234 " pdb=" C GLY D 234 " pdb=" N LYS D 235 " pdb=" CA LYS D 235 " ideal model delta harmonic sigma weight residual 180.00 -147.75 -32.25 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA MET A 794 " pdb=" C MET A 794 " pdb=" N LYS A 795 " pdb=" CA LYS A 795 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 14649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3370 0.100 - 0.200: 283 0.200 - 0.300: 25 0.300 - 0.400: 2 0.400 - 0.500: 4 Chirality restraints: 3684 Sorted by residual: chirality pdb=" CG LEU B 845 " pdb=" CB LEU B 845 " pdb=" CD1 LEU B 845 " pdb=" CD2 LEU B 845 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CG LEU A 845 " pdb=" CB LEU A 845 " pdb=" CD1 LEU A 845 " pdb=" CD2 LEU A 845 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CG LEU B 760 " pdb=" CB LEU B 760 " pdb=" CD1 LEU B 760 " pdb=" CD2 LEU B 760 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.08e+00 ... (remaining 3681 not shown) Planarity restraints: 4138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 145 " 0.036 2.00e-02 2.50e+03 3.43e-02 2.94e+01 pdb=" CG TRP B 145 " -0.093 2.00e-02 2.50e+03 pdb=" CD1 TRP B 145 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 145 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 145 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 145 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 145 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 145 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 145 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 145 " -0.036 2.00e-02 2.50e+03 3.42e-02 2.93e+01 pdb=" CG TRP A 145 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 TRP A 145 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP A 145 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 145 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 145 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 145 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 145 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 145 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 145 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 844 " 0.019 2.00e-02 2.50e+03 3.17e-02 1.76e+01 pdb=" CG PHE A 844 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 844 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 844 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 844 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 844 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 844 " -0.002 2.00e-02 2.50e+03 ... (remaining 4135 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 6523 2.82 - 3.34: 19697 3.34 - 3.86: 40092 3.86 - 4.38: 44423 4.38 - 4.90: 75402 Nonbonded interactions: 186137 Sorted by model distance: nonbonded pdb=" O ILE B 756 " pdb=" OG1 THR B 759 " model vdw 2.306 3.040 nonbonded pdb=" O ILE A 756 " pdb=" OG1 THR A 759 " model vdw 2.306 3.040 nonbonded pdb=" OE1 GLU A 35 " pdb=" OG SER A 94 " model vdw 2.312 3.040 nonbonded pdb=" OE1 GLU B 35 " pdb=" OG SER B 94 " model vdw 2.312 3.040 nonbonded pdb=" O ASN E 237 " pdb=" OG1 THR E 241 " model vdw 2.332 3.040 ... (remaining 186132 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 27.090 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 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 : 0.005 0.078 23766 Z= 0.246 Angle : 1.167 22.779 32094 Z= 0.587 Chirality : 0.060 0.500 3684 Planarity : 0.007 0.083 4138 Dihedral : 15.526 78.109 9008 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.08 % Allowed : 18.27 % Favored : 81.65 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.13), residues: 2960 helix: -2.62 (0.10), residues: 1304 sheet: -0.34 (0.22), residues: 558 loop : -1.03 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 725 TYR 0.027 0.002 TYR E 247 PHE 0.072 0.003 PHE A 54 TRP 0.093 0.004 TRP B 145 HIS 0.011 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00484 (23766) covalent geometry : angle 1.16692 (32094) hydrogen bonds : bond 0.15055 ( 1210) hydrogen bonds : angle 7.72969 ( 3576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8958 (ppp) cc_final: 0.8743 (tmm) REVERT: A 491 ASP cc_start: 0.8667 (t0) cc_final: 0.8296 (t0) REVERT: A 652 ASP cc_start: 0.8543 (t70) cc_final: 0.8329 (t0) REVERT: A 845 LEU cc_start: 0.9148 (mm) cc_final: 0.8798 (pt) REVERT: A 857 LEU cc_start: 0.9157 (mm) cc_final: 0.8889 (mm) REVERT: B 95 MET cc_start: 0.8907 (ppp) cc_final: 0.8685 (tmm) REVERT: B 638 ASP cc_start: 0.8868 (m-30) cc_final: 0.8611 (m-30) REVERT: B 845 LEU cc_start: 0.9178 (mm) cc_final: 0.8823 (pt) REVERT: B 857 LEU cc_start: 0.9173 (mm) cc_final: 0.8894 (mm) REVERT: D 167 TYR cc_start: 0.7704 (m-80) cc_final: 0.7222 (m-80) REVERT: E 256 LYS cc_start: 0.6445 (mmmt) cc_final: 0.6198 (mtpp) outliers start: 2 outliers final: 1 residues processed: 193 average time/residue: 0.1493 time to fit residues: 47.9730 Evaluate side-chains 164 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 356 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 GLN A 774 GLN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS B 356 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 GLN B 774 GLN B 792 ASN C 23 HIS ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN C 248 GLN ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 HIS ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 246 ASN E 248 GLN F 209 HIS ** F 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.135843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087614 restraints weight = 79483.292| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.13 r_work: 0.3129 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 23766 Z= 0.337 Angle : 0.768 11.975 32094 Z= 0.393 Chirality : 0.047 0.214 3684 Planarity : 0.005 0.072 4138 Dihedral : 5.004 46.569 3178 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 2.69 % Allowed : 16.34 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 2960 helix: -0.90 (0.12), residues: 1338 sheet: -0.06 (0.24), residues: 526 loop : -0.68 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 244 TYR 0.070 0.002 TYR C 247 PHE 0.023 0.002 PHE A 404 TRP 0.045 0.002 TRP A 145 HIS 0.007 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00738 (23766) covalent geometry : angle 0.76829 (32094) hydrogen bonds : bond 0.05085 ( 1210) hydrogen bonds : angle 5.30188 ( 3576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7575 (mmp) cc_final: 0.7304 (mmm) REVERT: B 84 MET cc_start: 0.7406 (mmp) cc_final: 0.7189 (mmm) REVERT: B 757 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8621 (pp30) REVERT: C 256 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8453 (mmmt) REVERT: D 167 TYR cc_start: 0.8294 (m-80) cc_final: 0.7827 (m-80) REVERT: E 57 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7119 (t80) REVERT: F 167 TYR cc_start: 0.7996 (m-80) cc_final: 0.7675 (m-80) outliers start: 71 outliers final: 28 residues processed: 218 average time/residue: 0.1572 time to fit residues: 56.0554 Evaluate side-chains 184 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 583 MET Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 248 GLN Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 166 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 183 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 245 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 220 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 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 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN D 209 HIS D 229 ASN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.136946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.089756 restraints weight = 78368.985| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.11 r_work: 0.3171 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23766 Z= 0.148 Angle : 0.615 13.331 32094 Z= 0.311 Chirality : 0.043 0.201 3684 Planarity : 0.004 0.058 4138 Dihedral : 4.555 45.569 3178 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.27 % Allowed : 16.45 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 2960 helix: -0.05 (0.13), residues: 1338 sheet: -0.13 (0.23), residues: 552 loop : -0.58 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 15 TYR 0.058 0.002 TYR C 247 PHE 0.013 0.001 PHE F 104 TRP 0.036 0.002 TRP A 145 HIS 0.002 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00318 (23766) covalent geometry : angle 0.61530 (32094) hydrogen bonds : bond 0.03955 ( 1210) hydrogen bonds : angle 4.85056 ( 3576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 0.951 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: A 32 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8381 (p) REVERT: A 46 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8911 (pp) REVERT: A 95 MET cc_start: 0.9009 (ppp) cc_final: 0.8486 (ppp) REVERT: A 500 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9285 (p) REVERT: A 651 GLU cc_start: 0.8988 (tp30) cc_final: 0.8777 (tp30) REVERT: B 32 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8379 (p) REVERT: B 46 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8965 (pp) REVERT: B 95 MET cc_start: 0.9064 (ppp) cc_final: 0.8593 (ppp) REVERT: B 500 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.9276 (p) REVERT: B 651 GLU cc_start: 0.8886 (tp30) cc_final: 0.8581 (tp30) REVERT: C 256 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8414 (mmmt) REVERT: D 13 MET cc_start: 0.6990 (pmm) cc_final: 0.6731 (pmm) REVERT: D 167 TYR cc_start: 0.8267 (m-80) cc_final: 0.7849 (m-80) REVERT: F 13 MET cc_start: 0.7089 (pmm) cc_final: 0.6797 (pmm) outliers start: 60 outliers final: 33 residues processed: 203 average time/residue: 0.1473 time to fit residues: 50.5419 Evaluate side-chains 188 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 271 TRP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 229 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 123 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 256 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 280 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 309 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.136305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089223 restraints weight = 78123.622| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.06 r_work: 0.3162 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23766 Z= 0.159 Angle : 0.604 13.270 32094 Z= 0.302 Chirality : 0.043 0.197 3684 Planarity : 0.004 0.053 4138 Dihedral : 4.353 45.347 3178 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.84 % Allowed : 16.60 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 2960 helix: 0.42 (0.14), residues: 1350 sheet: -0.11 (0.23), residues: 552 loop : -0.37 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 15 TYR 0.049 0.001 TYR C 247 PHE 0.022 0.001 PHE C 255 TRP 0.027 0.002 TRP A 145 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00346 (23766) covalent geometry : angle 0.60363 (32094) hydrogen bonds : bond 0.03789 ( 1210) hydrogen bonds : angle 4.65866 ( 3576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 163 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 MET cc_start: 0.8892 (mmm) cc_final: 0.8633 (mmm) REVERT: A 651 GLU cc_start: 0.8975 (tp30) cc_final: 0.8721 (tp30) REVERT: B 381 MET cc_start: 0.8906 (mmm) cc_final: 0.8615 (mmm) REVERT: B 651 GLU cc_start: 0.8883 (tp30) cc_final: 0.8428 (tp30) REVERT: B 763 MET cc_start: 0.7558 (mtm) cc_final: 0.7208 (ptm) REVERT: B 857 LEU cc_start: 0.9229 (mm) cc_final: 0.9000 (mm) REVERT: C 256 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8489 (mmmt) REVERT: D 13 MET cc_start: 0.7033 (pmm) cc_final: 0.6747 (pmm) REVERT: D 167 TYR cc_start: 0.8221 (m-80) cc_final: 0.7518 (m-80) REVERT: F 13 MET cc_start: 0.7078 (pmm) cc_final: 0.6786 (pmm) outliers start: 75 outliers final: 43 residues processed: 213 average time/residue: 0.1420 time to fit residues: 51.3628 Evaluate side-chains 198 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 805 HIS Chi-restraints excluded: chain A residue 925 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 925 HIS Chi-restraints excluded: chain B residue 929 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 134 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 264 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.136110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.088854 restraints weight = 78373.448| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.07 r_work: 0.3159 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23766 Z= 0.150 Angle : 0.601 13.036 32094 Z= 0.298 Chirality : 0.042 0.196 3684 Planarity : 0.003 0.051 4138 Dihedral : 4.216 45.330 3178 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.20 % Allowed : 17.59 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 2960 helix: 0.69 (0.14), residues: 1342 sheet: 0.04 (0.23), residues: 532 loop : -0.34 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 15 TYR 0.024 0.001 TYR D 107 PHE 0.014 0.001 PHE B 54 TRP 0.025 0.002 TRP A 145 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00329 (23766) covalent geometry : angle 0.60131 (32094) hydrogen bonds : bond 0.03613 ( 1210) hydrogen bonds : angle 4.55964 ( 3576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8337 (mt-10) REVERT: A 381 MET cc_start: 0.8961 (mmm) cc_final: 0.8689 (mmm) REVERT: A 651 GLU cc_start: 0.8975 (tp30) cc_final: 0.8751 (tp30) REVERT: B 29 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7860 (mppt) REVERT: B 381 MET cc_start: 0.8968 (mmm) cc_final: 0.8693 (mmm) REVERT: B 651 GLU cc_start: 0.8864 (tp30) cc_final: 0.8398 (tp30) REVERT: B 857 LEU cc_start: 0.9221 (mm) cc_final: 0.8986 (mm) REVERT: D 13 MET cc_start: 0.6951 (pmm) cc_final: 0.6713 (pmm) REVERT: D 107 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.7022 (p90) REVERT: D 167 TYR cc_start: 0.8327 (m-80) cc_final: 0.7773 (m-80) REVERT: F 13 MET cc_start: 0.7064 (pmm) cc_final: 0.6858 (pmm) outliers start: 58 outliers final: 37 residues processed: 209 average time/residue: 0.1441 time to fit residues: 49.3645 Evaluate side-chains 193 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 925 HIS Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 925 HIS Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 28 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 200 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 186 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 280 optimal weight: 40.0000 chunk 269 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.134583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087266 restraints weight = 77812.113| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.99 r_work: 0.3121 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23766 Z= 0.224 Angle : 0.651 12.234 32094 Z= 0.325 Chirality : 0.044 0.200 3684 Planarity : 0.004 0.093 4138 Dihedral : 4.256 45.986 3178 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 2.58 % Allowed : 17.97 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2960 helix: 0.75 (0.14), residues: 1356 sheet: -0.02 (0.23), residues: 532 loop : -0.36 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 86 TYR 0.024 0.002 TYR D 107 PHE 0.019 0.002 PHE B 404 TRP 0.024 0.002 TRP E 169 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00495 (23766) covalent geometry : angle 0.65110 (32094) hydrogen bonds : bond 0.03955 ( 1210) hydrogen bonds : angle 4.59976 ( 3576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: A 381 MET cc_start: 0.9051 (mmm) cc_final: 0.8843 (mmm) REVERT: A 651 GLU cc_start: 0.8993 (tp30) cc_final: 0.8747 (tp30) REVERT: A 679 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 857 LEU cc_start: 0.9290 (mm) cc_final: 0.9078 (mm) REVERT: B 29 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7735 (mppt) REVERT: B 289 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8416 (mt-10) REVERT: B 381 MET cc_start: 0.9053 (mmm) cc_final: 0.8839 (mmm) REVERT: B 651 GLU cc_start: 0.8904 (tp30) cc_final: 0.8462 (tp30) REVERT: B 679 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 763 MET cc_start: 0.7676 (mtm) cc_final: 0.7432 (ptp) REVERT: B 857 LEU cc_start: 0.9230 (mm) cc_final: 0.9015 (mm) REVERT: D 107 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6943 (p90) REVERT: D 167 TYR cc_start: 0.8324 (m-80) cc_final: 0.7870 (m-80) outliers start: 68 outliers final: 44 residues processed: 219 average time/residue: 0.1394 time to fit residues: 50.6014 Evaluate side-chains 204 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 925 HIS Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 925 HIS Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1026 VAL Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 172 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 243 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 71 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 GLN ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN E 61 GLN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.134307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.086929 restraints weight = 77735.120| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.02 r_work: 0.3119 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23766 Z= 0.213 Angle : 0.649 12.492 32094 Z= 0.323 Chirality : 0.043 0.202 3684 Planarity : 0.004 0.050 4138 Dihedral : 4.246 46.060 3178 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 2.62 % Allowed : 18.20 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2960 helix: 0.86 (0.14), residues: 1340 sheet: 0.04 (0.23), residues: 528 loop : -0.33 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 15 TYR 0.025 0.002 TYR D 107 PHE 0.017 0.002 PHE A 404 TRP 0.026 0.002 TRP C 169 HIS 0.005 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00470 (23766) covalent geometry : angle 0.64881 (32094) hydrogen bonds : bond 0.03856 ( 1210) hydrogen bonds : angle 4.63870 ( 3576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: A 381 MET cc_start: 0.9047 (mmm) cc_final: 0.8847 (mmm) REVERT: A 851 ASP cc_start: 0.9464 (m-30) cc_final: 0.9243 (m-30) REVERT: A 857 LEU cc_start: 0.9270 (mm) cc_final: 0.9065 (mm) REVERT: B 29 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7806 (mppt) REVERT: B 97 MET cc_start: 0.7932 (mmm) cc_final: 0.7636 (mmm) REVERT: B 289 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: B 651 GLU cc_start: 0.8882 (tp30) cc_final: 0.8442 (tp30) REVERT: B 679 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 690 MET cc_start: 0.9087 (ttt) cc_final: 0.8793 (tpt) REVERT: B 763 MET cc_start: 0.7894 (mtm) cc_final: 0.7622 (ptp) REVERT: B 857 LEU cc_start: 0.9257 (mm) cc_final: 0.9033 (mm) REVERT: D 107 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.7033 (p90) REVERT: D 167 TYR cc_start: 0.8262 (m-80) cc_final: 0.7849 (m-80) REVERT: E 211 ASP cc_start: 0.6982 (m-30) cc_final: 0.5608 (t70) REVERT: E 247 TYR cc_start: 0.5478 (m-80) cc_final: 0.5050 (m-80) outliers start: 69 outliers final: 50 residues processed: 218 average time/residue: 0.1124 time to fit residues: 42.4151 Evaluate side-chains 211 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 925 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 925 HIS Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 172 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 278 optimal weight: 40.0000 chunk 79 optimal weight: 30.0000 chunk 44 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** E 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.134910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088123 restraints weight = 78098.272| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.02 r_work: 0.3146 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23766 Z= 0.144 Angle : 0.634 11.264 32094 Z= 0.309 Chirality : 0.043 0.357 3684 Planarity : 0.003 0.046 4138 Dihedral : 4.140 45.788 3178 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 2.39 % Allowed : 18.31 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.16), residues: 2960 helix: 0.94 (0.14), residues: 1360 sheet: 0.00 (0.23), residues: 530 loop : -0.23 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 15 TYR 0.027 0.002 TYR D 107 PHE 0.020 0.001 PHE F 104 TRP 0.031 0.002 TRP C 169 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00320 (23766) covalent geometry : angle 0.63354 (32094) hydrogen bonds : bond 0.03539 ( 1210) hydrogen bonds : angle 4.55895 ( 3576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8308 (mt-10) REVERT: A 857 LEU cc_start: 0.9295 (mm) cc_final: 0.9068 (mm) REVERT: B 29 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7826 (mppt) REVERT: B 97 MET cc_start: 0.8009 (mmm) cc_final: 0.7766 (mmm) REVERT: B 289 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8306 (mt-10) REVERT: B 381 MET cc_start: 0.9010 (mmm) cc_final: 0.8648 (mpp) REVERT: B 651 GLU cc_start: 0.8828 (tp30) cc_final: 0.8368 (tp30) REVERT: B 763 MET cc_start: 0.7912 (mtm) cc_final: 0.7624 (ptp) REVERT: B 857 LEU cc_start: 0.9254 (mm) cc_final: 0.9036 (mm) REVERT: D 13 MET cc_start: 0.6676 (pmm) cc_final: 0.6453 (pmm) REVERT: D 107 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.7073 (p90) REVERT: D 167 TYR cc_start: 0.8232 (m-80) cc_final: 0.7861 (m-80) REVERT: E 211 ASP cc_start: 0.7023 (m-30) cc_final: 0.5680 (t70) REVERT: F 71 TYR cc_start: 0.6139 (m-10) cc_final: 0.5746 (m-80) outliers start: 63 outliers final: 47 residues processed: 215 average time/residue: 0.1283 time to fit residues: 47.2127 Evaluate side-chains 208 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 925 HIS Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 925 HIS Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 172 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 204 optimal weight: 50.0000 chunk 235 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 232 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN E 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.134731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.087914 restraints weight = 78973.850| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.01 r_work: 0.3144 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23766 Z= 0.147 Angle : 0.649 11.205 32094 Z= 0.315 Chirality : 0.044 0.344 3684 Planarity : 0.003 0.045 4138 Dihedral : 4.087 45.616 3178 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % Rotamer: Outliers : 2.12 % Allowed : 18.84 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2960 helix: 1.02 (0.14), residues: 1342 sheet: -0.00 (0.23), residues: 530 loop : -0.20 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 15 TYR 0.027 0.001 TYR D 107 PHE 0.019 0.001 PHE F 104 TRP 0.030 0.002 TRP E 169 HIS 0.008 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00326 (23766) covalent geometry : angle 0.64868 (32094) hydrogen bonds : bond 0.03525 ( 1210) hydrogen bonds : angle 4.54080 ( 3576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: A 857 LEU cc_start: 0.9302 (mm) cc_final: 0.9084 (mm) REVERT: B 97 MET cc_start: 0.8008 (mmm) cc_final: 0.7753 (mmm) REVERT: B 289 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: B 381 MET cc_start: 0.9025 (mmm) cc_final: 0.8608 (mpp) REVERT: B 651 GLU cc_start: 0.8826 (tp30) cc_final: 0.8358 (tp30) REVERT: B 690 MET cc_start: 0.9026 (ttt) cc_final: 0.8717 (tpt) REVERT: B 763 MET cc_start: 0.8005 (mtm) cc_final: 0.7663 (ptp) REVERT: B 857 LEU cc_start: 0.9262 (mm) cc_final: 0.9052 (mm) REVERT: D 13 MET cc_start: 0.6763 (pmm) cc_final: 0.6558 (pmm) REVERT: D 107 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.7091 (p90) REVERT: D 167 TYR cc_start: 0.8197 (m-80) cc_final: 0.7848 (m-80) REVERT: E 211 ASP cc_start: 0.7056 (m-30) cc_final: 0.5740 (t70) REVERT: E 256 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8611 (tppt) REVERT: F 71 TYR cc_start: 0.6189 (m-10) cc_final: 0.5820 (m-80) REVERT: F 107 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6943 (p90) outliers start: 56 outliers final: 45 residues processed: 206 average time/residue: 0.1343 time to fit residues: 47.6985 Evaluate side-chains 207 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 925 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 925 HIS Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 248 GLN Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 294 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 GLN ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** E 248 GLN ** 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 = 0.4451 r_free = 0.4451 target = 0.132651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.084737 restraints weight = 80312.508| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.05 r_work: 0.3078 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23766 Z= 0.279 Angle : 0.740 13.530 32094 Z= 0.363 Chirality : 0.046 0.362 3684 Planarity : 0.004 0.043 4138 Dihedral : 4.332 46.509 3178 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.98 % Rotamer: Outliers : 2.24 % Allowed : 19.03 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 2960 helix: 0.87 (0.14), residues: 1344 sheet: 0.03 (0.24), residues: 494 loop : -0.40 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 15 TYR 0.030 0.002 TYR E 247 PHE 0.022 0.002 PHE B 404 TRP 0.035 0.002 TRP C 169 HIS 0.008 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00616 (23766) covalent geometry : angle 0.73967 (32094) hydrogen bonds : bond 0.04235 ( 1210) hydrogen bonds : angle 4.76654 ( 3576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: A 381 MET cc_start: 0.9100 (mmm) cc_final: 0.8699 (mpp) REVERT: B 29 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7977 (mppt) REVERT: B 97 MET cc_start: 0.8102 (mmm) cc_final: 0.7876 (mmm) REVERT: B 289 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: B 381 MET cc_start: 0.9114 (mmm) cc_final: 0.8635 (mpp) REVERT: B 651 GLU cc_start: 0.8884 (tp30) cc_final: 0.8440 (tp30) REVERT: B 763 MET cc_start: 0.8167 (mtm) cc_final: 0.7799 (ptp) REVERT: B 823 LEU cc_start: 0.9512 (mt) cc_final: 0.9303 (mt) REVERT: B 857 LEU cc_start: 0.9289 (mm) cc_final: 0.9038 (mm) REVERT: D 13 MET cc_start: 0.6983 (pmm) cc_final: 0.6776 (pmm) REVERT: D 107 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.7129 (p90) REVERT: D 167 TYR cc_start: 0.8211 (m-80) cc_final: 0.7888 (m-80) REVERT: E 211 ASP cc_start: 0.7091 (m-30) cc_final: 0.5748 (t70) REVERT: F 71 TYR cc_start: 0.6251 (m-10) cc_final: 0.5977 (m-80) REVERT: F 107 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.7010 (p90) outliers start: 59 outliers final: 46 residues processed: 211 average time/residue: 0.1407 time to fit residues: 50.7968 Evaluate side-chains 206 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 925 HIS Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 805 HIS Chi-restraints excluded: chain B residue 826 SER Chi-restraints excluded: chain B residue 925 HIS Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 172 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 86 optimal weight: 40.0000 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN E 248 GLN F 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.134682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.088197 restraints weight = 78155.861| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.98 r_work: 0.3156 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23766 Z= 0.117 Angle : 0.670 13.196 32094 Z= 0.321 Chirality : 0.044 0.356 3684 Planarity : 0.004 0.043 4138 Dihedral : 4.105 45.845 3178 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 1.74 % Allowed : 19.45 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.16), residues: 2960 helix: 1.10 (0.14), residues: 1336 sheet: 0.01 (0.23), residues: 530 loop : -0.16 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 15 TYR 0.028 0.001 TYR D 107 PHE 0.019 0.001 PHE F 104 TRP 0.032 0.002 TRP E 169 HIS 0.009 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00257 (23766) covalent geometry : angle 0.66968 (32094) hydrogen bonds : bond 0.03445 ( 1210) hydrogen bonds : angle 4.55667 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7736.23 seconds wall clock time: 133 minutes 0.88 seconds (7980.88 seconds total)